• Publications of Rytas J. Vilgalys

      • Papers Published

          • S Branco, P Gladieux, CE Ellison, A Kuo, K LaButti, A Lipzen, IV Grigoriev, HL Liao, R Vilgalys, KG Peay, JW Taylor and TD Bruns.
          • (2015).
          • Genetic isolation between two recently diverged populations of a symbiotic fungus..
          • Molecular ecology
          • ,
          • 24
          • (11)
          • ,
          • 2747-2758.
          • [web]
          Publication Description

          Fungi are an omnipresent and highly diverse group of organisms, making up a significant part of eukaryotic diversity. Little is currently known about the drivers of fungal population differentiation and subsequent divergence of species, particularly in symbiotic, mycorrhizal fungi. Here, we investigate the population structure and environmental adaptation in Suillus brevipes (Peck) Kuntze, a wind-dispersed soil fungus that is symbiotic with pine trees. We assembled and annotated the reference genome for Su. brevipes and resequenced the whole genomes of 28 individuals from coastal and montane sites in California. We detected two clearly delineated coast and mountain populations with very low divergence. Genomic divergence was restricted to few regions, including a region of extreme divergence containing a gene encoding for a membrane Na(+) /H(+) exchanger known for enhancing salt tolerance in plants and yeast. Our results are consistent with a very recent split between the montane and coastal Su. brevipes populations, with few small genomic regions under positive selection and a pattern of dispersal and/or establishment limitation. Furthermore, we identify a putatively adaptive gene that motivates further functional analyses to link genotypes and phenotypes and shed light on the genetic basis of adaptive traits.

          • CR Kuske, CN Hesse, JF Challacombe, D Cullen, JR Herr, RC Mueller, A Tsang and R Vilgalys.
          • (2015).
          • Prospects and challenges for fungal metatranscriptomics of complex communities.
          • Fungal Ecology
          • ,
          • 14
          • ,
          • 133-137.
          • [web]
          • SI Glassman, KG Peay, JM Talbot, DP Smith, JA Chung, JW Taylor, R Vilgalys and TD Bruns.
          • (2015).
          • A continental view of pine-associated ectomycorrhizal fungal spore banks: a quiescent functional guild with a strong biogeographic pattern..
          • The New phytologist
          • ,
          • 205
          • (4)
          • ,
          • 1619-1631.
          • [web]
          Publication Description

          Ecologists have long acknowledged the importance of seed banks; yet, despite the fact that many plants rely on mycorrhizal fungi for survival and growth, the structure of ectomycorrhizal (ECM) fungal spore banks remains poorly understood. The primary goal of this study was to assess the geographic structure in pine-associated ECM fungal spore banks across the North American continent. Soils were collected from 19 plots in forests across North America. Fresh soils were pyrosequenced for fungal internal transcribed spacer (ITS) amplicons. Adjacent soil cores were dried and bioassayed with pine seedlings, and colonized roots were pyrosequenced to detect resistant propagules of ECM fungi. The results showed that ECM spore banks correlated strongly with biogeographic location, but not with the identity of congeneric plant hosts. Minimal community overlap was found between resident ECM fungi vs those in spore banks, and spore bank assemblages were relatively simple and dominated by Rhizopogon, Wilcoxina, Cenococcum, Thelephora, Tuber, Laccaria and Suillus. Similar to plant seed banks, ECM fungal spore banks are, in general, depauperate, and represent a small and rare subset of the mature forest soil fungal community. Yet, they may be extremely important in fungal colonization after large-scale disturbances such as clear cuts and forest fires.

          • V Hofstetter, SA Redhead, F Kauff, J-M Moncalvo, PB Matheny and R Vilgalys.
          • (2014).
          • Taxonomic Revision and Examination of Ecological Transitions of the Lyophyllaceae (Basidiomycota, Agaricales) Based on a Multigene Phylogeny.
          • Cryptogamie, Mycologie
          • ,
          • 35
          • (4)
          • ,
          • 399-425.
          • [web]
          • HL Liao, Y Chen, TD Bruns, KG Peay, JW Taylor, S Branco, JM Talbot and R Vilgalys.
          • (2014).
          • Metatranscriptomic analysis of ectomycorrhizal roots reveals genes associated with Piloderma-Pinus symbiosis: improved methodologies for assessing gene expression in situ..
          • Environmental microbiology
          • ,
          • 16
          • (12)
          • ,
          • 3730-3742.
          • [web]
          Publication Description

          Ectomycorrhizal (EM) fungi form symbiotic associations with plant roots that regulate nutrient exchange between forest plants and soil. Environmental metagenomics approaches that employ next-generation sequencing show great promise for studying EM symbioses; however, metatranscriptomic studies have been constrained by the inherent difficulties associated with isolation and sequencing of RNA from mycorrhizae. Here we apply an optimized method for combined DNA/RNA extraction using field-collected EM fungal-pine root clusters, together with protocols for taxonomic identification of expressed ribosomal RNA, and inference of EM function based on plant and fungal metatranscriptomics. We used transcribed portions of ribosomal RNA genes to identify several transcriptionally dominant fungal taxa associated with loblolly pine including Amphinema, Russula and Piloderma spp. One taxon, Piloderma croceum, has a publically available genome that allowed us to identify patterns of gene content and transcript abundance. Over 1500 abundantly expressed Piloderma genes were detected from mycorrhizal roots, including genes for protein metabolism, cell signalling, electron transport, terpene synthesis and other extracellular activities. In contrast, Piloderma gene encoding an ammonia transporter showed highest transcript abundance in soil samples. Our methodology highlights the potential of metatranscriptomics to identify genes associated with symbiosis and ecosystem function using field-collected samples.

          • G Bonito, H Reynolds, MS Robeson, J Nelson, BP Hodkinson, G Tuskan, CW Schadt and R Vilgalys.
          • (2014).
          • Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants.
          • Molecular Ecology
          • ,
          • 23
          • (13)
          • ,
          • 3356-3370.
          • [web]
          • JM Talbot, TD Bruns, JW Taylor, DP Smith, S Branco, SI Glassman, S Erlandson, R Vilgalys, HL Liao, ME Smith and KG Peay.
          • (2014).
          • Endemism and functional convergence across the North American soil mycobiome..
          • Proceedings of the National Academy of Sciences of the United States of America
          • ,
          • 111
          • (17)
          • ,
          • 6341-6346.
          • [web]
          Publication Description

          Identifying the ecological processes that structure communities and the consequences for ecosystem function is a central goal of ecology. The recognition that fungi, bacteria, and viruses control key ecosystem functions has made microbial communities a major focus of this field. Because many ecological processes are apparent only at particular spatial or temporal scales, a complete understanding of the linkages between microbial community, environment, and function requires analysis across a wide range of scales. Here, we map the biological and functional geography of soil fungi from local to continental scales and show that the principal ecological processes controlling community structure and function operate at different scales. Similar to plants or animals, most soil fungi are endemic to particular bioregions, suggesting that factors operating at large spatial scales, like dispersal limitation or climate, are the first-order determinants of fungal community structure in nature. By contrast, soil extracellular enzyme activity is highly convergent across bioregions and widely differing fungal communities. Instead, soil enzyme activity is correlated with local soil environment and distribution of fungal traits within the community. The lack of structure-function relationships for soil fungal communities at continental scales indicates a high degree of functional redundancy among fungal communities in global biogeochemical cycles.

          • L Losada, SB Pakala, ND Fedorova, V Joardar, SA Shabalina, J Hostetler, SM Pakala, N Zafar, E Thomas, M Rodriguez-Carres, R Dean, R Vilgalys, WC Nierman and MA Cubeta.
          • (2014).
          • Mobile elements and mitochondrial genome expansion in the soil fungus and potato pathogenAG-3.
          • FEMS Microbiology Letters
          • ,
          • 352
          • (2)
          • ,
          • 165-173.
          • [web]
          • DJ Lodge, M Padamsee, PB Matheny, MC Aime, SA Cantrell, D Boertmann, A Kovalenko, A Vizzini, BTM Dentinger, PM Kirk, AM Ainsworth, J-M Moncalvo, R Vilgalys, E Larsson, R Lücking, GW Griffith, ME Smith, LL Norvell, DE Desjardin, SA Redhead, CL Ovrebo, EB Lickey, E Ercole, KW Hughes, R Courtecuisse, A Young, M Binder, AM Minnis, DL Lindner, B Ortiz-Santana, J Haight, T Læssøe, TJ Baroni, J Geml and T Hattori.
          • (2014).
          • Molecular phylogeny, morphology, pigment chemistry and ecology in Hygrophoraceae (Agaricales).
          • Fungal Diversity
          • ,
          • 64
          • (1)
          • ,
          • 1-99.
          • [web]
          • L Losada, SB Pakala, ND Fedorova, V Joardar, SA Shabalina, J Hostetler, SM Pakala, N Zafar, E Thomas, M Rodriguez-Carres, R Dean, R Vilgalys, WC Nierman and MA Cubeta.
          • (2014).
          • Mobile elements and mitochondrial genome expansion in the soil fungus and potato pathogen Rhizoctonia solani AG-3.
          • FEMS Microbiology Letters
          • ,
          • 352
          • (2)
          • ,
          • 165-173.
          • [web]
          Publication Description

          The soil fungus Rhizoctonia solani is an economically important pathogen of agricultural and forestry crops. Here, we present the complete sequence and analysis of the mitochondrial genome of R. solani, field isolate Rhs1AP. The genome (235 849 bp) is the largest mitochondrial genome of a filamentous fungus sequenced to date and exhibits a rich accumulation of introns, novel repeat sequences, homing endonuclease genes, and hypothetical genes. Stable secondary structures exhibited by repeat sequences suggest that they comprise functional, possibly catalytic RNA elements. RNA-Seq expression profiling confirmed that the majority of homing endonuclease genes and hypothetical genes are transcriptionally active. Comparative analysis suggests that the mitochondrial genome of R. solani is an example of a dynamic history of expansion in filamentous fungi. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

          • MS Benítez, MH Hersh, R Vilgalys and JS Clark.
          • (December, 2013).
          • Pathogen regulation of plant diversity via effective specialization..
          • Trends Ecol Evol
          • ,
          • 28
          • (12)
          • ,
          • 705-711.
          • [web]
          Publication Description

          The Janzen-Connell (JC) hypothesis, one of the most influential hypotheses explaining forest diversity, is inconsistent with evidence that tree species share the same natural enemies. Through the discussion of seedling diseases from a pathogen-centered perspective, we expand the JC hypothesis to tie in host-pathogen-environment interactions at three levels: local adaptation, host specificity of the combined effect of multiple infections, and environmental modulation of disease. We present evidence from plant pathology, disease ecology, and host-parasite evolution relevant to (but not commonly associated with) forest species diversity maintenance. This expanded view of the JC hypothesis suggests ways to direct new experiments to integrate research on pathogen local adaptation, co-infection, and environmental effects on infection by using high-throughput molecular techniques and statistical models.

          • MS Benítez, MH Hersh, R Vilgalys and JS Clark.
          • (2013).
          • Pathogen regulation of plant diversity via effective specialization.
          • Trends in Ecology and Evolution
          • ,
          • 28
          • (12)
          • ,
          • 705-711.
          • [web]
          Publication Description

          The Janzen-Connell (JC) hypothesis, one of the most influential hypotheses explaining forest diversity, is inconsistent with evidence that tree species share the same natural enemies. Through the discussion of seedling diseases from a pathogen-centered perspective, we expand the JC hypothesis to tie in host-pathogen-environment interactions at three levels: local adaptation, host specificity of the combined effect of multiple infections, and environmental modulation of disease. We present evidence from plant pathology, disease ecology, and host-parasite evolution relevant to (but not commonly associated with) forest species diversity maintenance. This expanded view of the JC hypothesis suggests ways to direct new experiments to integrate research on pathogen local adaptation, co-infection, and environmental effects on infection by using high-throughput molecular techniques and statistical models. © 2013 Elsevier Ltd.

          • Lodge, D Jean and Padamsee, M and Matheny, P B and Aime, M C and Cantrell, S A and Boertmann, D and Kovalenko, A, Vizzini, A, Dentinger, B T M and Kirk, P M and Ainsworth, A M and Moncalvo, J and Vilgalys, R and Larsson, E and Lucking, R and Griffith, G W and Smith, M E and Norvell, L L and Desjardin, D E and Redhead, S A and Ovrebo, C L and Lickey, E B and Ercole, E and Hughes, K W and Courtecuisse, R and Young, A and Binder, M and Minnis, A M and Lindner, D L and Ortiz-Santana, B and Haight, J and Laessoe, T and Baroni, T J and Geml, J and Hattori, T.
          • (2013).
          • Molecular phylogeny, morphology, pigment chemistry and ecology in Hygrophoraceae (Agaricales).
          • Fungal Diversity
          • .
          • Gryganskyi, A P and Humber, R A and Smith, M E and Hodge, K and Huang, B and Voigt, K and Vilgalys, R.
          • (2013).
          • Phylogenetic lineages in Entomophthoromycota.
          • Persoonia - Molecular Phylogeny and Evolution of Fungi
          • ,
          • 30
          • (1)
          • ,
          • 94--105.
          • Smith, M E and Henkel, T W and Uehling, J K and Fremier, A K and Clarke, H D and Vilgalys, R.
          • (2013).
          • The Ectomycorrhizal Fungal Community in a Neotropical Forest Dominated by the Endemic Dipterocarp Pakaraimaea dipterocarpacea.
          • PLoS ONE
          • ,
          • 8
          • (1)
          • ,
          • e55160.
          • M Shakya, N Gottel, H Castro, ZK Yang, L Gunter, J Labbé, W Muchero, G Bonito, R Vilgalys, G Tuskan and E al.
          • (2013).
          • A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature Populus deltoides Trees.
          • PLoS ONE
          • ,
          • 8
          • (10)
          • ,
          • e76382.
          • [web]
          Publication Description

          Bacterial and fungal communities associated with plant roots are central to the host health, survival and growth. However, a robust understanding of the root-microbiome and the factors that drive host associated microbial community structure have remained elusive, especially in mature perennial plants from natural settings. Here, we investigated relationships of bacterial and fungal communities in the rhizosphere and root endosphere of the riparian tree species Populus deltoides, and the influence of soil parameters, environmental properties (host phenotype and aboveground environmental settings), host plant genotype (Simple Sequence Repeat (SSR) markers), season (Spring vs. Fall) and geographic setting (at scales from regional watersheds to local riparian zones) on microbial community structure. Each of the trees sampled displayed unique aspects to its associated community structure with high numbers of Operational Taxonomic Units (OTUs) specific to an individual trees (bacteria >90%, fungi >60%). Over the diverse conditions surveyed only a small number of OTUs were common to all samples within rhizosphere (35 bacterial and 4 fungal) and endosphere (1 bacterial and 1 fungal) microbiomes. As expected, Proteobacteria and Ascomycota were dominant in root communities (>50%) while other higher-level phylogenetic groups (Chytridiomycota, Acidobacteria) displayed greatly reduced abundance in endosphere compared to the rhizosphere. Variance partitioning partially explained differences in microbiome composition between all sampled roots on the basis of seasonal and soil properties (4% to 23%). While most variation remains unattributed, we observed significant differences in the microbiota between watersheds (Tennessee vs. North Carolina) and seasons (Spring vs. Fall). SSR markers clearly delineated two host populations associated with the samples taken in TN vs. NC, but overall host genotypic distances did not have a significant effect on corresponding communities that could be separated from other measured effects. © 2013 Shakya et al.

          • CF Weber, R Vilgalys and CR Kuske.
          • (2013).
          • Changes in fungal community composition in response to elevated atmospheric CO2 and nitrogen fertilization varies with soil horizon.
          • Frontiers in Microbiology
          • ,
          • 4
          • (APR)
          • ,
          • 1--14.
          • [web]
          Publication Description

          Increasing levels of atmospheric carbon dioxide (CO2) and rates of nitrogen (N)-deposition to forest ecosystems are predicted to alter the structure and function of soil fungal communities, but the spatially heterogeneous distribution of soil fungi has hampered investigations aimed at understanding such impacts. We hypothesized that soil physical and chemical properties and fungal community composition would be differentially impacted by elevated atmospheric CO2 (eCO2) and N-fertilization in spatially separated field samples, in the forest floor, 0-2, 2-5, and 5-10 cm depth intervals in a loblolly pine Free-Air Carbon Dioxide Enrichment (FACE) experiment. In all soils, quantitative PCR-based estimates of fungal biomass were highest in the forest floor. Fungal richness, based on pyrosequencing of the fungal ribosomal large subunit gene, increased in response to N-fertilization in 0-2 cm and forest floor intervals. Composition shifted in forest floor, 0-2 and 2-5 cm intervals in response to N-fertilization, but the shift was most distinct in the 0-2 cm interval, in which the largest number of statistically significant changes in soil chemical parameters (i.e., phosphorus, organic matter, calcium, pH) was also observed. In the 0-2 cm interval, increased recovery of sequences from the Thelephoraceae, Tricholomataceae, Hypocreaceae, Clavicipitaceae, and Herpotrichiellaceae families and decreased recovery of sequences from the Amanitaceae correlated with N-fertilization. In this same depth interval, Amanitaceae, Tricholomataceae, and Herpotriciellaceae sequences were recovered less frequently from soils exposed to eCO2 relative to ambient conditions. These results demonstrated that vertical stratification should be taken into consideration in future efforts to elucidate environmental impacts on fungal communities and their feedbacks on ecosystem processes. © 2013 Weber, Vilgalys and Kuske.

          • AP Gryganskyi, RA Humber, JE Stajich, B Mullens, IM Anishchenko and R Vilgalys.
          • (2013).
          • Sequential Utilization of Hosts from Different Fly Families by Genetically Distinct, Sympatric Populations within the Entomophthora muscae Species Complex.
          • PLoS ONE
          • ,
          • 8
          • (8)
          • ,
          • e71168.
          • [web]
          Publication Description

          The fungus Entomophthora muscae (Entomophthoromycota, Entomophthorales, Entomophthoraceae) is a widespread insect pathogen responsible for fatal epizootic events in many dipteran fly hosts. During epizootics in 2011 and 2012 in Durham, North Carolina, we observed a transition of fungal infections from one host, the plant-feeding fly Delia radicum, to a second host, the predatory fly Coenosia tigrina. Infections first appeared on Delia in the middle of March, but by the end of May, Coenosia comprised 100% of infected hosts. Multilocus sequence typing revealed that E. muscae in Durham comprises two distinct subpopulations (clades) with several haplotypes in each. Fungi from either clade are able to infect both fly species, but vary in their infection phenologies and host-specificities. Individuals of the more phylogenetically diverse clade I predominated during the beginning of the spring epizootic, infecting mostly phytophagous Delia flies. Clade II dominated in late April and May and affected mostly predatory Coenosia flies. Analysis of population structure revealed two subpopulations within E. muscae with limited gene exchange. This study provides the first evidence of recombination and population structure within the E. muscae species complex, and illustrates the complexity of insect-fungus relationships that should be considered for development of biological control methods.

          • AP Gryganskyi, RA Humber, ME Smith, J Miadlikovska, S Wu, K Voigt, G Walther, IM Anishchenko and R Vilgalys.
          • (2013).
          • Corrigendum to "Molecular phylogeny of the Entomophthoromycota" [Mol. Phylogenet. Evol. 65 (2012) 682-694].
          • Molecular Phylogenetics and Evolution
          • ,
          • 66
          • (3)
          • ,
          • 1099-.
          • [web]
          • AM Golonka and R Vilgalys.
          • (2013).
          • Nectar inhabiting yeasts in Virginian populations of Silene latifolia (Caryophyllaceae) and coflowering species.
          • American Midland Naturalist
          • ,
          • 169
          • (2)
          • ,
          • 235-258.
          • [web]
          Publication Description

          Nectar inhabiting yeasts are commonly found in many plant species. Even though these microorganisms are abundant, much is still unknown about the communities of these microorganisms within and among plant species as well as the diversity of these microorganisms within and among seasons. This study examines the presence and diversity of these microorganisms in the dioecious plant species Silene latifolia as well as coflowering plants in Virginia, U.S. The majority of previous research on nectarivorous yeasts has been on hermaphroditic plant species. This is one of the few studies examining a dioecious plant species. Yeast species were isolated from the floral nectar of S. latifolia and associated plant species in 1999-2001, morphotyped into 37 morphospecies, and identified into 26 operational taxonomic units (OTUs) by sequencing the D1/D2 domain of the large subunit nrDNA. Yeast species from ascomycetes and basidiomycetes were isolated from nectar, including nectar associated ascomycetous Metschnikowia species and the basidiomycetous anther smut Microbotryum violaceum; however, ascomycetes dominated the samples. Metschnikowia species only accounted for 21% of the yeast isolates, a much lower percentage than in other studies. There was evidence of both host specificity and widespread dispersal of yeast species with Microbotryum violaceum found in nectar from both healthy and consistently diseased plant populations, indicating long distance dispersal of this fungus. There were no consistent differences among the sexes of S. latifolia, but male floral nectar appeared to have a higher diversity and species richness in some years. There was some indication of seasonality of yeast abundance in nectar as well as differences among years, potentially due to drought conditions. These results support the current body of evidence by researchers that, although not diverse in terms of the number of different yeast species found in nectar, yeasts are abundant in the nectar of plants. © 2013, American Midland Naturalist.

          • JM Talbot, TD Bruns, DP Smith, S Branco, SI Glassman, S Erlandson, R Vilgalys and KG Peay.
          • (2013).
          • Independent roles of ectomycorrhizal and saprotrophic communities in soil organic matter decomposition.
          • Soil Biology and Biochemistry
          • ,
          • 57
          • ,
          • 282-291.
          • [web]
          Publication Description

          The relative roles of ectomycorrhizal (ECM) and saprotrophic communities in controlling the decomposition of soil organic matter remain unclear. We tested the hypothesis that ECM community structure and activity influences the breakdown of nutrient-rich biopolymers in soils, while saprotrophic communities primarily regulate the breakdown of carbon-rich biopolymers. To test this hypothesis, we used high-throughput techniques to measure ECM and saprotrophic community structure, soil resource availability, and extracellular enzyme activity in whole soils and on ECM root tips in a coastal pine forest. We found that ECM and saprotroph richness did not show spatial structure and did not co-vary with any soil resource. However, species richness of ECM fungi explained variation in the activity of enzymes targeting recalcitrant N sources (protease and peroxidase) in bulk soil. Activity of carbohydrate- and organic P- targeting enzymes (e.g. cellobiohydrolase, β-glucosidase, α-glucosidase, hemicellulases, N-acetyl-glucosaminidase, and acid phosphatase) was correlated with saprotroph community structure and soil resource abundance (total soil C, N, and moisture), both of which varied along the soil profile. These observations suggest independent roles of ECM fungi and saprotrophic fungi in the cycling of N-rich, C-rich, and P-rich molecules through soil organic matter. Enzymatic activity on ECM root tips taken from the same soil cores used for bulk enzyme analysis did not correlate with the activity of any enzyme measured in the bulk soil, suggesting that ECM contributions to larger-scale soil C and nutrient cycling may occur primarily via extramatrical hyphae outside the rhizosphere. © 2012.

          • G Bonito, ME Smith, M Nowak, RA Healy, G Guevara, E Cázares, A Kinoshita, ER Nouhra, LS Domínguez, L Tedersoo, C Murat, Y Wang, BA Moreno, DH Pfister, K Nara, A Zambonelli, JM Trappe and R Vilgalys.
          • (2013).
          • Historical biogeography and diversification of truffles in the Tuberaceae and their newly identified southern hemisphere sister lineage..
          • PLoS One
          • ,
          • 8
          • (1)
          • ,
          • e52765.
          • [web]
          Publication Description

          Truffles have evolved from epigeous (aboveground) ancestors in nearly every major lineage of fleshy fungi. Because accelerated rates of morphological evolution accompany the transition to the truffle form, closely related epigeous ancestors remain unknown for most truffle lineages. This is the case for the quintessential truffle genus Tuber, which includes species with socio-economic importance and esteemed culinary attributes. Ecologically, Tuber spp. form obligate mycorrhizal symbioses with diverse species of plant hosts including pines, oaks, poplars, orchids, and commercially important trees such as hazelnut and pecan. Unfortunately, limited geographic sampling and inconclusive phylogenetic relationships have obscured our understanding of their origin, biogeography, and diversification. To address this problem, we present a global sampling of Tuberaceae based on DNA sequence data from four loci for phylogenetic inference and molecular dating. Our well-resolved Tuberaceae phylogeny shows high levels of regional and continental endemism. We also identify a previously unknown epigeous member of the Tuberaceae--the South American cup-fungus Nothojafnea thaxteri (E.K. Cash) Gamundí. Phylogenetic resolution was further improved through the inclusion of a previously unrecognized Southern hemisphere sister group of the Tuberaceae. This morphologically diverse assemblage of species includes truffle (e.g. Gymnohydnotrya spp.) and non-truffle forms that are endemic to Australia and South America. Southern hemisphere taxa appear to have diverged more recently than the Northern hemisphere lineages. Our analysis of the Tuberaceae suggests that Tuber evolved from an epigeous ancestor. Molecular dating estimates Tuberaceae divergence in the late Jurassic (~156 million years ago), with subsequent radiations in the Cretaceous and Paleogene. Intra-continental diversification, limited long-distance dispersal, and ecological adaptations help to explain patterns of truffle evolution and biodiversity.

          • AP Gryganskyi, RA Humber, ME Smith, J Miadlikowska, S Wu, K Voigt, G Walther, IM Anishchenko and R Vilgalys.
          • (2012).
          • Molecular phylogeny of the Entomophthoromycota..
          • Mol Phylogenet Evol
          • ,
          • 65
          • (2)
          • ,
          • 682-694.
          • [web]
          Publication Description

          The Entomophthoromycota is a ubiquitous group of fungi best known as pathogens of a wide variety of economically important insect pests, and other soil invertebrates. This group of fungi also includes a small number of parasites of reptiles, vertebrates (including humans), macromycetes, fern gametophytes, and desmid algae, as well as some saprobic species. Here we report on recent studies to resolve the phylogenetic relationships within the Entomophthoromycota and to reliably place this group among other basal fungal lineages. Bayesian Interference (BI) and Maximum Likelihood (ML) analyses of three genes (nuclear 18S and 28S rDNA, mitochondrial 16S, and the protein-coding RPB2) as well as non-molecular data consistently and unambiguously identify 31 taxa of Entomophthoromycota as a monophyletic group distinct from other Zygomycota and flagellated fungi. Using the constraints of our multi-gene dataset we constructed the most comprehensive rDNA phylogeny yet available for Entomophthoromycota. The taxa studied here belong to five distinct, well-supported lineages. The Basidiobolus clade is the earliest diverging lineage, comprised of saprobe species of Basidiobolus and the undescribed snake parasite Schizangiella serpentis nom. prov. The Conidiobolus lineage is represented by a paraphyletic grade of trophically diverse species that include saprobes, insect pathogens, and facultative human pathogens. Three well supported and exclusively entomopathogenic lineages in the Entomophthoraceae center around the genera Batkoa, Entomophthora and Zoophthora, although several genera within this crown clade are resolved as non-monophyletic. Ancestral state reconstruction suggests that the ancestor of all Entomophthoromycota was morphologically similar to species of Conidiobolus. Analyses using strict, relaxed, and local molecular clock models documented highly variable DNA substitution rates among lineages of Entomophthoromycota. Despite the complications caused by different rates of molecular evolution among lineages, our dating analysis indicates that the Entomophthoromycota originated 405±90 million years ago. We suggest that entomopathogenic lineages in Entomophthoraceae probably evolved from saprobic or facultatively pathogenic ancestors during or shortly after the evolutionary radiation of the arthropods.

          • MH Hersh, R Vilgalys and JS Clark.
          • (2012).
          • Evaluating the impacts of multiple generalist fungal pathogens on temperate tree seedling survival..
          • Ecology
          • ,
          • 93
          • (3)
          • ,
          • 511-520.
          • [web]
          Publication Description

          Host-specific mortality driven by natural enemies is a widely discussed mechanism for explaining plant diversity. In principle, populations of plant species can be regulated by distinct host-specific natural enemies that have weak or nonexistent effects on heterospecific competitors, preventing any single species from becoming dominant and thus promoting diversity. Two of the first steps in exploring the role of natural enemies in diversity regulation are to (1) identify potential enemies and (2) evaluate their levels of host specificity by determining if interactions between any one host and its enemy have equivalent survival impacts on co-occurring host species. We developed a bioinformatics framework to evaluate impacts of potential pathogens on seedling survival, for both single and multiple infections. Importantly, we consider scenarios not only if there are specialist pathogens for each plant, but also when generalist pathogens have differential effects on multiple host species, and when co-infection has species-specific effects. We then applied this analytical framework to a field experiment using molecular techniques to detect potential fungal pathogens on co-occurring tree seedling hosts. Combinatorial complexity created by 160 plant-fungus interactions was reduced to eight combinations that affect seedling survival. Potential fungal pathogens had broad host ranges, but seedling species were each regulated by different combinations of fungi or by generalist fungi that had differential effects on multiple plant species. Soil moisture can have the potential to shift the nature of the interactions in some plant-fungal combinations from neutral to detrimental. Reassessing the assumption of single-enemy-single-host interactions broadens the mechanisms through which natural enemies can influence plant diversity.

          • Bonito, G., Timothy Brenneman and Rytas Vilgalys..
          • (2012).
          • Ectomycorrhizal fungal diversity in orchards of cultivated pecan (Carya illinoinensis; Juglandaceae). ..
          • Mycorrhiza.
          • ,
          • 601-612.
          • RA Healy, ME Smith, GM Bonito, DH Pfister, ZW Ge, GG Guevara, G Williams, K Stafford, L Kumar, T Lee and E al.
          • (2012).
          • High diversity and widespread occurrence of mitotic spore mats in ectomycorrhizal Pezizales.
          • Molecular Ecology
          • ,
          • 22
          • (6)
          • ,
          • 1717-1732.
          • [web]
          Publication Description

          Fungal mitospores may function as dispersal units and/or spermatia and thus play a role in distribution and/or mating of species that produce them. Mitospore production in ectomycorrhizal (EcM) Pezizales is rarely reported, but here we document mitospore production by a high diversity of EcM Pezizales on three continents, in both hemispheres. We sequenced the internal transcribed spacer (ITS) and partial large subunit (LSU) nuclear rDNA from 292 spore mats (visible mitospore clumps) collected in Argentina, Chile, China, Mexico and the USA between 2009 and 2012. We collated spore mat ITS sequences with 105 fruit body and 47 EcM root sequences to generate operational taxonomic units (OTUs). Phylogenetic inferences were made through analyses of both molecular data sets. A total of 48 OTUs from spore mats represented six independent EcM Pezizales lineages and included truffles and cup fungi. Three clades of seven OTUs have no known meiospore stage. Mitospores failed to germinate on sterile media, or form ectomycorrhizas on Quercus, Pinus and Populus seedlings, consistent with a hypothesized role of spermatia. The broad geographic range, high frequency and phylogenetic diversity of spore mats produced by EcM Pezizales suggests that a mitospore stage is important for many species in this group in terms of mating, reproduction and/or dispersal. © 2012 Blackwell Publishing Ltd.

          • AP Gryganskyi, RA Humber, ME Smith, J Miadlikovska, S Wu, K Voigt, G Walther, IM Anishchenko and R Vilgalys.
          • (2012).
          • Corrigendum to "Molecular phylogeny of the Entomophthoromycota" [Mol. Phylogenet. Evol. 65 (2012) 682-694] (DOI:10.1016/j.ympev.2012.07.026).
          • Molecular Phylogenetics and Evolution
          • .
          • [web]
          • G Bonito, ME Smith, T Brenneman and R Vilgalys.
          • (2012).
          • Assessing ectomycorrhizal fungal spore banks of truffle producing soils with pecan seedling trap-plants.
          • Plant and Soil
          • ,
          • 356
          • (1-2)
          • ,
          • 357-366.
          • [web]
          Publication Description

          Background and Aims: Recently, the truffle species Tuber lyonii Butters was found to be dominant in ectomycorrhizal (EcM) fungal communities of cultivated pecan (Carya illinoinensis (Wangenh.) K. Koch). Many truffle fungi exhibit the trait of effectively colonizing plant roots via spores. We hypothesized that T. lyonii would be well represented in the spore bank of pecan orchard soils where it is found. Methods: We used axenically-grown pecan seedlings as trap-plants to bait for EcM associates in soils collected beneath truffle-producing pecan trees. EcM fungi on seedlings were characterized through rDNA sequencing and were compared to EcM communities of adult trees in these orchards. Results: Tuber lyonii mycorrhizas were well formed on seedlings inoculated with truffle spores, but were limited to just a few of the trap-plants grown in field soils. We compared EcM communities of adult pecan orchard trees to those on trap-plants and found distinct communities on each, with a high degree of similarity at the ordinal but not species level. Conclusions: Although species of Pezizales are abundant in pecan EcM communities and as propagules in their soil spore banks, only a low level of T. lyonii was detected in soil spore banks beneath orchard trees naturally colonized by T. lyonii. Other factors including land-use history or orchard management may better explain this truffle species presence and abundance in pecan EcM communities. © 2012 Springer Science+Business Media B.V.

          • JK Uehling, TW Henkel, MC Aime, R Vilgalys and ME Smith.
          • (2012).
          • New species and distribution records for Clavulina (Cantharellales, Basidiomycota) from the Guiana Shield, with a key to the lowland neotropical taxa.
          • Fungal Biology
          • ,
          • 116
          • (12)
          • ,
          • 1263-1274.
          • [web]
          Publication Description

          Three new and one previously described species of Clavulina (Clavulinaceae, Cantharellales, Basidiomycota) are reported from the central Guiana Shield region from tropical rainforests dominated by ectomycorrhizal trees of the leguminous genus Dicymbe (Fabaceae subfam. Caesalpinioideae). We provide morphological, DNA sequence, habitat, and fruiting occurrence data for each species. The new species conform to a generic concept of Clavulina that includes coralloid, branched basidiomata with amphigenous hymenia, basidia with two or 2-4 incurved sterigmata and postpartal septa present or absent, and smooth, hyaline, guttulate basidiospores. Placements of the new species in Clavulina were corroborated with DNA sequence data from the internal transcribed spacer and large subunit of the nuclear ribosomal repeat, and their infrageneric relationships were examined with phylogenetic analyses based on DNA from the region coding for the second largest subunit of DNA-dependent RNA polymerase II (rpb2). To facilitate future studies of the genus in the neotropics, a key is provided for all Clavulina species described from the lowland neotropics. © 2012 The British Mycological Society.

          • JK Uehling, TW Henkel, R Vilgalys and ME Smith.
          • (2012).
          • Membranomyces species are common ectomycorrhizal symbionts in Northern Hemisphere forests.
          • Mycorrhiza
          • ,
          • 22
          • (7)
          • ,
          • 577-581.
          • [web]
          Publication Description

          Membranomyces (Clavulinaceae, Cantharellales) Jülich consists of two described species of resupinate (crust-like) basidiomycetes. Previous studies indicated that Membranomyces falls within the Clavulinaceae, but the phylogenetic position of the genus has not been fully resolved. Membranomyces species were thought to be saprotrophic until 2003 when Tedersoo et al. detected Membranomyces delectabilis on ectomycorrhizal roots of Populus and Picea. Membranomyces was previously known only from collections made in eastern Canada and Europe. We recently sequenced the ITS rDNA barcode region from Scandinavian herbarium specimens identified as M. delectabilis and Membranomyces spurius. Phylogenetic analyses of these sporocarp sequences and similar environmental sequences indicated that Membranomyces is more diverse than previously thought and forms ectomycorrhizas with hosts from a diverse range of plant families in many north temperate ecosystems. © 2012 Springer-Verlag.

          • JK Uehling, TW Henkel, MC Aime, R Vilgalys and ME Smith.
          • (2012).
          • Four new species of Clavulina (Cantharellales, Basidiomycota) from the Guiana Shield, and a key to the lowland neotropical species..
          • Fungal Biology. In Press
          • .
          Publication Description

          19.. (2013) F

          • JK Uehling, TW Henkel, MC Aime, R Vilgalys and ME Smith.
          • (2012).
          • New species of Clavulina (Cantharellales, Basidiomycota) with resupinate and effused basidiomata from the Guiana Shield.
          • Mycologia
          • ,
          • 103
          • (2)
          • ,
          • 883-894.
          • [web]
          Publication Description

          18. Uehling JK, Henkel TW, Aime MC, Vilgalys R, Smith ME. (2012).

          • ME Smith, TW Henkel, JK Uehling, AK Fremier, HD Clarke and R Vilgalys.
          • (2012).
          • Ectomycorrhizal fungal community in a tropical forest dominated by the Neotropical Dipterocarp, Pakaraimea dipterocarpaceae.
          • PLOS ONE (in press)
          • .
          Publication Description

          16. Smith ME, Henkel TW, Uehling JK, Fremier AK, Clarke HD, Vilgalys R. (2013) Ectomycorrhizal fungal community in a tropical forest dominated by the Neotropical Dipterocarp, Pakaraimea dipterocarpaceae. PloS One. In press

          • TW Henkel, MC Aime, MML Chin, SL Miller, R Vilgalys and ME Smith.
          • (2012).
          • Ectomycorrhizal fungal sporocarp diversity and discovery of new taxa in Dicymbe monodominant forests of the Guiana Shield.
          • Biodiversity and Conservation
          • ,
          • 21
          • (9)
          • ,
          • 2195-2220.
          • [web]
          Publication Description

          Ectomycorrhizal (ECM) fungi historically were considered poorly represented in Neotropical forests but in the central Guiana Shield substantial areas are dominated by leguminous ECM trees. In the Upper Potaro Basin of Western Guyana, ECM fungi were sampled for 7 years during the rainy seasons of 2000-2008 in three 1-ha plots in primary monodominant forests of the ECM canopy tree Dicymbe corymbosa (Fabaceae subfam. Caesalpinioideae). Over the plot sampling period sporocarps of 126 species of putative or confirmed ECM fungi were recovered. These taxa represented 13 families and 25 genera of primarily Agaricomycetes, but also Ascomycota (Elaphomycetaceae), the majority of which are new to science. Russulaceae contained the most species (20 Russula; 9 Lactarius), followed by Boletaceae (8 genera, 25 spp.), Clavulinaceae (17 Clavulina), and Amanitaceae (16 Amanita). An additional 46 species of ECM fungi were collected in forests of the Upper Potaro Basin outside the study plots between 2000 and 2010, bringing the regional number of ECM species known from sporocarps to 172. This is the first long-term ECM macrofungal dataset from an ECM-dominated Neotropical forest, and sporocarp diversity is comparable to that recorded for ECM-diverse temperate and boreal forests. While a species accumulation curve indicated that ECM sporocarp diversity was not fully recovered inside of the plots, ~80% of the total species were recovered in the first year. Sequence data from ECM roots have confirmed the ECM status of 56 taxa represented by corresponding sporocarp data. However, >50% of ECM fungal species from roots remain undiscovered as sporocarps, leading to a conservative estimate of >250 ECM species at the Potaro site. Dicymbe forests in Guyana are a hotspot for ECM fungal diversity in the Neotropics. © 2011 Springer Science+Business Media B.V.

          • Guevara, Gonzalo, G Bonito, JM Trappe, E Cázares, G Williams, RA Healy, CW Schadt and R Vilgalys.
          • (2012).
          • New North American truffles (Tuber spp.) and their ectomycorrhizal associations..
          • Mycologia
          • ,
          • 2012
          • (1)
          • ,
          • 194--209.
          • AP Gryganskyi, RA Humber, ME Smith, K Hodge, B Huang, K Voigt and R Vilgalys.
          • (2012).
          • Phylogenetic lineages in Entomophthoromycota..
          • Persoonia.
          • .
          • TW Henkel, D Husbands, GM Bonito, R Vilgalys and ME Smith.
          • (2012).
          • New species of Xerocomus (Boletales) from the Guiana Shield, with notes on their mycorrhizal status and fruiting occurrence.
          • Mycologia
          • ,
          • in press
          • (2)
          • ,
          • 422--435.
          Publication Description

          . (2013). Mycologia. In Press.

          • J Dunbar, SA Eichorst, LV Gallegos-Graves, S Silva, G Xie, NW Hengartner, RD Evans, BA Hungate, RB Jackson, JP Megonigal, CW Schadt, R Vilgalys, DR Zak and CR Kuske.
          • (2012).
          • Common bacterial responses in six ecosystems exposed to 10 years of elevated atmospheric carbon dioxide.
          • Environmental Microbiology
          • ,
          • 14
          • (5)
          • ,
          • 1145-1158.
          • [web]
          Publication Description

          Six terrestrial ecosystems in the USA were exposed to elevated atmospheric CO2 in single or multifactorial experiments for more than a decade to assess potential impacts. We retrospectively assessed soil bacterial community responses in all six-field experiments and found ecosystem-specific and common patterns of soil bacterial community response to elevated CO2. Soil bacterial composition differed greatly across the six ecosystems. No common effect of elevated atmospheric CO2 on bacterial biomass, richness and community composition across all of the ecosystems was identified, although significant responses were detected in individual ecosystems. The most striking common trend across the sites was a decrease of up to 3.5-fold in the relative abundance of Acidobacteria Group 1 bacteria in soils exposed to elevated CO2 or other climate factors. The Acidobacteria Group 1 response observed in exploratory 16S rRNA gene clone library surveys was validated in one ecosystem by 100-fold deeper sequencing and semi-quantitative PCR assays. Collectively, the 16S rRNA gene sequencing approach revealed influences of elevated CO2 on multiple ecosystems. Although few common trends across the ecosystems were detected in the small surveys, the trends may be harbingers of more substantive changes in less abundant, more sensitive taxa that can only be detected by deeper surveys. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.

          • AD Thaler, CLV Dover and R Vilgalys.
          • (2012).
          • Ascomycete phylotypes recovered from a Gulf of Mexico methane seep are identical to an uncultured deep-sea fungal clade from the Pacific.
          • Fungal Ecology
          • ,
          • 5
          • (2)
          • ,
          • 270-273.
          • [web]
          Publication Description

          Deep-sea endemic fungi are one component of an under-sampled invisible biosphere whose contribution to benthic ecosystems is not yet understood. In the last decade, molecular techniques have facilitated the discovery of several new deep-sea fungal groups, especially in habitats such as hydrothermal vents and methane seeps. We assessed fungal diversity at a methane seep in the Gulf of Mexico by sequencing partial ITS and LSU gene regions from environmental DNA recovered from microoxic and anoxic sediment. While most phylotypes were closely allied with common fungal species, the dominant phylotype did not match any known terrestrial species and aligned with an uncultured deep-sea fungus found in oxygen-depleted sediment at multiple sites in the Pacific Ocean. Despite its apparently broad distribution and frequent occurrence in oxygen-depleted sediment, the ecological role of this phylotype is not yet known. © 2011 Elsevier Ltd and The British Mycological Society.

          • G Bonito, JM Trappe, S Donovan and R Vilgalys.
          • (2011).
          • The Asian black truffle Tuber indicum can form ectomycorrhizas with North American host plants and complete its life cycle in non-native soils.
          • Fungal Ecology
          • ,
          • 4
          • (1)
          • ,
          • 83-93.
          • [web]
          Publication Description

          The Asian black truffle Tuber indicum is morphologically and phylogenetically similar to the European black truffle Tuber melanosporum. T. indicum is considered a threat to T. melanosporum trufficulture due to its presumed competitiveness and broad host compatibility. Recently, in independent events, T. indicum was found fruiting in a forest in Oregon, USA, and was detected as ectomycorrhizas within a truffle orchard established with trees believed to have been inoculated with T. melanosporum. We used haplotype networking to assess intraspecific ITS rDNA diversity among Asian and North American T. indicum group B isolates. To further assess the potential of T. indicum to spread onto native host plants it was inoculated onto seedlings of loblolly pine (Pinus taeda) and pecan (Carya illinoinensis, Juglandaceae), species endemic to North America. T. indicum formed ectomycorrhizas on both host species examined. This supports previous studies from Europe and Asia that indicate T. indicum has a broad host spectrum, an ecological trait that may be important to its invasion ecology. This is the first report of T. indicum introductions in North America and of this species fruiting outside of its native range. To help prevent further unintended truffle introductions we recommend that fruitbodies used by the truffle industry for inoculating seedlings first be identified with DNA methods. © 2010 Elsevier Ltd and The British Mycological Society.

          • TJ Baroni, V Hofstetter, DL Largent and R Vilgalys.
          • (2011).
          • Entocybe is proposed as a new genus in the Entolomataceae (Agaricomycetes, Basidiomycota) based on morphological and molecular evidence.
          • North American Fungi
          • ,
          • 6
          • (12)
          • ,
          • 1-19.
          • [web]
          Publication Description

          Morphological and molecular characteristics support the recognition of a welldefined taxonomic group within the Entolomataceae. The distinctive basidiospore form and a three locus DNA analysis separate the species that share these characteristics from other species of Entoloma s. l. We propose here a new genus, Entocybe, to accommodate these taxa. © 2011 Pacific Northwest Fungi Project. All rights reserved.

          • ME Smith, TW Henkel, MC Aime, AK Fremier and R Vilgalys.
          • (2011).
          • Ectomycorrhizal fungal diversity and community structure on three co-occurring leguminous canopy tree species in a Neotropical rainforest.
          • New Phytologist
          • ,
          • 192
          • (3)
          • ,
          • 699-712.
          • [web]
          Publication Description

          Summary: • The ectomycorrhizal (ECM) symbiosis was historically considered restricted to the temperate zones, but recent studies have shown the importance of this symbiosis across the tropics. We examined ECM fungal diversity, host plant phylogeny and ECM host preferences in a rainforest dominated by the leguminous host plants Dicymbe corymbosa, Dicymbe altsonii and Aldina insignis. • Ectomycorrhizal fungi were identified by internal transcribed spacer rDNA sequencing and host species were verified with chloroplast trnL sequencing. To test whether Dicymbe and Aldina represent independent gains of the ECM symbiosis, we constructed a Fabaceae phylogeny using MatK and trnL. We identified four independent ECM lineages within the Fabaceae. • We detected a diverse community of 118 ECM species dominated by the /clavulina, /russula-lactarius, /boletus, and /tomentella-thelephora lineages. Ectomycorrhizal species in Agaricales, Atheliales and Polyporales may represent previously unrecognized tropical-endemic ECM lineages. Previous studies suggested that ECM fungi did not diversify in the tropics, but the /clavulina lineage appears to have a center of diversity in tropical South America. • Dicymbe and Aldina represent independent gains of the ECM symbiosis in Fabaceae but their fungal symbionts showed no host preferences. Spatial factors are more important than hosts in structuring the ECM fungal community in this ecosystem. © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.

          • TM Porter, W Martin, TY James, JE Longcore, FH Gleason, PH Adler, PM Letcher and R Vilgalys.
          • (2011).
          • Molecular phylogeny of the Blastocladiomycota (Fungi) based on nuclear ribosomal DNA.
          • Fungal Biology
          • ,
          • 115
          • (4-5)
          • ,
          • 381-392.
          • [web]
          Publication Description

          The Blastocladiomycota is a recently described phylum of ecologically diverse zoosporic fungi whose species have not been thoroughly sampled and placed within a molecular phylogeny. In this study, we investigated the phylogeny of the Blastocladiomycota based on ribosomal DNA sequences from strains identified by traditional morphological and ultrastructural characters. Our results support the monophyly of the Coelomomycetaceae and Physodermataceae but the Blastocladiaceae and Catenariaceae are paraphyletic or polyphyletic. The data support two clades within Allomyces with strains identified as Allomyces arbusculus in both clades, suggesting that species concepts in Allomyces are in need of revision. A clade of Catenaria species isolated from midge larvae group separately from other Catenaria species, suggesting that this genus may need revision. In the Physodermataceae, Urophlyctis species cluster with a clade of Physoderma species. The algal parasite Paraphysoderma sedebokerensis nom. prov. clusters sister to other taxa in the Physodermataceae. Catenomyces persicinus, which has been classified in the Catenariaceae, groups with the Chytridiomycota rather than Blastocladiomycota. The rDNA operon seems to be suitable for classification within the Blastocladiomycota and distinguishes among genera; however, this region alone is not suitable to determine the position of the Blastocladiomycota among other basal fungal phyla with statistical support. A focused effort to find and isolate, or directly amplify DNA from additional taxa will be necessary to evaluate diversity in this phylum. We provide this rDNA phylogeny as a preliminary framework to guide further taxon and gene sampling and to facilitate future ecological, morphological, and systematic studies. © 2011 The British Mycological Society.

          • G Bonito, T Brenneman and R Vilgalys.
          • (2011).
          • Ectomycorrhizal fungal diversity in orchards of cultivated pecan (Carya illinoinensis; Juglandaceae).
          • Mycorrhiza
          • ,
          • 21
          • (7)
          • ,
          • 601-612.
          • [web]
          Publication Description

          Carya illinoinensis (pecan) belongs to the Juglandaceae (walnut family) and is a major economic nut crop in the southern USA. Although evidence suggests that some species in the Juglandaceae are ectomycorrhizal, investigations on their ectomycorrhizal fungal symbionts are quite limited. Here we assessed the ectomycorrhizal fungal diversity in cultivated orchards of C. illinoinensis. Five pecan orchards in southern Georgia, USA, were studied, three of which were known to fruit the native edible truffle species Tuber lyonii. We sequenced rDNA from single ectomycorrhizal root tips sampled from a total of 50 individual trees. Mycorrhizae were identified by ITS and LSU rDNA sequence-based methods. Forty-four distinct ectomycorrhizal taxa were detected. Sequestrate taxa including Tuber and Scleroderma were particularly abundant. The two most abundant sequence types belonged to T. lyonii (17%) and an undescribed Tuber species (~20%). Because of our interest in the ecology of T. lyonii, we also conducted greenhouse studies to determine whether this species would colonize and form ectomycorrhizae on roots of pecan, oak, or pine species endemic to the region. T. lyonii ectomycorrhizae were formed on pecan and oak seedlings, but not pine, when these were inoculated with spores. That oak and pecan seedling roots were receptive to truffle spores indicates that spore slurry inoculation could be a suitable method for commercial use and that, ecologically, T. lyonii may function as a pioneer ectomycorrhizal species for these hosts. © 2011 Springer-Verlag.

          • NR Gottel, HF Castro, M Kerley, Z Yang, DA Pelletier, M Podar, T Karpinets, E Uberbacher, GA Tuskan, R Vilgalys, MJ Doktycz and CW Schadt.
          • (2011).
          • Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types.
          • Applied and Environmental Microbiology
          • ,
          • 77
          • (17)
          • ,
          • 5934-5944.
          • [web]
          Publication Description

          The root-rhizosphere interface of Populus is the nexus of a variety of associations between bacteria, fungi, and the host plant and an ideal model for studying interactions between plants and microorganisms. However, such studies have generally been confined to greenhouse and plantation systems. Here we analyze microbial communities from the root endophytic and rhizospheric habitats of Populus deltoides in mature natural trees from both upland and bottomland sites in central Tennessee. Community profiling utilized 454 pyrosequencing with separate primers targeting the V4 region for bacterial 16S rRNA and the D1/D2 region for fungal 28S rRNA genes. Rhizosphere bacteria were dominated by Acidobacteria (31%) and Alphaproteobacteria (30%), whereas most endophytes were from the Gammaproteobacteria (54%) as well as Alphaproteobacteria (23%). A single Pseudomonas-like operational taxonomic unit (OTU) accounted for 34% of endophytic bacterial sequences. Endophytic bacterial richness was also highly variable and 10-fold lower than in rhizosphere samples originating from the same roots. Fungal rhizosphere and endophyte samples had approximately equal amounts of the Pezizomycotina (40%), while the Agaricomycotina were more abundant in the rhizosphere (34%) than endosphere (17%). Both fungal and bacterial rhizosphere samples were highly clustered compared to the more variable endophyte samples in a UniFrac principal coordinates analysis, regardless of upland or bottomland site origin. Hierarchical clustering of OTU relative abundance patterns also showed that the most abundant bacterial and fungal OTUs tended to be dominant in either the endophyte or rhizosphere samples but not both. Together, these findings demonstrate that root endophytic communities are distinct assemblages rather than opportunistic subsets of the rhizosphere. © 2011, American Society for Microbiology.

          • CF Weber, DR Zak, BA Hungate, RB Jackson, R Vilgalys, RD Evans, CW Schadt, JP Megonigal and CR Kuske.
          • (2011).
          • Responses of soil cellulolytic fungal communities to elevated atmospheric CO 2 are complex and variable across five ecosystems.
          • Environmental Microbiology
          • ,
          • 13
          • (10)
          • ,
          • 2778-2793.
          • [web]
          Publication Description

          Elevated atmospheric CO 2 generally increases plant productivity and subsequently increases the availability of cellulose in soil to microbial decomposers. As key cellulose degraders, soil fungi are likely to be one of the most impacted and responsive microbial groups to elevated atmospheric CO 2. To investigate the impacts of ecosystem type and elevated atmospheric CO 2 on cellulolytic fungal communities, we sequenced 10677 cbhI gene fragments encoding the catalytic subunit of cellobiohydrolase I, across five distinct terrestrial ecosystem experiments after a decade of exposure to elevated CO 2. The cbhI composition of each ecosystem was distinct, as supported by weighted Unifrac analyses (all P-values;<0.001), with few operational taxonomic units (OTUs) being shared across ecosystems. Using a 114-member cbhI sequence database compiled from known fungi, less than 1% of the environmental sequences could be classified at the family level indicating that cellulolytic fungi in situ are likely dominated by novel fungi or known fungi that are not yet recognized as cellulose degraders. Shifts in fungal cbhI composition and richness that were correlated with elevated CO 2 exposure varied across the ecosystems. In aspen plantation and desert creosote bush soils, cbhI gene richness was significantly higher after exposure to elevated CO 2 (550μmol mol -1) than under ambient CO 2 (360μmol mol -1 CO 2). In contrast, while the richness was not altered, the relative abundance of dominant OTUs in desert soil crusts was significantly shifted. This suggests that responses are complex, vary across different ecosystems and, in at least one case, are OTU-specific. Collectively, our results document the complexity of cellulolytic fungal communities in multiple terrestrial ecosystems and the variability of their responses to long-term exposure to elevated atmospheric CO 2. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

          • G Bonito, OS Isikhuemhen and R Vilgalys.
          • (2010).
          • Identification of fungi associated with municipal compost using DNA-based techniques.
          • Bioresource Technology
          • ,
          • 101
          • (3)
          • ,
          • 1021-1027.
          • [web]
          Publication Description

          Fungi are important in terrestrial decay processes. However, fungi associated with organic decay during composting are still not well known. In this study culture-independent methods were used to identify fungi associated with composting organic municipal wastes to gain a better understanding of the diversity of fungi associated with this process. Fungal communities from 0, 210, and 410 day-old compost samples were assessed with DNA fingerprinting using denaturing gradient gel electrophoresis (DGGE) and by the analysis of DNA sequences from rDNA clone libraries. From 207 rDNA sequences, 82 fungal OTU's were detected. A disproportionate number of yeast sequences were detected in Day 0 clone libraries, including the human pathogens Candida tropicalis and Candida krusei (Saccharomycetales). Basidiomycetes accounted for over half of the clones from the Day 210 sample. Clones of Cercophora and Neurospora species accounted for most of the fungal clones of the Day 410 sample. No Zygomycetes or Aspergillus species were detected in this study. These findings call for a reassessment of long held views about the organisms involved in the composting of organic municipal wastes. © 2009 Elsevier Ltd. All rights reserved.

          • G Bonito, JM Trappe, P Rawlinson and R Vilgalys.
          • (2010).
          • Improved resolution of major clades within Tuber and taxonomy of species within the Tuber gibbosum complex.
          • Mycologia
          • ,
          • 102
          • (5)
          • ,
          • 1042-1057.
          • [web]
          Publication Description

          Tuber gibbosum Harkn., described from northern California, originally was thought to be a single, variable species that fruited from autumn through winter to spring. It has become popular as a culinary truffle in northwestern USA, where it is commercially harvested. Morphological studies suggested it might be a complex that includes at least two species. We conducted morphological and phylogenetic studies of the complex to determine how many species it might contain and how they differed morphologically, geographically and seasonally. We also provide the first LSU phylogeny for the genus Tuber. Phylogenetic analyses resolve nine major clades in the genus with high bootstrap support and distinguish the Gibbosum clade from the Aestivum, Excavatum, Macrosporum, Magnatum, Melanosporum, Puberulum, Rufum and Spinoreticulatum clades. Further analyses of ITS and LSU regions revealed four distinct species in the Gibbosum complex. Although morphologically similar the four species differ in spore size and shape and in peridial anatomy. These species share the synapomorphy of having suprapellis hyphae with distinctive, irregular wall swellings at maturity; we have not seen this hyphal type in any other Tuber spp. worldwide. The three new species are named and described as T. bellisporum Bonito & Trappe, T. castellanoi Bonito & Trappe and T. oregonense Trappe, Bonito & Rawlinson. © 2010 by The Mycological Society of America.

          • GM Bonito, AP Gryganskyi, JM Trappe and R Vilgalys.
          • (2010).
          • A global meta-analysis of Tuber ITS rDNA sequences: Species diversity, host associations and long-distance dispersal.
          • Molecular Ecology
          • ,
          • 19
          • (22)
          • ,
          • 4994-5008.
          • [web]
          Publication Description

          Truffles (Tuber) are ectomycorrhizal fungi characterized by hypogeous fruitbodies. Their biodiversity, host associations and geographical distributions are not well documented. ITS rDNA sequences of Tuber are commonly recovered from molecular surveys of fungal communities, but most remain insufficiently identified making it difficult to determine whether these sequences represent conspecific or novel taxa. In this meta-analysis, over 2000 insufficiently identified Tuber sequences from 76 independent studies were analysed within a phylogenetic framework. Species ranges, host associates, geographical distributions and intra- and interspecific ITS variability were assessed. Over 99% of the insufficiently identified Tuber sequences grouped within clades composed of species with little culinary value (Maculatum, Puberulum and Rufum). Sixty-four novel phylotypes were distinguished including 36 known only from ectomycorrhizae or soil. Most species of Tuber showed 1-3% intraspecific ITS variability and >4% interspecific ITS sequence variation. We found 123 distinct phylotypes based on 96% ITS sequence similarity and estimated that Tuber contains a minimum of 180 species. Based on this meta-analysis, species in Excavatum, Maculatum and Rufum clades exhibit preference for angiosperm hosts, whereas those in the Gibbosum clade are preferential towards gymnosperms. Sixteen Tuber species (>13% of the known diversity) have putatively been introduced to continents or islands outside their native range. © 2010 Blackwell Publishing Ltd.

          • AP Gryganskyi, SC Lee, AP Litvintseva, ME Smith, G Bonito, TM Porter, IM Anishchenko, J Heitman and R Vilgalys.
          • (2010).
          • Structure, function, and phylogeny of the mating locus in the Rhizopus oryzae complex.
          • PLoS ONE
          • ,
          • 5
          • (12)
          • ,
          • e15273.
          • [web]
          Publication Description

          The Rhizopus oryzae species complex is a group of zygomycete fungi that are common, cosmopolitan saprotrophs. Some strains are used beneficially for production of Asian fermented foods but they can also act as opportunistic human pathogens. Although R. oryzae reportedly has a heterothallic (+/2) mating system, most strains have not been observed to undergo sexual reproduction and the genetic structure of its mating locus has not been characterized. Here we report on the mating behavior and genetic structure of the mating locus for 54 isolates of the R. oryzae complex. All 54 strains have a mating locus similar in overall organization to Phycomyces blakesleeanus and Mucor circinelloides (Mucoromycotina, Zygomycota). In all of these fungi, the minus (2) allele features the SexM high mobility group (HMG) gene flanked by an RNA helicase gene and a TP transporter gene (TPT). Within the R. oryzae complex, the plus (+) mating allele includes an inserted region that codes for a BTB/POZ domain gene and the SexP HMG gene. Phylogenetic analyses of multiple genes, including the mating loci (HMG, TPT, RNA helicase), ITS1-5.8S-ITS2 rDNA, RPB2, and LDH genes, identified two distinct groups of strains. These correspond to previously described sibling species R. oryzae sensu stricto and R. delemar. Within each species, discordant gene phylogenies among multiple loci suggest an outcrossing population structure. The hypothesis of random-mating is also supported by a 50:50 ratio of plus and minus mating types in both cryptic species. When crossed with tester strains of the opposite mating type, most isolates of R. delemar failed to produce zygospores, while isolates of R. oryzae produced sterile zygospores. In spite of the reluctance of most strains to mate in vitro, the conserved sex locus structure and evidence for outcrossing suggest that a normal sexual cycle occurs in both species. © 2010 Gryganskyi et al.

          • K Findley, M Rodriguez-Carres, B Metin, J Kroiss, Á Fonseca, R Vilgalys and J Heitman.
          • (2009).
          • Phylogeny and phenotypic characterization of pathogenic Cryptococcus species and closely related saprobic taxa in the tremellales.
          • Eukaryotic Cell
          • ,
          • 8
          • (3)
          • ,
          • 353-361.
          • [web]
          Publication Description

          The basidiomycetous yeasts Cryptococcus neoformans and Cryptococcus gattii are closely related sibling species that cause respiratory and neurological disease in humans and animals. Within these two recognized species, phylogenetic analysis reveals at least six cryptic species defined as molecular types (VNI/II/B, VNIV, VGI, VGII, VGIII, and VGIV) that comprise the pathogenic Cryptococcus species complex. These pathogenic species are clustered in the Filobasidiella clade within the order Tremellales. Previous studies have shown that the Filobasidiella clade also includes several saprobic fungi isolated from insect frass, but information evaluating the relatedness of the saprobes and pathogens within this cluster is limited. Here, the phylogeny encompassing a subset of species in the Tremellales lineage that clusters closely with the pathogenic Cryptococcus species complex was resolved by employing a multilocus sequencing approach for phylogenetic analysis. Six highly conserved genomic loci from 15 related basidiomycete species were sequenced, and the alignments from the concatenated gene sequences were evaluated with different tree-building criteria. Furthermore, these 15 species were subjected to virulence and phenotype assays to evaluate their pathogenic potential. These studies revealed that Cryptococcus amylolentus and Tsuchiyaea wingfieldii, two nonpathogenic sibling species, are the taxa most closely related to the pathogens C. neoformans and C. gattii and together with Filobasidiella depauperata form a Cryptococcus sensu stricto group. Five other saprobic yeast species form the Kwoniella clade, which appears to be a part of a more distantly related sensu lato group. This study establishes a foundation for future comparative genomic approaches that will provide insight into the structure, function, and evolution of the mating type locus, the transitions in modes of sexual reproduction, and the emergence of human pathogenic species from related or ancestral saprobic species. Copyright © 2009, American Society for Microbiology. All Rights Reserved.

          • DJ McLaughlin, DS Hibbett, F Lutzoni, JW Spatafora and R Vilgalys.
          • (2009).
          • The search for the fungal tree of life.
          • Trends in Microbiology
          • ,
          • 17
          • (11)
          • ,
          • 488-497.
          • [web]
          Publication Description

          The Fungi comprise a diverse kingdom of eukaryotes that are characterized by a typically filamentous but sometimes unicellular vegetative form, and heterotrophic, absorptive nutrition. Their simple morphologies and variable ecological strategies have confounded efforts to elucidate their limits, phylogenetic relationships, and diversity. Here we review progress in developing a phylogenetic classification of Fungi since Darwin's On the Origin of Species. Knowledge of phylogenetic relationships has been driven by the available characters that have ranged from morphological and ultrastructural to biochemical and genomic. With the availability of multiple gene phylogenies a well-corroborated phylogenetic classification has now begun to emerge. In the process some fungus-like heterotrophs have been shown to belong elsewhere, and several groups of enigmatic eukaryotic microbes have been added to the Fungi. © 2009 Elsevier Ltd. All rights reserved.

          • JL Parrent and R Vilgalys.
          • (2009).
          • Expression of genes involved in symbiotic carbon and nitrogen transport in Pinus taeda mycorrhizal roots exposed to CO2 enrichment and nitrogen fertilization..
          • Mycorrhiza
          • ,
          • 19
          • (7)
          • ,
          • 469-479.
          • [web]
          Publication Description

          As atmospheric carbon dioxide (CO(2)) concentrations rise, one important mechanism by which plants can gain greater access to necessary soil nutrients is through greater investment in their mycorrhizal symbionts. In this study, we tested the hypotheses that (1) plants increase C allocation to ectomycorrhizal fungi (EMF) under elevated CO(2) conditions, (2) N fertilization decreases C allocation to EMF, and (3) EMF activity at the site of symbiotic C and nutrient exchange is enhanced with CO(2) enrichment. To test these hypotheses, we examined expression levels of Pinus taeda genes encoding monosaccharide transport (MST) and ammonium transport (AMT) proteins thought to be involved in symbiotic C and N movement, respectively, from mycorrhizal root tips exposed to CO(2) and N fertilization. We also examined EMF ribosomal RNA expression (18S rRNA) to determine EMF activity. There was a trend toward lower relative MST expression with increased CO(2). AMT expression levels showed no significant differences between control and treatment plots. EMF 18S rRNA expression was increased in CO(2)-enriched plots and there was a marginally significant positive interactive effect of CO(2) and N fertilization on expression (p = 0.09 and 0.10, respectively). These results are consistent with greater C allocation to EMF and greater EMF metabolic activity under elevated CO(2) conditions, although selective allocation of C to particular EMF species and greater fungal biomass on roots are plausible alternative hypotheses.

          • TY James, AP Litvintseva, R Vilgalys, JAT Morgan, JW Taylor, MC Fisher, L Berger, C Weldon, LD Preez and JE Longcore.
          • (2009).
          • Rapid global expansion of the fungal disease chytridiomycosis into declining and healthy amphibian populations.
          • PLoS Pathogens
          • ,
          • 5
          • (5)
          • ,
          • e1000458.
          • [web]
          Publication Description

          The fungal disease chytridiomycosis, caused by Batrachochytrium dendrobatidis, is enigmatic because it occurs globally in both declining and apparently healthy (non-declining) amphibian populations. This distribution has fueled debate concerning whether, in sites where it has recently been found, the pathogen was introduced or is endemic. In this study, we addressed the molecular population genetics of a global collection of fungal strains from both declining and healthy amphibian populations using DNA sequence variation from 17 nuclear loci and a large fragment from the mitochondrial genome. We found a low rate of DNA polymorphism, with only two sequence alleles detected at each locus, but a high diversity of diploid genotypes. Half of the loci displayed an excess of heterozygous genotypes, consistent with a primarily clonal mode of reproduction. Despite the absence of obvious sex, genotypic diversity was high (44 unique genotypes out of 59 strains). We provide evidence that the observed genotypic variation can be generated by loss of heterozygosity through mitotic recombination. One strain isolated from a bullfrog possessed as much allelic diversity as the entire global sample, suggesting the current epidemic can be traced back to the outbreak of a single clonal lineage. These data are consistent with the current chytridiomycosis epidemic resulting from a novel pathogen undergoing a rapid and recent range expansion. The widespread occurrence of the same lineage in both healthy and declining populations suggests that the outcome of the disease is contingent on environmental factors and host resistance. © 2009 James et al.

          • WH Hartman, CJ Richardson, R Vilgalys and GL Bruland.
          • (2008).
          • Environmental and anthropogenic controls over bacterial communities in wetland soils..
          • Proc Natl Acad Sci U S A
          • ,
          • 105
          • (46)
          • ,
          • 17842-17847.
          • [web]
          Publication Description

          Soil bacteria regulate wetland biogeochemical processes, yet little is known about controls over their distribution and abundance. Bacteria in North Carolina swamps and bogs differ greatly from Florida Everglades fens, where communities studied were unexpectedly similar along a nutrient enrichment gradient. Bacterial composition and diversity corresponded strongly with soil pH, land use, and restoration status, but less to nutrient concentrations, and not with wetland type or soil carbon. Surprisingly, wetland restoration decreased bacterial diversity, a response opposite to that in terrestrial ecosystems. Community level patterns were underlain by responses of a few taxa, especially the Acidobacteria and Proteobacteria, suggesting promise for bacterial indicators of restoration and trophic status.

          • TM Porter, CW Schadt, L Rizvi, AP Martin, SK Schmidt, L Scott-Denton, R Vilgalys and JM Moncalvo.
          • (2008).
          • Widespread occurrence and phylogenetic placement of a soil clone group adds a prominent new branch to the fungal tree of life.
          • Molecular Phylogenetics and Evolution
          • ,
          • 46
          • (2)
          • ,
          • 635-644.
          • [web]
          Publication Description

          Fungi are one of the most diverse groups of Eukarya and play essential roles in terrestrial ecosystems as decomposers, pathogens and mutualists. This study unifies disparate reports of unclassified fungal sequences from soils of diverse origins and anchors many of them in a well-supported clade of the Ascomycota equivalent to a subphylum. We refer to this clade as Soil Clone Group I (SCGI). We expand the breadth of environments surveyed and develop a taxon-specific primer to amplify 2.4 kbp rDNA fragments directly from soil. Our results also expand the known range of this group from North America to Europe and Australia. The ancient origin of SCGI implies that it may represent an important transitional form among the basal Ascomycota groups. SCGI is unusual because it currently represents the only major fungal lineage known only from sequence data. This is an important contribution towards building a more complete fungal phylogeny and highlights the need for further work to determine the function and biology of SCGI taxa. © 2007 Elsevier Inc. All rights reserved.

          • PB Matheny, JM Curtis, V Hofstetter, MC Aime, JM Moncalvo, ZW Ge, JC Slot, JF Ammirati, TJ Baroni, NL Bougher, KW Hughes, DJ Lodge, RW Kerrigan, MT Seidl, DK Aanen, M DeNitis, GM Daniele, DE Desjardin, BR Kropp, LL Norvell, A Parker, EC Vellinga, R Vilgalys, DS Hibbett.
          • (2007).
          • Major clades of Agaricales: a multilocus phylogenetic overview..
          • Mycologia, United States
          • ,
          • 98
          • (6)
          • ,
          • 982-95.
          Publication Description

          An overview of the phylogeny of the Agaricales is presented based on a multilocus analysis of a six-gene region supermatrix. Bayesian analyses of 5611 nucleotide characters of rpb1, rpb1-intron 2, rpb2 and 18S, 25S, and 5.8S ribosomal RNA genes recovered six major clades, which are recognized informally and labeled the Agaricoid, Tricholomatoid, Marasmioid, Pluteoid, Hygrophoroid and Plicaturopsidoid clades. Each clade is discussed in terms of key morphological and ecological traits. At least 11 origins of the ectomycorrhizal habit appear to have evolved in the Agaricales, with possibly as many as nine origins in the Agaricoid plus Tricholomatoid clade alone. A family-based phylogenetic classification is sketched for the Agaricales, in which 30 families, four unplaced tribes and two informally named clades are recognized.

          • JM Moncalvo, RH Nilsson, B Koster, SM Dunham, T Bernauer, PB Matheny, TM Porter, S Margaritescu, M Weiss, S Garnica, E Danell, G Langer, E Langer, E Larsson, KH Larsson, R Vilgalys.
          • (2007).
          • The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods..
          • Mycologia, United States
          • ,
          • 98
          • (6)
          • ,
          • 937-48.
          Publication Description

          We reassessed the circumscription of the cantharelloid clade and identified monophyletic groups by using nLSU, nSSU, mtSSU and RPB2 sequence data. Results agreed with earlier studies that placed the genera Cantharellus, Craterellus, Hydnum, Clavulina, Membranomyces, Multiclavula, Sistotrema, Botryobasidium and the family Ceratobasidiaceae in that clade. Phylogenetic analyses support monophyly of all genera except Sistotrema, which was highly polyphyletic. Strongly supported monophyletic groups were: (i) Cantharellus-Craterellus, Hydnum, and the Sistotrema confluens group; (ii) Clavulina-Membranomyces and the S. brinkmannii-oblongisporum group, with Multiclavula being possibly sister of that clade; (iii) the Sistotrema eximum-octosporum group; (iv) Sistotrema adnatum and S. coronilla. Positions of Sistotrema raduloides and S. athelioides were unresolved, as were basal relationships. Botryobasidium was well supported as the sister taxon of all the above taxa, while Ceratobasidiaceae was the most basal lineage. The relationship between Tulasnella and members of the cantharelloid clade will require further scrutiny, although there is cumulative evidence that they are probably sister groups. The rates of molecular evolution of both the large and small nuclear ribosomal RNA genes (nuc-rDNA) are much higher in Cantharellus, Craterellus and Tulasnella than in the other cantharelloid taxa, and analyses of nuc-rDNA sequences strongly placed Tulasnella close to Cantharellus-Craterellus. In contrast analyses with RPB2 and mtSSU sequences placed Tulasnella at the base of the cantharelloid clade. Our attempt to reconstruct a "supertree" from tree topologies resulting from separate analyses that avoided phylogenetic reconstruction problems associated with missing data and/or unalignable sequences proved unsuccessful.

          • TY James, PM Letcher, JE Longcore, SE Mozley-Standridge, D Porter, MJ Powell, GW Griffith, R Vilgalys.
          • (2007).
          • A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota)..
          • Mycologia, United States
          • ,
          • 98
          • (6)
          • ,
          • 860-71.
          Publication Description

          Chytridiomycota (chytrids) is the only phylum of true Fungi that reproduces with motile spores (zoospores). Chytrids currently are classified into five orders based on habitat, zoospore characters and life cycles. In this paper we estimate the phylogeny of the chytrids with DNA sequences from the ribosomal RNA operon (18S+5.8S+28S subunits). To our surprise the morphologically reduced parasites Olpidium and Rozella comprise two entirely new, and separate, lineages on the fungal tree. Olpidium brassicae groups among the Zygomycota, and Rozella spp. are the earliest branch to diverge in the fungal kingdom. The phylogeny also suggests that Chytridiomycota is not monophyletic and there are four major lineages of chytrids: Rozella spp., Olpidium brassicae, the Blastocladiales and a "core chytrid clade" containing the remaining orders and families and the majority of flagellated fungi. Within the core chytrid group 11 subclades can be identified, each of which correlates well with zoospore ultrastructure or morphology. We provide a synopsis of each clade and its morphological circumscription. The Blastocladiales appears to be the sister taxon of most nonflagellated fungi. Based on molecular phylogenetic and ultrastructural characters this order is elevated to a phylum, the Blastocladiomycota.

          • AE Arnold, DA Henk, RL Eells, F Lutzoni, R Vilgalys.
          • (2007).
          • Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR..
          • Mycologia, United States
          • ,
          • 99
          • (2)
          • ,
          • 185-206.
          Publication Description

          We examined endophytic fungi in asymptomatic foliage of loblolly pine (Pinus taeda) in North Carolina, U.S.A., with four goals: (i) to evaluate morphotaxa, BLAST matches and groups based on sequence similarity as functional taxonomic units; (ii) to explore methods to maximize phylogenetic signal for environmental datasets, which typically contain many taxa but few characters; (iii) to compare culturing vs. culture-free methods (environmental PCR of surface sterilized foliage) for estimating endophyte diversity and species composition; and (iv) to investigate the relationships between traditional ecological indices (e.g. Shannon index) and phylogenetic diversity (PD) in estimating endophyte diversity and spatial heterogeneity. Endophytes were recovered in culture from 87 of 90 P. taeda leaves sampled, yielding 439 isolates that represented 24 morphotaxa. Sequence data from the nuclear ribosomal internal transcribed spacer (ITS) for 150 isolates revealed 59 distinct ITS genotypes that represented 24 and 37 unique groups based on 90% and 95% sequence similarity, respectively. By recoding ambiguously aligned regions to extract phylogenetic signal and implementing a conservative phylogenetic backbone constraint, we recovered well supported phylogenies based on ca. 600 bp of the nuclear ribosomal large subunit (LSUrDNA) for 72 Ascomycota and Basidiomycota, 145 cultured endophytes and 33 environmental PCR samples. Comparisons with LSUrDNA-delimited species showed that morphotaxa adequately estimated total species richness but rarely corresponded to biologically meaningful groups. ITS BLAST results were variable in their utility, but ITS genotype groups based on 90% sequence similarity were concordant with LSUrDNA-delimited species. Environmental PCR yielded more genotypes per sampling effort and recovered several distinct clades relative to culturing, but some commonly cultured clades were never found (Sordariomycetes) or were rare relative to their high frequency among cultures (Leotiomycetes). In contrast to traditional indices, PD demonstrated spatial heterogeneity in endophyte assemblages among P. taeda trees and study plots. Our results highlight the need for caution in designating taxonomic units based on gross cultural morphology or ITS BLAST matches, the utility of phylogenetic tools for extracting robust phylogenies from environmental samples, the complementarity of culturing and environmental PCR, the utility of PD relative to traditional ecological indices, and the remarkably high diversity of foliar fungal endophytes in this simplified temperate ecosystem.

          • AE Arnold, DA Henk, RL Eells, F Lutzoni, R Vilgalys.
          • (2007).
          • Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR..
          • Mycologia, United States
          • ,
          • 99
          • (2)
          • ,
          • 185-206.
          Publication Description

          We examined endophytic fungi in asymptomatic foliage of loblolly pine (Pinus taeda) in North Carolina, U.S.A., with four goals: (i) to evaluate morphotaxa, BLAST matches and groups based on sequence similarity as functional taxonomic units; (ii) to explore methods to maximize phylogenetic signal for environmental datasets, which typically contain many taxa but few characters; (iii) to compare culturing vs. culture-free methods (environmental PCR of surface sterilized foliage) for estimating endophyte diversity and species composition; and (iv) to investigate the relationships between traditional ecological indices (e.g. Shannon index) and phylogenetic diversity (PD) in estimating endophyte diversity and spatial heterogeneity. Endophytes were recovered in culture from 87 of 90 P. taeda leaves sampled, yielding 439 isolates that represented 24 morphotaxa. Sequence data from the nuclear ribosomal internal transcribed spacer (ITS) for 150 isolates revealed 59 distinct ITS genotypes that represented 24 and 37 unique groups based on 90% and 95% sequence similarity, respectively. By recoding ambiguously aligned regions to extract phylogenetic signal and implementing a conservative phylogenetic backbone constraint, we recovered well supported phylogenies based on ca. 600 bp of the nuclear ribosomal large subunit (LSUrDNA) for 72 Ascomycota and Basidiomycota, 145 cultured endophytes and 33 environmental PCR samples. Comparisons with LSUrDNA-delimited species showed that morphotaxa adequately estimated total species richness but rarely corresponded to biologically meaningful groups. ITS BLAST results were variable in their utility, but ITS genotype groups based on 90% sequence similarity were concordant with LSUrDNA-delimited species. Environmental PCR yielded more genotypes per sampling effort and recovered several distinct clades relative to culturing, but some commonly cultured clades were never found (Sordariomycetes) or were rare relative to their high frequency among cultures (Leotiomycetes). In contrast to traditional indices, PD demonstrated spatial heterogeneity in endophyte assemblages among P. taeda trees and study plots. Our results highlight the need for caution in designating taxonomic units based on gross cultural morphology or ITS BLAST matches, the utility of phylogenetic tools for extracting robust phylogenies from environmental samples, the complementarity of culturing and environmental PCR, the utility of PD relative to traditional ecological indices, and the remarkably high diversity of foliar fungal endophytes in this simplified temperate ecosystem.

          • AE Arnold, DA Henk, RL Eells, F Lutzoni and R Vilgalys.
          • (2007).
          • Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR..
          • Mycologia
          • ,
          • 99
          • (2)
          • ,
          • 185-206.
          • [web]
          Publication Description

          We examined endophytic fungi in asymptomatic foliage of loblolly pine (Pinus taeda) in North Carolina, U.S.A., with four goals: (i) to evaluate morphotaxa, BLAST matches and groups based on sequence similarity as functional taxonomic units; (ii) to explore methods to maximize phylogenetic signal for environmental datasets, which typically contain many taxa but few characters; (iii) to compare culturing vs. culture-free methods (environmental PCR of surface sterilized foliage) for estimating endophyte diversity and species composition; and (iv) to investigate the relationships between traditional ecological indices (e.g. Shannon index) and phylogenetic diversity (PD) in estimating endophyte diversity and spatial heterogeneity. Endophytes were recovered in culture from 87 of 90 P. taeda leaves sampled, yielding 439 isolates that represented 24 morphotaxa. Sequence data from the nuclear ribosomal internal transcribed spacer (ITS) for 150 isolates revealed 59 distinct ITS genotypes that represented 24 and 37 unique groups based on 90% and 95% sequence similarity, respectively. By recoding ambiguously aligned regions to extract phylogenetic signal and implementing a conservative phylogenetic backbone constraint, we recovered well supported phylogenies based on ca. 600 bp of the nuclear ribosomal large subunit (LSUrDNA) for 72 Ascomycota and Basidiomycota, 145 cultured endophytes and 33 environmental PCR samples. Comparisons with LSUrDNA-delimited species showed that morphotaxa adequately estimated total species richness but rarely corresponded to biologically meaningful groups. ITS BLAST results were variable in their utility, but ITS genotype groups based on 90% sequence similarity were concordant with LSUrDNA-delimited species. Environmental PCR yielded more genotypes per sampling effort and recovered several distinct clades relative to culturing, but some commonly cultured clades were never found (Sordariomycetes) or were rare relative to their high frequency among cultures (Leotiomycetes). In contrast to traditional indices, PD demonstrated spatial heterogeneity in endophyte assemblages among P. taeda trees and study plots. Our results highlight the need for caution in designating taxonomic units based on gross cultural morphology or ITS BLAST matches, the utility of phylogenetic tools for extracting robust phylogenies from environmental samples, the complementarity of culturing and environmental PCR, the utility of PD relative to traditional ecological indices, and the remarkably high diversity of foliar fungal endophytes in this simplified temperate ecosystem.

          • PC Ceresini, HD Shew, TY James, RJ Vilgalys and MA Cubeta.
          • (2007).
          • Phylogeography of the Solanaceae-infecting Basidiomycota fungus Rhizoctonia solani AG-3 based on sequence analysis of two nuclear DNA loci..
          • BMC Evol Biol
          • ,
          • 7
          • ,
          • 163.
          • [web]
          Publication Description

          BACKGROUND: The soil fungus Rhizoctonia solani anastomosis group 3 (AG-3) is an important pathogen of cultivated plants in the family Solanaceae. Isolates of R. solani AG-3 are taxonomically related based on the composition of cellular fatty acids, phylogenetic analysis of nuclear ribosomal DNA (rDNA) and beta-tubulin gene sequences, and somatic hyphal interactions. Despite the close genetic relationship among isolates of R. solani AG-3, field populations from potato and tobacco exhibit comparative differences in their disease biology, dispersal ecology, host specialization, genetic diversity and population structure. However, little information is available on how field populations of R. solani AG-3 on potato and tobacco are shaped by population genetic processes. In this study, two field populations of R. solani AG-3 from potato in North Carolina (NC) and the Northern USA; and two field populations from tobacco in NC and Southern Brazil were examined using sequence analysis of two cloned regions of nuclear DNA (pP42F and pP89). RESULTS: Populations of R. solani AG-3 from potato were genetically diverse with a high frequency of heterozygosity, while limited or no genetic diversity was observed within the highly homozygous tobacco populations from NC and Brazil. Except for one isolate (TBR24), all NC and Brazilian isolates from tobacco shared the same alleles. No alleles were shared between potato and tobacco populations of R. solani AG-3, indicating no gene flow between them. To infer historical events that influenced current geographical patterns observed for populations of R. solani AG-3 from potato, we performed an analysis of molecular variance (AMOVA) and a nested clade analysis (NCA). Population differentiation was detected for locus pP89 (Phi ST = 0.257, significant at P

          • DS Hibbett, M Binder, JF Bischoff, M Blackwell, PF Cannon, OE Eriksson, S Huhndorf, T James, PM Kirk, R Lücking, HT Lumbsch, F Lutzoni, PB Matheny, DJ McLaughlin, MJ Powell, S Redhead, CL Schoch, JW Spatafora, JA Stalpers, R Vilgalys, MC Aime, A Aptroot, R Bauer, D Begerow, GL Benny, LA Castlebury, PW Crous, YC Dai, W Gams, DM Geiser, GW Griffith, C Gueidan, DL Hawksworth, G Hestmark, K Hosaka, RA Humber, KD Hyde, JE Ironside, U Kõljalg, CP Kurtzman, KH Larsson, R Lichtwardt, J Longcore, J Miadlikowska, A Miller, JM Moncalvo, S Mozley-Standridge, F Oberwinkler, E Parmasto, V Reeb, JD Rogers, C Roux, L Ryvarden, JP Sampaio, A Schüßler, J Sugiyama, RG Thorn, L Tibell, WA Untereiner, C Walker, Z Wang, A Weir, M Weiss, MM White, K Winka, YJ Yao and N Zhang.
          • (2007).
          • A higher-level phylogenetic classification of the Fungi.
          • Mycological Research
          • ,
          • 111
          • (5)
          • ,
          • 509-547.
          • [web]
          Publication Description

          A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community. The classification includes 195 taxa, down to the level of order, of which 16 are described or validated here: Dikarya subkingdom nov.; Chytridiomycota, Neocallimastigomycota phyla nov.; Monoblepharidomycetes, Neocallimastigomycetes class. nov.; Eurotiomycetidae, Lecanoromycetidae, Mycocaliciomycetidae subclass. nov.; Acarosporales, Corticiales, Baeomycetales, Candelariales, Gloeophyllales, Melanosporales, Trechisporales, Umbilicariales ords. nov. The clade containing Ascomycota and Basidiomycota is classified as subkingdom Dikarya, reflecting the putative synapomorphy of dikaryotic hyphae. The most dramatic shifts in the classification relative to previous works concern the groups that have traditionally been included in the Chytridiomycota and Zygomycota. The Chytridiomycota is retained in a restricted sense, with Blastocladiomycota and Neocallimastigomycota representing segregate phyla of flagellated Fungi. Taxa traditionally placed in Zygomycota are distributed among Glomeromycota and several subphyla incertae sedis, including Mucoromycotina, Entomophthoromycotina, Kickxellomycotina, and Zoopagomycotina. Microsporidia are included in the Fungi, but no further subdivision of the group is proposed. Several genera of 'basal' Fungi of uncertain position are not placed in any higher taxa, including Basidiobolus, Caulochytrium, Olpidium, and Rozella. © 2007 The British Mycological Society.

          • JL Parrent and R Vilgalys.
          • (2007).
          • Biomass and compositional responses of ectomycorrhizal fungal hyphae to elevated CO2 and nitrogen fertilization.
          • New Phytologist
          • ,
          • 176
          • (1)
          • ,
          • 164-174.
          • [web]
          Publication Description

          • The extramatrical mycelia (EMM) of ectomycorrhizal fungi make up a large proportion of the microbial diversity and biomass in temperate forest soils. Thus, their response to elevated CO2 can have large effects on plant nutrient acquisition and carbon movement through forests. • Here, the effects of CO2 and nitrogen (N) fertilization on EMM biomass and community structure in Pinus taeda forest plots were examined using sand-filled mesh bags buried in the field, the contents of which were analyzed by phospholipid fatty acid (PLFA) and DNA sequencing. • A total of 2138 sequences comprising 295 taxa were recovered; most (83.5%) were from ectomycorrhizal fungal taxa. No biomass increase was detected in elevated CO2 plots relative to control plots, but individual taxa responded to both CO2 and N fertilization, four of the six most abundant taxa were less frequent in N-fertilized plots. Thelephoroid and athelioid taxa were both frequent and abundant as EMM, and thelephoroid richness was extremely high. Russula and Cortinariaceae taxa were less abundant and boletoid taxa were more abundant as EMM relative to ectomycorrhizas. • The EMM community, sampled across seasons and years, was dynamic with a high degree of interspecific variation in response to CO2 enrichment and N fertilization. © The Authors (2007).

          • DA Henk and R Vilgalys.
          • (2007).
          • Molecular phylogeny suggests a single origin of insect symbiosis in the Pucciniomycetes with support for some relationships within the genus Septobasidium.
          • American Journal of Botany
          • ,
          • 94
          • (9)
          • ,
          • 1515-1526.
          • [web]
          Publication Description

          In the Pucciniomycetes, a class of fungi that includes the plant pathogenic rust fungi, insect parasitism is restricted to a single family, the Septobasidiaceae. The Septobasidiaceae form a variety of symbioses with scale insects and have remained largely unstudied since the 1930s. Transitions between plant and animal parasitism and between mutualism and parasitism cannot be fully addressed in the Basidiomycota without a clear phylogenetic hypothesis for the Septobasidiales. Here, molecular phylogenetic methods were applied to understand the origin of scale insect parasitism, test the monophyly of the order Septobasidiales, and evaluate the infrageneric concepts in the largest genus of scale insect parasites, Septobasidium. DNA sequence data from rRNA genes were used to infer higher-level relationships within the Pucciniomycetes, and data from translation elongation factor 1-alpha (tef1) were added for phylogenetic inference within the Septobasidiaceae. Data from tef1 revealed different intron arrangements within Septobasidium, but the molecule did not provide much additional phylogenetically informative data. Likelihood-model- based phylogenetic analyses of 44 Pucciniomycotina taxa provided moderate support for a single origin of insect parasitism. Within the Septobasidiaceae, there was little or no support for a monophyletic Septobasidium, and well-resolved subclades of Septobasidium species contradict previous morphological delimitations of groups within the genus.

          • TY James, F Kauff, CL Schoch, PB Matheny, V Hofstetter, CJ Cox, G Celio, C Gueidan, E Fraker, J Miadlikowska, HT Lumbsch, A Rauhut, V Reeb, AE Arnold, A Amtoft, JE Stajich, K Hosaka, GH Sung, D Johnson, B O'Rourke, M Crockett, M Binder, JM Curtis, JC Slot, Z Wang, AW Wilson, A Schüssler, JE Longcore, K O'Donnell, S Mozley-Standridge, D Porter, PM Letcher, MJ Powell, JW Taylor, MM White, GW Griffith, DR Davies, RA Humber, JB Morton, J Sugiyama, AY Rossman, JD Rogers, DH Pfister, D Hewitt, K Hansen, S Hambleton, RA Shoemaker, J Kohlmeyer, B Volkmann-Kohlmeyer, RA Spotts, M Serdani, PW Crous, KW Hughes, K Matsuura, E Langer, G Langer, WA Untereiner, R Lücking, B Büdel, DM Geiser, A Aptroot, P Diederich, I Schmitt, M Schultz, R Yahr, DS Hibbett, F Lutzoni, DJ McLaughlin, JW Spatafora and R Vilgalys.
          • (2006).
          • Reconstructing the early evolution of Fungi using a six-gene phylogeny..
          • Nature
          • ,
          • 443
          • (7113)
          • ,
          • 818-822.
          • [web]
          Publication Description

          The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extant phylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore flagellum, leading to the diversification of terrestrial fungi. Here we develop phylogenetic hypotheses for Fungi using data from six gene regions and nearly 200 species. Our results indicate that there may have been at least four independent losses of the flagellum in the kingdom Fungi. These losses of swimming spores coincided with the evolution of new mechanisms of spore dispersal, such as aerial dispersal in mycelial groups and polar tube eversion in the microsporidia (unicellular forms that lack mitochondria). The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree.

          • JL Parrent, WF Morris, R Vilgalys.
          • (2006).
          • CO2-enrichment and nutrient availability alter ectomycorrhizal fungal communities..
          • Ecology, United States
          • ,
          • 87
          • (9)
          • ,
          • 2278-87.
          Publication Description

          Ectomycorrhizal fungi (EMF), a phylogenetically and physiologically diverse guild, form symbiotic associations with many trees and greatly enhance their uptake of nutrients and water. Elevated CO2, which increases plant carbon supply and demand for mineral nutrients, may change the composition of the EMF community, possibly altering nutrient uptake and ultimately forest productivity. To assess CO2 effects on EMF communities, we sampled mycorrhizae from the FACTS-I (Forest-Atmosphere Carbon Transfer and Storage) research site in Duke Forest, Orange County, North Carolina, USA, where Pinus taeda forest plots are maintained at either ambient or elevated CO2 (200 ppm above ambient) concentrations. Mycorrhizae were identified by DNA sequence similarity of the internal transcribed spacer ribosomal RNA gene region. EMF richness was very high; 72 distinct phylotypes were detected from 411 mycorrhizal samples. Overall EMF richness and diversity were not affected by elevated CO2, but increased CO2 concentrations altered the relative abundances of particular EMF taxa colonizing fine roots, increased prevalence of unique EMF species, and led to greater EMF community dissimilarity among individual study plots. Natural variation among plots in mean potential net nitrogen (N) mineralization rates was a key determinant of EMF community structure; increasing net N mineralization rate was negatively correlated with EMF richness and had differential effects on the abundance of particular EMF taxa. Our results predict that, at CO2 concentrations comparable to that predicted for the year 2050, EMF community composition and structure will change, but diversity will be maintained. In contrast, high soil N concentrations can negatively affect EMF diversity; this underscores the importance of considering CO2 effects on forest ecosystems in the context of background soil chemical parameters and other environmental perturbations such as acid deposition or fertilizer runoff.

          • JL Parrent, WF Morris and R Vilgalys.
          • (2006).
          • CO2-enrichment and nutrient availability alter ectomycorrhizal fungal communities..
          • Ecology
          • ,
          • 87
          • (9)
          • ,
          • 2278-2287.
          • [web]
          Publication Description

          Ectomycorrhizal fungi (EMF), a phylogenetically and physiologically diverse guild, form symbiotic associations with many trees and greatly enhance their uptake of nutrients and water. Elevated CO2, which increases plant carbon supply and demand for mineral nutrients, may change the composition of the EMF community, possibly altering nutrient uptake and ultimately forest productivity. To assess CO2 effects on EMF communities, we sampled mycorrhizae from the FACTS-I (Forest-Atmosphere Carbon Transfer and Storage) research site in Duke Forest, Orange County, North Carolina, USA, where Pinus taeda forest plots are maintained at either ambient or elevated CO2 (200 ppm above ambient) concentrations. Mycorrhizae were identified by DNA sequence similarity of the internal transcribed spacer ribosomal RNA gene region. EMF richness was very high; 72 distinct phylotypes were detected from 411 mycorrhizal samples. Overall EMF richness and diversity were not affected by elevated CO2, but increased CO2 concentrations altered the relative abundances of particular EMF taxa colonizing fine roots, increased prevalence of unique EMF species, and led to greater EMF community dissimilarity among individual study plots. Natural variation among plots in mean potential net nitrogen (N) mineralization rates was a key determinant of EMF community structure; increasing net N mineralization rate was negatively correlated with EMF richness and had differential effects on the abundance of particular EMF taxa. Our results predict that, at CO2 concentrations comparable to that predicted for the year 2050, EMF community composition and structure will change, but diversity will be maintained. In contrast, high soil N concentrations can negatively affect EMF diversity; this underscores the importance of considering CO2 effects on forest ecosystems in the context of background soil chemical parameters and other environmental perturbations such as acid deposition or fertilizer runoff.

          • D González, MA Cubeta, R Vilgalys.
          • (2006).
          • Phylogenetic utility of indels within ribosomal DNA and beta-tubulin sequences from fungi in the Rhizoctonia solani species complex..
          • Molecular phylogenetics and evolution, United States
          • ,
          • 40
          • (2)
          • ,
          • 459-70.
          • [web]
          Publication Description

          The genus Rhizoctonia consists of a diverse assemblage of anamorphic fungi frequently associated with plants and soil throughout the world. Some anamorphs are related with teleomorphs (sexual stage) in different taxonomic classes, orders, and families. The fungus may exist as pathogen, saprophyte, or mycorrhizal symbiont and shows extensive variation in characteristics such as geographic location, morphology, host specificity, and pathogenicity. In this study, phylogenetic analyses were performed in the Rhizoctonia solani species complex with individual and combined data sets from three gene partitions (ITS, LSU rDNA, and beta-tubulin). To explore whether indels were a source of phylogenetically informative characters, single-site indels were treated as a new state, while indels greater than one contiguous nucleotide were analyzed by including them as ambiguous data (Coding A); excluding them from the analyses (Coding B), and with three distinct codes: multistate for different sequence (Coding C); multistate for different length (Coding D) and different characters for each distinct sequence (Coding E). Results suggest that indels in noncoding regions contain phylogenetic information and support the fact that the R. solani species complex is not monophyletic. Six clades within R. solani (teleomorph=Thanatephorus) representing distinct anastomosis groups and five clades within binucleate Rhizoctonia (teleomorph=Ceratobasidium) were well supported in all analyses. The data suggest that clades with representatives of R. solani fungi belonging to anastomosis groups 1, 4, 6, and 8 should be recognized as phylogenetic species.

          • AP Litvintseva, R Thakur, R Vilgalys, TG Mitchell.
          • (2006).
          • Multilocus sequence typing reveals three genetic subpopulations of Cryptococcus neoformans var. grubii (serotype A), including a unique population in Botswana..
          • Genetics, United States
          • ,
          • 172
          • (4)
          • ,
          • 2223-38.
          • [web]
          Publication Description

          We applied multilocus sequence typing (MLST) to investigate the population structure and mode of reproduction of Cryptococcus neoformans var. grubii (serotype A). This MLST system utilizes 12 unlinked polymorphic loci, which are dispersed on nine different chromosomes, and allows the unambiguous identification of closely related strains of serotype A. We compared MLST analyses with the conventional genotyping method of detecting amplified fragment length polymorphisms (AFLPs), and there was excellent correlation between the MLST and AFLP results. However, MLST differentiated a larger number of strains. We analyzed a global collection of isolates of serotype A using both methods, and the results identified at least three genetically distinct subpopulations, designated groups VNI, VNII, and VNB. Groups VNI and VNII are widespread, dominated by isolates with the MATalpha mating type, and predominantly clonal. Conversely, isolates of group VNB are unique to Botswana, include a significant proportion of fertile strains with the MATa mating type, and manifest compelling evidence of recombination. We have AFLP genotyped >1000 strains of serotype A from different parts of the world, including isolates from several African countries, and, to date, haploid serotype A isolates of group VNB have been found only in Botswana.

          • AP Litvintseva, R Thakur, R Vilgalys and TG Mitchell.
          • (2006).
          • Multilocus sequence typing reveals three genetic subpopulations of Cryptococcus neoformans var. grubii (serotype A), including a unique population in Botswana..
          • Genetics
          • ,
          • 172
          • (4)
          • ,
          • 2223-2238.
          • [web]
          Publication Description

          We applied multilocus sequence typing (MLST) to investigate the population structure and mode of reproduction of Cryptococcus neoformans var. grubii (serotype A). This MLST system utilizes 12 unlinked polymorphic loci, which are dispersed on nine different chromosomes, and allows the unambiguous identification of closely related strains of serotype A. We compared MLST analyses with the conventional genotyping method of detecting amplified fragment length polymorphisms (AFLPs), and there was excellent correlation between the MLST and AFLP results. However, MLST differentiated a larger number of strains. We analyzed a global collection of isolates of serotype A using both methods, and the results identified at least three genetically distinct subpopulations, designated groups VNI, VNII, and VNB. Groups VNI and VNII are widespread, dominated by isolates with the MATalpha mating type, and predominantly clonal. Conversely, isolates of group VNB are unique to Botswana, include a significant proportion of fertile strains with the MATa mating type, and manifest compelling evidence of recombination. We have AFLP genotyped >1000 strains of serotype A from different parts of the world, including isolates from several African countries, and, to date, haploid serotype A isolates of group VNB have been found only in Botswana.

          • TY James, P Srivilai, U Kües, R Vilgalys.
          • (2006).
          • Evolution of the bipolar mating system of the mushroom Coprinellus disseminatus from its tetrapolar ancestors involves loss of mating-type-specific pheromone receptor function..
          • Genetics, United States
          • ,
          • 172
          • (3)
          • ,
          • 1877-91.
          • [web]
          Publication Description

          Mating incompatibility in mushroom fungi is controlled by the mating-type loci. In tetrapolar species, two unlinked mating-type loci exist (A and B), whereas in bipolar species there is only one locus. The A and B mating-type loci encode homeodomain transcription factors and pheromones and pheromone receptors, respectively. Most mushroom species have a tetrapolar mating system, but numerous transitions to bipolar mating systems have occurred. Here we determined the genes controlling mating type in the bipolar mushroom Coprinellus disseminatus. Through positional cloning and degenerate PCR, we sequenced both the transcription factor and pheromone receptor mating-type gene homologs from C. disseminatus. Only the transcription factor genes segregate with mating type, discounting the hypothesis of genetic linkage between the A and B mating-type loci as the causal origin of bipolar mating behavior. The mating-type locus of C. disseminatus is similar to the A mating-type locus of the model species Coprinopsis cinerea and encodes two tightly linked pairs of homeodomain transcription factor genes. When transformed into C. cinerea, the C. disseminatus A and B homologs elicited sexual reactions like native mating-type genes. Although mating type in C. disseminatus is controlled by only the transcription factor genes, cellular functions appear to be conserved for both groups of genes.

          • James TY, Kauff F, Schoch CL, Matheny PB, Hofstetter V, Cox CJ, Celio G, Gueidan C, Fraker E, Miadlikowska J, Lumbsch HT, Rauhut A, Reeb V, Arnold AE, Amtoft A, Stajich JE, Hosaka K, Sung GH, Johnson D, O'Rourke B, Crockett M, Binder M, Curtis JM, Slot JC, Wang Z, Wilson AW, Schussler A, Longcore JE, O'Donnell K, Mozley-Standridge S, Porter D, Letcher PM, Powell MJ, Taylor JW, White MM, Griffith GW, Davies DR, Humber RA, Morton JB, Sugiyama J, Rossman AY, Rogers JD, Pfister DH, Hewitt D, Hansen K, Hambleton S, Shoemaker RA, Kohlmeyer J, Volkmann-Kohlmeyer B, Spotts RA, Serdani M, Crous PW, Hughes KW, Matsuura K, Langer E, Langer G, Untereiner WA, Lucking R, Budel B, Geiser DM, Aptroot A, Diederich P, Schmitt I, Schultz M, Yahr R, Hibbett DS, Lutzoni F, McLaughlin DJ, Spatafora JW, Vilgalys R.
          • (2006).
          • Reconstructing the early evolution of Fungi using a six-gene phylogeny.
          • Nature
          • ,
          • 443
          • ,
          • 818-822.
          • R Yahr, R Vilgalys and PT DePriest.
          • (2006).
          • Erratum: Geographic variation in algal partners of Cladonia subtenuis (Cladoniaceae) highlights the dynamic nature of a lichen symbiosis (New Phytologist (2006) 171 (847-860)).
          • New Phytologist
          • ,
          • 172
          • (2)
          • ,
          • 377-.
          • [web]
          • TY James, PM Letcher, JE Longcore, SE Mozley-Standridge, D Porter, MJ Powell, GW Griffith and R Vilgalys.
          • (2006).
          • A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota).
          • Mycologia
          • ,
          • 98
          • (6)
          • ,
          • 860-871.
          • [web]
          Publication Description

          Chytridiomycota (chytrids) is the only phylum of true Fungi that reproduces with motile spores (zoospores). Chytrids currently are classified into five orders based on habitat, zoospore characters and life cycles. In this paper we estimate the phylogeny of the chytrids with DNA sequences from the ribosomal RNA operon (18S+5.8S+28S subunits). To our surprise the morphologically reduced parasites Olpidium and Rozella comprise two entirely new, and separate, lineages on the fungal tree. Olpidium brassicae groups among the Zygomycota, and Rozella spp. are the earliest branch to diverge in the fungal kingdom. The phylogeny also suggests that Chytridiomycota is not monophyletic and there are four major lineages of chytrids: Rozella spp., Olpidium brassicae, the Blastocladiales and a "core chytrid clade" containing the remaining orders and families and the majority of flagellated fungi. Within the core chytrid group 11 subclades can be identified, each of which correlates well with zoospore ultrastructure or morphology. We provide a synopsis of each clade and its morphological circumscription. The Blastocladiales appears to be the sister taxon of most nonflagellated fungi. Based on molecular phylogenetic and ultrastructural characters this order is elevated to a phylum, the Blastocladiomycota. © 2006 by The Mycological Society of America.

          • JM Moncalvo, RH Nilsson, B Koster, SM Dunham, T Bernauer, PB Matheny, TM Porter, S Margaritescu, M Weiß, S Garnica, E Danell, G Langer, E Langer, E Larsson, KH Larsson and R Vilgalys.
          • (2006).
          • The cantharelloid clade: Dealing with incongruent gene trees and phylogenetic reconstruction methods.
          • Mycologia
          • ,
          • 98
          • (6)
          • ,
          • 937-948.
          • [web]
          Publication Description

          We reassessed the circumscription of the cantharelloid clade and identified monophyletic groups by using nLSU, nSSU, mtSSU and RPB2 sequence data. Results agreed with earlier studies that placed the genera Cantharellus, Craterellus, Hydnum, Clavulina, Membranomyces, Multiclavula, Sistotrema, Botryobasidium and the family Ceratobasidiaceae in that clade. Phylogenetic analyses support monophyly of all genera except Sistotrema, which was highly polyphyletic. Strongly supported monophyletic groups were: (i) Cantharellus-Craterellus, Hydnum, and the Sistotrema confluens group; (ii) Clavulina-Membranomyces and the S. brinkmannii-oblongisporum group, with Multiclavula being possibly sister of that clade; (iii) the Sistotrema eximum-octosporum group; (iv) Sistotrema adnatum and S. coronilla. Positions of Sistotrema raduloides and S. athelioides were unresolved, as were basal relationships. Botryobasidium was well supported as the sister taxon of all the above taxa, while Ceratobasidiaceae was the most basal lineage. The relationship between Tulasnella and members of the cantharelloid clade will require further scrutiny, although there is cumulative evidence that they are probably sister groups. The rates of molecular evolution of both the large and small nuclear ribosomal RNA genes (nuc-rDNA) are much higher in Cantharellus, Craterellus and Tulasnella than in the other cantharelloid taxa, and analyses of nuc-rDNA sequences strongly placed Tulasnella close to Cantharellus-Craterellus. In contrast analyses with RPB2 and mtSSU sequences placed Tulasnella at the base of the cantharelloid clade. Our attempt to reconstruct a "supertree" from tree topologies resulting from separate analyses that avoided phylogenetic reconstruction problems associated with missing data and/or unalignable sequences proved unsuccessful. © 2006 by The Mycological Society of America.

          • PB Matheny, JM Curtis, V Hofstetter, MC Aime, JM Moncalvo, ZW Ge, ZL Yang, JC Slot, JF Ammirati, TJ Baroni, NL Bougher, KW Hughes, DJ Lodge, RW Kerrigan, MT Seidl, DK Aanen, M DeNitis, GM Daniele, DE Desjardin, BR Kropp, LL Norvell, A Parker, EC Vellinga, R Vilgalys and DS Hibbett.
          • (2006).
          • Major clades of Agaricales: A multilocus phylogenetic overview.
          • Mycologia
          • ,
          • 98
          • (6)
          • ,
          • 982-995.
          • [web]
          Publication Description

          An overview of the phylogeny of the Agaricales is presented based on a multilocus analysis of a six-gene region supermatrix. Bayesian analyses of 5611 nucleotide characters of rpb1, rpb1-intron 2, rpb2 and 18S, 25S, and 5.8S ribosomal RNA genes recovered six major clades, which are recognized informally and labeled the Agaricoid, Tricholomatoid, Marasmioid, Pluteoid, Hygrophoroid and Plicaturopsidoid clades. Each clade is discussed in terms of key morphological and ecological traits. At least 11 origins of the ectomycorrhizal habit appear to have evolved in the Agaricales, with possibly as many as nine origins in the Agaricoid plus Tricholomatoid clade alone. A family-based phylogenetic classification is sketched for the Agaricales, in which 30 families, four unplaced tribes and two informally named clades are recognized. © 2006 by The Mycological Society of America.

          • D González, MA Cubeta and R Vilgalys.
          • (2006).
          • Phylogenetic utility of indels within ribosomal DNA and β-tubulin sequences from fungi in the Rhizoctonia solani species complex.
          • Molecular Phylogenetics and Evolution
          • ,
          • 40
          • (2)
          • ,
          • 459-470.
          • [web]
          Publication Description

          The genus Rhizoctonia consists of a diverse assemblage of anamorphic fungi frequently associated with plants and soil throughout the world. Some anamorphs are related with teleomorphs (sexual stage) in different taxonomic classes, orders, and families. The fungus may exist as pathogen, saprophyte, or mycorrhizal symbiont and shows extensive variation in characteristics such as geographic location, morphology, host specificity, and pathogenicity. In this study, phylogenetic analyses were performed in the Rhizoctonia solani species complex with individual and combined data sets from three gene partitions (ITS, LSU rDNA, and β-tubulin). To explore whether indels were a source of phylogenetically informative characters, single-site indels were treated as a new state, while indels greater than one contiguous nucleotide were analyzed by including them as ambiguous data (Coding A); excluding them from the analyses (Coding B), and with three distinct codes: multistate for different sequence (Coding C); multistate for different length (Coding D) and different characters for each distinct sequence (Coding E). Results suggest that indels in noncoding regions contain phylogenetic information and support the fact that the R. solani species complex is not monophyletic. Six clades within R. solani (teleomorph = Thanatephorus) representing distinct anastomosis groups and five clades within binucleate Rhizoctonia (teleomorph = Ceratobasidium) were well supported in all analyses. The data suggest that clades with representatives of R. solani fungi belonging to anastomosis groups 1, 4, 6, and 8 should be recognized as phylogenetic species. © 2006 Elsevier Inc. All rights reserved.

          • TY James, P Srivilai, U Kües and R Vilgalys.
          • (2006).
          • Evolution of the bipolar mating system of the mushroom Coprinellus disseminatus from its tetrapolar ancestors involves loss of mating-type-specific pheromone receptor function.
          • Genetics
          • ,
          • 172
          • (3)
          • ,
          • 1877-1891.
          • [web]
          Publication Description

          Mating incompatibility in mushroom fungi is controlled by the mating-type loci. In tetrapolar species, two unlinked mating-type loci exist (A and B), whereas in bipolar species there is only one locus. The A and B mating-type loci encode homeodomain transcription factors and pheromones and pheromone receptors, respectively. Most mushroom species have a tetrapolar mating system, but numerous transitions to bipolar mating systems have occurred. Here we determined the genes controlling mating type in the bipolar mushroom Coprinellus disseminatus. Through positional cloning and degenerate PCR, we sequenced both the transcription factor and pheromone receptor mating-type gene homologs from C. disseminatus. Only the transcription factor genes segregate with mating type, discounting the hypothesis of genetic linkage between the A and B mating-type loci as the causal origin of bipolar mating behavior. The mating-type locus of C. disseminatus is similar to the A mating-type locus of the model species Coprinopsis cinerea and encodes two tightly linked pairs of homeodomain transcription factor genes. When transformed into C. cinerea, the C. disseminatus A and B homologs elicited sexual reactions like native matingtype genes. Although mating type in C. disseminatus is controlled by only the transcription factor genes, cellular functions appear to be conserved for both groups of genes. Copyright © 2006 by the Genetics Society of America.

          • R Yahr, R Vilgalys and PT Depriest.
          • (2006).
          • Geographic variation in algal partners of Cladonia subtenuis (Cladoniaceae) highlights the dynamic nature of a lichen symbiosis.
          • New Phytologist
          • ,
          • 171
          • (4)
          • ,
          • 847-860.
          • [web]
          Publication Description

          • Multiple interacting factors may explain variation present in symbiotic associations, including fungal specificity, algal availability, mode of transmission and fungal selectivity. To separate these factors, we sampled the lichenized Cladonia subtenuis and associated Asterochloris algae across a broad geographic range. • We sampled 87 thalli across 11 sites using sequence data to test for fungal specificity (phylogenetic range of association) and selectivity (frequency of association), fungal reproductive mode, and geographic structure among populations. Permutation tests were used to examine symbiont transmission. • Four associated algal clades were found. Analysis of molecular variation (AMOVA) and partial Mantel tests suggested that the frequency of associated algal genotypes was significantly different among sites and habitats, but at random with respect to fungal genotype and clade. The apparent specificity for Clade II algae in the fungal species as a whole did not scale down to further within-species lineage-dependent specificity for particular algae. Fungal genotypes were not structured according to site and appeared to be recombining. • We suggest that ecological specialization exists for a specific lichen partnership and a site, and that this selectivity is dynamic and environment-dependent. We present a working model combining algal availability, fungal specificity and selectivity, which maintains variation in symbiotic composition across landscapes. © The Authors (2006).

          • R Yahr, R Vilgalys, PT DePriest.
          • (2006).
          • Geographic variation in algal partners of Cladonia subtenuis (Cladoniaceae) highlights the dynamic nature of a lichen symbiosis..
          • The New phytologist, England
          • ,
          • 171
          • (4)
          • ,
          • 847-60.
          • [web]
          Publication Description

          Multiple interacting factors may explain variation present in symbiotic associations, including fungal specificity, algal availability, mode of transmission and fungal selectivity. To separate these factors, we sampled the lichenized Cladonia subtenuis and associated Asterochloris algae across a broad geographic range. We sampled 87 thalli across 11 sites using sequence data to test for fungal specificity (phylogenetic range of association) and selectivity (frequency of association), fungal reproductive mode, and geographic structure among populations. Permutation tests were used to examine symbiont transmission. Four associated algal clades were found. Analysis of molecular variation (amova) and partial Mantel tests suggested that the frequency of associated algal genotypes was significantly different among sites and habitats, but at random with respect to fungal genotype and clade. The apparent specificity for Clade II algae in the fungal species as a whole did not scale down to further within-species lineage-dependent specificity for particular algae. Fungal genotypes were not structured according to site and appeared to be recombining. We suggest that ecological specialization exists for a specific lichen partnership and a site, and that this selectivity is dynamic and environment-dependent. We present a working model combining algal availability, fungal specificity and selectivity, which maintains variation in symbiotic composition across landscapes.

          • HE O'Brien, JL Parrent, JA Jackson, JM Moncalvo and R Vilgalys.
          • (2005).
          • Fungal community analysis by large-scale sequencing of environmental samples..
          • Appl Environ Microbiol
          • ,
          • 71
          • (9)
          • ,
          • 5544-5550.
          • [web]
          Publication Description

          Fungi are an important and diverse component of soil communities, but these communities have proven difficult to study in conventional biotic surveys. We evaluated soil fungal diversity at two sites in a temperate forest using direct isolation of small-subunit and internal transcribed spacer (ITS) rRNA genes by PCR and high-throughput sequencing of cloned fragments. We identified 412 sequence types from 863 fungal ITS sequences, as well as 112 ITS sequences from other eukaryotic microorganisms. Equal proportions of Basidiomycota and Ascomycota sequences were present in both the ITS and small-subunit libraries, while members of other fungal phyla were recovered at much lower frequencies. Many sequences closely matched sequences from mycorrhizal, plant-pathogenic, and saprophytic fungi. Compositional differences were observed among samples from different soil depths, with mycorrhizal species predominating deeper in the soil profile and saprophytic species predominating in the litter layer. Richness was consistently lowest in the deepest soil horizon samples. Comparable levels of fungal richness have been observed following traditional specimen-based collecting and culturing surveys, but only after much more extensive sampling. The high rate at which new sequence types were recovered even after sampling 863 fungal ITS sequences and the dominance of fungi in our libraries relative to other eukaryotes suggest that the abundance and diversity of fungi in forest soils may be much higher than previously hypothesized. All sequences were deposited in GenBank, with accession numbers AY 969316 to AY 970290 for the ITS sequences and AY 969135 to AY 969315 for the SSU sequences.

          • N Fierer, JA Jackson, R Vilgalys, RB Jackson.
          • (2005).
          • Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays..
          • Applied and environmental microbiology, United States
          • ,
          • 71
          • (7)
          • ,
          • 4117-20.
          • [web]
          Publication Description

          Here we describe a quantitative PCR-based approach to estimating the relative abundances of major taxonomic groups of bacteria and fungi in soil. Primers were thoroughly tested for specificity, and the method was applied to three distinct soils. The technique provides a rapid and robust index of microbial community structure.

          • N Fierer, JA Jackson, R Vilgalys and RB Jackson.
          • (2005).
          • Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays..
          • Appl Environ Microbiol
          • ,
          • 71
          • (7)
          • ,
          • 4117-4120.
          • [web]
          Publication Description

          Here we describe a quantitative PCR-based approach to estimating the relative abundances of major taxonomic groups of bacteria and fungi in soil. Primers were thoroughly tested for specificity, and the method was applied to three distinct soils. The technique provides a rapid and robust index of microbial community structure.

          • M Didukh, R Vilgalys, SP Wasser, OS Isikhuemhen and E Nevo.
          • (2005).
          • Notes on Agaricus section Duploannulati using molecular and morphological data..
          • Mycological research
          • ,
          • 109
          • (Pt 6)
          • ,
          • 729-740.
          • [web]
          Publication Description

          The position of several endemic and rare species in Agaricus sect. Dulploannulati and the limits of the section were investigated by analysis of sequence data from the ribosomal DNA ITS. The results supported the recognition of two groups, which we treat as subsections Chitonioides and Duploannulati. Most of the species studied proved to belong to subsect. Chitonioides. Species excluded from the section, as well as other potential members of sect. Duploannulati, are considered. Morphological traits deemed important for identification of A. nevoi, A. pequinii, A. gennadii, A. rollanii, and A. padanus are discussed. Taxonomic positions of these species in morphologically-based systems and according to molecular systematics data are compared and analyzed.

          • AP Litvintseva, L Kestenbaum, R Vilgalys, TG Mitchell.
          • (2005).
          • Comparative analysis of environmental and clinical populations of Cryptococcus neoformans..
          • Journal of clinical microbiology, United States
          • ,
          • 43
          • (2)
          • ,
          • 556-64.
          • [web]
          Publication Description

          Cryptococcus neoformans is a major, global cause of meningoencephalitis in immunocompromised patients. Despite advances in the molecular epidemiology of C. neoformans, its population structure and mode of reproduction are not well understood. In the environment, it is associated with avian guano or vegetation. We collected nearly 800 environmental isolates from three locations in the United States (viz., North Carolina, California, and Texas) and compared them with one another and with clinical isolates from North Carolina. As expected, they consisted of the most prevalent serotypes, serotypes A and D, as well as serotype AD hybrids. The majority of environmental isolates were obtained from pigeon excreta. All environmental and clinical isolates of serotype A or D had the MATalpha mating-type allele. However, the AD hybrids included MATa alleles typical of serotypes A and D. Using an amplified fragment length polymorphism fingerprinting technique with two primer pairs, we identified 12 genotypes among the isolates of serotype A. Six of these genotypes were present in both the clinical and the environmental populations. However, one of the most prevalent environmental genotypes was absent from the clinical samples, and two other genotypes were isolated only from patients. The combined molecular data suggest that this environmental population of C. neoformans is predominantly clonal, although there was evidence for recent or past recombination.

          • AP Litvintseva, L Kestenbaum, R Vilgalys and TG Mitchell.
          • (2005).
          • Comparative analysis of environmental and clinical populations of Cryptococcus neoformans..
          • J Clin Microbiol
          • ,
          • 43
          • (2)
          • ,
          • 556-564.
          • [web]
          Publication Description

          Cryptococcus neoformans is a major, global cause of meningoencephalitis in immunocompromised patients. Despite advances in the molecular epidemiology of C. neoformans, its population structure and mode of reproduction are not well understood. In the environment, it is associated with avian guano or vegetation. We collected nearly 800 environmental isolates from three locations in the United States (viz., North Carolina, California, and Texas) and compared them with one another and with clinical isolates from North Carolina. As expected, they consisted of the most prevalent serotypes, serotypes A and D, as well as serotype AD hybrids. The majority of environmental isolates were obtained from pigeon excreta. All environmental and clinical isolates of serotype A or D had the MATalpha mating-type allele. However, the AD hybrids included MATa alleles typical of serotypes A and D. Using an amplified fragment length polymorphism fingerprinting technique with two primer pairs, we identified 12 genotypes among the isolates of serotype A. Six of these genotypes were present in both the clinical and the environmental populations. However, one of the most prevalent environmental genotypes was absent from the clinical samples, and two other genotypes were isolated only from patients. The combined molecular data suggest that this environmental population of C. neoformans is predominantly clonal, although there was evidence for recent or past recombination.

          • James, T. Y. and R. Vilgalys.
          • (2005).
          • Chytrid fungi as agents of amphibian decline- what can we learn from the earliest diverging fungi?.
          • Fungal Molecular principles of fungal pathogenesis, ASM Press. Joe Heitman, Scott Filler, and Aaron Mitchell-eds
          • .
          • MC Aime, R Vilgalys and OKM Jr.
          • (2005).
          • The crepidotaceae (Basidiomycota, Agaricales): Phylogeny and taxonomy of the genera and revision of the family based on molecular evidence.
          • American Journal of Botany
          • ,
          • 92
          • (1)
          • ,
          • 74-82.
          • [web]
          Publication Description

          Advances in phylogenetic systematics have clarified the position of most major homobasidiomycete lineages. In contrast, the status of the Crepidotaceae, a historically controversial family of dark-spored agarics, remains unaddressed. In this paper, current morphology-based classifications of the agaric genera of the Crepidotaceae were evaluated by parsimony and constraint analyses of sequence data from the nuclear large subunit rDNA. Taxa analyzed included the type species for each agaric genus allied in the family by Singer: Crepidotus, Simocybe, Pleurotellus, Tubaria, and Melanomphalia. Contrary to traditional classifications, results suggest that the crepidotoid fungi have three separate origins within the euagarics. The Crepidotaceae sensu stricto (s.s.) includes Crepidotus and Simocybe and represents a separate lineage of dark-spored euagarics. Pleurotellus is congeneric with Crepidotus. Results indicate the exclusion of both Tubaria and Melanomphalia from the Crepidotaceae s.s. Tubaria is allied with the strophariaceous taxa Phaeomarasmius and Flammulaster, while Melanomphalia has arisen from within a lineage of light-spored omphalinoid euagarics representing an independent acquisition of basidiospore pigmentation. Other pleisiomorphic and newly uncovered synapomorphic characters are discussed in detail along with the taxonomic status of each genus, and a revised family description is provided.

          • MD Wallenstein and RJ Vilgalys.
          • (2005).
          • Quantitative analyses of nitrogen cycling genes in soils.
          • Pedobiologia
          • ,
          • 49
          • (6)
          • ,
          • 665-672.
          • [web]
          Publication Description

          Soil nitrogen cycling is accomplished by a diverse microbial community using several nitrogen functional genes (NFGs). The relationship between the composition of these communities and nitrogen cycling processes is poorly understood. We developed techniques to quantify several important NFGs nitrogen transformations including fixation (nifH), ammonia oxidation (amoA), nitrogen reduction (nirS and nirK), and nitrous oxide reduction (nosZ) using quantitative real-time PCR with SybrGreen. Standard curves with known gene copies of each target molecule were developed using genomic DNA extracted from pure cultures. Primers from previously published studies were successfully used to amplify and quantify each NFGs in DNA extracted from two forest soils. Some soil samples inhibited PCR amplification of positive control DNA, and required further purification, which alleviated the problem. Two forest soils from Harvard Forest, MA and Duke Forest, NC differed greatly in their relative abundance of NFGs. The abundance of the amoA gene, associated with ammonia oxidation, was greater at Harvard Forest. The nifH gene, associated with N fixation, was more abundant at Duke Forest. These differences may reflect contrasting N cycling processes, however other published data do not indicate strong differences in gross N cycling rates. This technique can be widely adapted to quantify functional genes from a variety of complex environmental samples, and its utility could be further extended by amplifying mRNA using a reverse transcriptase-PCR procedure. © 2005 Elsevier GmbH. All rights reserved.

          • M Didukh, R Vilgalys, SP Wasser, OS Isikhuemhen and E Nevo.
          • (2005).
          • Notes on Agaricus section Duploannulati using molecular and morphological data.
          • Mycological Research
          • ,
          • 109
          • (6)
          • ,
          • 729-740.
          • [web]
          Publication Description

          The position of several endemic and rare species in Agaricus sect. Duploannulati and the limits of the section were investigated by analysis of sequence data from the ribosomal DNA ITS. The results supported the recognition of two groups, which we treat as subsections Chitonioides and Duploannulati. Most of the species studied proved to belong to subsect. Chitonioides. Species excluded from the section, as well as other potential members of sect. Duploannulati, are considered. Morphological traits deemed important for identification of A. nevoi, A. pequinii, A. gennadii, A. rollanii, and A. padanus are discussed. Taxonomic positions of these species in morphologically-based systems and according to molecular systematics data are compared and analyzed. © The British Mycological Society.

          • S Diezmann, CJ Cox, G Schönian, RJ Vilgalys and TG Mitchell.
          • (2004).
          • Phylogeny and evolution of medical species of Candida and related taxa: a multigenic analysis..
          • J Clin Microbiol
          • ,
          • 42
          • (12)
          • ,
          • 5624-5635.
          • [web]
          Publication Description

          Hemiascomycetes are species of yeasts within the order Saccharomycetales. The order encompasses disparate genera with a variety of life styles, including opportunistic human pathogens (e.g., Candida albicans), plant pathogens (e.g., Eremothecium gossypii), and cosmopolitan yeasts associated with water and decaying vegetation. To analyze the phylogeny of medically important species of yeasts, we selected 38 human pathogenic and related strains in the order Saccharomycetales. The DNA sequences of six nuclear genes were analyzed by maximum likelihood and Bayesian phylogenetic methods. The maximum likelihood analysis of the combined data for all six genes resolved three major lineages with significant support according to Bayesian posterior probability. One clade was mostly comprised of pathogenic species of Candida. Another major group contained members of the family Metschnikowiaceae as a monophyletic group, three species of Debaryomyces, and strains of Candida guilliermondii. The third clade consisted exclusively of species of the family Saccharomycetaceae. Analysis of the evolution of key characters indicated that both codon reassignment and coenzyme Q(9) likely had single origins with multiple losses. Tests of correlated character evolution revealed that these two traits evolved independently.

          • F Lutzoni, F Kauff, CJ Cox, D McLaughlin, G Celio, B Dentinger, M Padamsee, D Hibbett, TY James, E Baloch, M Grube, V Reeb, V Hofstetter, C Schoch, AE Arnold, J Miadlikowska, J Spatafora, D Johnson, S Hambleton, M Crockett, R Shoemaker, GH Sung, R Lücking, T Lumbsch, K O'Donnell, M Binder, P Diederich, D Ertz, C Gueidan, K Hansen, RC Harris, K Hosaka, YW Lim, B Matheny, H Nishida, D Pfister, J Rogers, A Rossman, I Schmitt, H Sipman, J Stone, J Sugiyama, R Yahr and R Vilgalys.
          • (2004).
          • Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits..
          • Am J Bot
          • ,
          • 91
          • (10)
          • ,
          • 1446-1480.
          • [web]
          Publication Description

          Based on an overview of progress in molecular systematics of the true fungi (Fungi/Eumycota) since 1990, little overlap was found among single-locus data matrices, which explains why no large-scale multilocus phylogenetic analysis had been undertaken to reveal deep relationships among fungi. As part of the project "Assembling the Fungal Tree of Life" (AFTOL), results of four Bayesian analyses are reported with complementary bootstrap assessment of phylogenetic confidence based on (1) a combined two-locus data set (nucSSU and nucLSU rDNA) with 558 species representing all traditionally recognized fungal phyla (Ascomycota, Basidiomycota, Chytridiomycota, Zygomycota) and the Glomeromycota, (2) a combined three-locus data set (nucSSU, nucLSU, and mitSSU rDNA) with 236 species, (3) a combined three-locus data set (nucSSU, nucLSU rDNA, and RPB2) with 157 species, and (4) a combined four-locus data set (nucSSU, nucLSU, mitSSU rDNA, and RPB2) with 103 species. Because of the lack of complementarity among single-locus data sets, the last three analyses included only members of the Ascomycota and Basidiomycota. The four-locus analysis resolved multiple deep relationships within the Ascomycota and Basidiomycota that were not revealed previously or that received only weak support in previous studies. The impact of this newly discovered phylogenetic structure on supraordinal classifications is discussed. Based on these results and reanalysis of subcellular data, current knowledge of the evolution of septal features of fungal hyphae is synthesized, and a preliminary reassessment of ascomal evolution is presented. Based on previously unpublished data and sequences from GenBank, this study provides a phylogenetic synthesis for the Fungi and a framework for future phylogenetic studies on fungi.

          • RE Marra, JC Huang, E Fung, K Nielsen, J Heitman, R Vilgalys and TG Mitchell.
          • (2004).
          • A genetic linkage map of Cryptococcus neoformans variety neoformans serotype D (Filobasidiella neoformans)..
          • Genetics
          • ,
          • 167
          • (2)
          • ,
          • 619-631.
          • [web]
          Publication Description

          To construct a genetic linkage map of the heterothallic yeast, Cryptococcus neoformans (Filobasidiella neoformans), we crossed two mating-compatible strains and analyzed 94 progeny for the segregation of 301 polymorphic markers, consisting of 228 restriction site polymorphisms, 63 microsatellites, two indels, and eight mating-type (MAT)-associated markers. All but six markers showed no significant (P

          • GI Zervakis, JM Moncalvo and R Vilgalys.
          • (2004).
          • Molecular phylogeny, biogeography and speciation of the mushroom species Pleurotus cystidiosus and allied taxa..
          • Microbiology
          • ,
          • 150
          • (Pt 3)
          • ,
          • 715-726.
          Publication Description

          Members of the mushroom genus Pleurotus form a heterogeneous group of edible species of high commercial importance. Subgenus Coremiopleurotus includes taxa that produce synnematoid fructifications (anamorphic state). Several species, subspecies and varieties have been described in Coremiopleurotus: These taxa are discriminated by minute morphological differences and correspond to Pleurotus cystidiosus sensu lato. A worldwide geographical sampling of Coremiopleurotus taxa and nucleotide sequence data from the internal transcribed spacer of the nuclear rRNA genes (ITS) were used to produce a molecular phylogeny for the group. Also conducted were new interfertility studies, and a summary of the mating data currently available in the literature is provided. Both ITS phylogeny and mating data supported the distinction between Pleurotus australis (a species apparently endemic to New Zealand and Australia) and P. cystidiosus sensu lato. Within P. cystidiosus sensu lato, ITS phylogeny showed a deep split between Old and New World isolates and clearly distinguished four distinct clades that strongly corresponded to the geographical origin of the strains. In the Old World, one clade is composed of isolates from Europe and Africa, and one clade is composed of isolates from Asia (including collections from Hawaii). In the New World, one clade is restricted to isolates from Mexico, and one clade includes all the authors' North America isolates, one collection from Japan and one collection from South Africa. Mating data revealed a high level of interfertility among strains of P. cystidiosus sensu lato, except that isolates from Mexico were nearly fully intersterile with the other collections. Nucleotide sequence divergence in the ITS1-5.8S rDNA-ITS2 regions among intercompatible P. cystidiosus collections was very high (0-6.9 %) in comparison to that reported in other biological species of basidiomycetes (0-3 %), indicating significant genetic divergence between geographically isolated populations of the P. cystidiosus group. The phylogenetic species concept, as well as molecular, mating and geographical evidence, was used to recognize five species in the subgenus Coremiopleurotus: P. australis (in New Zealand and Australia), Pleurotus abalonus (in Asia and Hawaii), Pleurotus fuscosquamulosus (in Africa and Europe), Pleurotus smithii (in Mexico) and Pleurotus cystidiosus sensu stricto (in North America). However, geographical boundaries between these species are not strict, as rare events of long distance dispersal have occurred.

          • U Peintner, JM Moncalvo and R Vilgalys.
          • (2004).
          • Toward a better understanding of the infrageneric relationships in Cortinarius (Agaricales, Basidiomycota).
          • Mycologia
          • ,
          • 96
          • (5)
          • ,
          • 1042-1058.
          Publication Description

          Research on the molecular systematics of Cortinarius, a species-rich mushroom genus with nearly global distribution, is just beginning. The present study explores infrageneric relationships using rDNA ITS and LSU sequence data. One large dataset of 132 rDNA ITS sequences and one combined dataset with 54 rDNA ITS and LSU sequences were generated. Hebeloma was used as outgroup. Bayesian analyses and maximum-likelihood (ML) analyses were carried out. Bayesian phylogenetic inference performed equally well or better than ML, especially in large datasets. The phylogenetic analysis of the combined dataset with species representing all currently recognized subgenera recovered seven well-supported clades (Bayesian posterior probabilities BPP > 90%). These major clades are: /Myxacium s.l., /subg. Cortinarius, the /phlegmacioid clade (including the subclades /Phlegmacium and /Delibuti), the /calochroid clade (/Calochroi, /Ochroleuci and /Allutus), the /telamonioid clade (/Telamonia, /Orellani, /Anomali), /Dermocybe s.l. and /Myxotelamonia. Our results show that Cortinarius consists of many lineages, but the relationships among these clades could not be elucidated. On one hand, the low divergence in rDNA sequences can be held responsible for this; on the other hand, taxon sampling is problematic in Cortinarius phylogeny. Because of the incredibly high diversity (∼2000 Cortinarius species), our sampling included <5% of the known species. By choosing type species of subgenera and sections, our sampling is strongly biased toward Northern Hemisphere taxa. More extensive taxon sampling, especially of species from the Southern Hemisphere, is essential to resolve the phylogeny of this important genus of ectomycorrhizal fungi.

          • TY James, U Kües, SA Rehner and R Vilgalys.
          • (2004).
          • Evolution of the gene encoding mitochondrial intermediate peptidase and its cosegregation with the A mating-type locus of mushroom fungi.
          • Fungal Genetics and Biology
          • ,
          • 41
          • (3)
          • ,
          • 381-390.
          • [web]
          Publication Description

          The high level of DNA polymorphism at the mating-type loci of mushroom fungi has made the cloning of mating-type genes difficult. As an alternative to strategies that employ sequence conservation, an approach utilizing conserved gene order could facilitate the cloning of A mating-type genes from mushroom fungi. It has been shown that a gene encoding a mitochondrial intermediate peptidase (MIP) is very close (<1kbp) to the A mating-type locus of two model mushroom species. In this study, the cosegregation of MIP and the A mating-type locus was studied by genotyping progeny of seven additional mushroom species using PCR and genetic crosses. No evidence of any recombination between MIP and the A mating-type locus was detected among all seven species. Phylogenetic analysis of MIP sequences from diverse mushroom species agrees with the current organismal phylogeny, suggesting the sequences are generally orthologous. © 2003 Elsevier Inc. All rights reserved.

          • TY James, SR Liou and R Vilgalys.
          • (2004).
          • The genetic structure and diversity of the A and B mating-type genes from the tropical oyster mushroom, Pleurotus djamor.
          • Fungal Genetics and Biology
          • ,
          • 41
          • (8)
          • ,
          • 813-825.
          • [web]
          Publication Description

          In most heterothallic mushroom species, inbreeding is avoided by an incompatibility system determined by two loci each with multiple alleles (the A and B mating-type loci). In this study we investigated the genetic structure of the mating-type loci in the tropical oyster mushroom Pleurotus djamor using both positional cloning and degenerate PCR methods. DNA sequences from genomic regions cosegregating with the mating-type loci of P. djamor revealed homeodomain transcription factors (A) and pheromone receptors (B), suggesting the genetic basis for mating-type determination in P. djamor is the same as in the model mushroom species. Three pheromone receptors were detected in a single homokaryotic isolate of P. djamor. Only one pair of homeodomain genes was detected in the A mating-type region. It is hypothesized that the A mating-type locus of P. djamor is comprised of only one homeodomain pair, which may explain the lower number of A mating-type alleles relative to other mushroom species. © 2004 Elsevier Inc. All rights reserved.

          • R Yahr, R Vilgalys and PT Depriest.
          • (2004).
          • Strong fungal specificity and selectivity for algal symbionts in Florida scrub Cladonia lichens.
          • Molecular Ecology
          • ,
          • 13
          • (11)
          • ,
          • 3367-3378.
          • [web]
          Publication Description

          Symbiosis is a major theme in the history of life and can be an important force driving evolution. However, across symbioses, it is difficult to tease apart the mechanisms that structure the interactions among potential partners. We used genetic similarity and frequency-based methods to qualitatively and quantitatively examine the patterns of association among several co-occurring Cladonia lichen fungi and their algal photobionts in six disjunct Florida scrub sites. The patterns of association were described by the degree of specificity, i.e. the phylogenetic range of associated partners, and of selectivity, i.e. the frequency of association among partners. Six fungal species associated with only one algal internal transcribed spacer clade, with the remaining two fungi being associated with two algal clades. In all cases, the fungi associated in unequal frequencies with the observed algal photobiont genotypes within those clades - suggesting that both specificity and selectivity were higher than expected. Fungal species can be grouped into three significantly different specificity classes: photobiont specialists, intermediates and generalists. In contrast to the pronounced specificity for photobionts among fungal species, the different Florida scrub sites do not harbour distinct photobiont pools, and differential photobiont availability cannot explain the patterning of lichen associations at this spatial scale. Therefore, we conclude that fungal specificity and selectivity for algal photobionts are major factors in determining the local composition of symbiotic partnerships.

          • GI Zervakis, JM Moncalvo and R Vilgalys.
          • (2004).
          • Molecular phylogeny, biogeography and speciation of the mushroom species Pleurotus cystidiosus and allied taxa.
          • Microbiology
          • ,
          • 150
          • (3)
          • ,
          • 715-726.
          Publication Description

          Members of the mushroom genus Pleurotus form a heterogeneous group of edible species of high commercial importance. Subgenus Coremiopleurotus includes taxa that produce synnematoid fructifications (anamorphic state). Several species, subspecies and varieties have been described in Coremiopleurotus. These taxa are discriminated by minute morphological differences and correspond to Pleurotus cystidiosus sensu lato. A worldwide geographical sampling of Coremiopleurotus taxa and nucleotide sequence data from the internal transcribed spacer of the nuclear rRNA genes (ITS) were used to produce a molecular phylogeny for the group. Also conducted were new interfertility studies, and a summary of the mating data currently available in the literature is provided. Both ITS phylogeny and mating data supported the distinction between Pleurotus australis (a species apparently endemic to New Zealand and Australia) and P. cystidiosus sensu lato. Within P. cystidiosus sensu lato, ITS phylogeny showed a deep split between Old and New World isolates and clearly distinguished four distinct clades that strongly corresponded to the geographical origin of the strains. In the Old World, one clade is composed of isolates from Europe and Africa, and one clade is composed of isolates from Asia (including collections from Hawaii). In the New World, one clade is restricted to isolates from Mexico, and one clade includes all the authors' North America isolates, one collection from Japan and one collection from South Africa. Mating data revealed a high level of interfertility among strains of P. cystidiosus sensu lato, except that isolates from Mexico were nearly fully intersterile with the other collections. Nucleotide sequence divergence in the ITS1-5.8S rDNA-ITS2 regions among intercompatible P. cystidiosus collections was very high (0-6.9 %) in comparison to that reported in other biological species of basidiomycetes (0-3 %), indicating significant genetic divergence between geographically isolated populations of the P. cystidiosus group. The phylogenetic species concept, as well as molecular, mating and geographical evidence, was used to recognize five species in the subgenus Coremiopleurotus: P. australis (in New Zealand and Australia), Pleurotus abalonus (in Asia and Hawaii), Pleurotus fuscosquamulosus (in Africa and Europe), Pleurotus smithii (in Mexico) and Pleurotus cystidiosus sensu stricto (in North America). However, geographical boundaries between these species are not strict, as rare events of long distance dispersal have occurred. © 2004 SGM.

          • AP Litvintseva, RE Marra, K Nielsen, J Heitman, R Vilgalys and TG Mitchell.
          • (2003).
          • Evidence of sexual recombination among Cryptococcus neoformans serotype A isolates in sub-Saharan Africa..
          • Eukaryot Cell
          • ,
          • 2
          • (6)
          • ,
          • 1162-1168.
          • [web]
          Publication Description

          The most common cause of fungal meningitis in humans, Cryptococcus neoformans serotype A, is a basidiomycetous yeast with a bipolar mating system. However, the vast majority (>99.9%) of C. neoformans serotype A isolates possess only one of the two mating type alleles (MATalpha). Isolates with the other allele (MATa) were recently discovered and proven to mate in the laboratory. It has been a mystery whether and where C. neoformans strains undergo sexual reproduction. Here, we applied population genetic approaches to demonstrate that a population of C. neoformans serotype A clinical isolates from Botswana contains an unprecedented proportion of fertile MATa isolates and exhibits evidence of both clonal expansion and recombination within two partially genetically isolated subgroups. Our findings provide evidence for sexual recombination among some populations of C. neoformans serotype A from sub-Saharan Africa, which may have a direct impact on their evolution.

          • EC Davis, JB Franklin, AJ Shaw and R Vilgalys.
          • (2003).
          • Endophytic Xylaria (Xylariaceae) among liverworts and angiosperms: phylogenetics, distribution, and symbiosis..
          • Am J Bot
          • ,
          • 90
          • (11)
          • ,
          • 1661-1667.
          • [web]
          Publication Description

          Nuclear ribosomal 18S and internal transcribed spacer (ITS) sequence data were used to identify endophytic fungi cultured from six species of liverworts collected in Jamaica and North Carolina. Comparisons with other published fungal sequences and phylogenetic analyses yielded the following conclusions: (1) the endophytes belong to the ascomycete families Xylariaceae, Hypocreaceae, and Ophiostomataceae, and (2) liverwort endophytes in the genus Xylaria are closely related to each other and to endophytes isolated from angiosperms in China, Puerto Rico, and Europe. Liverwort endophytes are expected to be foragers or endophytic specialists, although little is known about the role of these fungi in symbioses. Features that may indicate a mutualistic role for these endophytes are discussed.

          • PC Ceresini, HD Shew, RJ Vilgalys, LR Gale and MA Cubeta.
          • (2003).
          • Detecting Migrants in Populations of Rhizoctonia solani Anastomosis Group 3 from Potato in North Carolina Using Multilocus Genotype Probabilities..
          • Phytopathology
          • ,
          • 93
          • (5)
          • ,
          • 610-615.
          • [web]
          Publication Description

          ABSTRACT The relative contribution of migration of Rhizoctonia solani anastomosis group 3 (AG-3) on infested potato seed tubers originating from production areas in Canada, Maine, and Wisconsin (source population) to the genetic diversity and structure of populations of R. solani AG-3 in North Carolina (NC) soil (recipient population) was examined. The frequency of alleles detected by multilocus polymerase chain reaction-restriction fragment length polymorphisms, heterozygosity at individual loci, and gametic phase disequilibrium between all pairs of loci were determined for subpopulations of R. solani AG-3 from eight sources of potato seed tubers and from five soils in NC. Analysis of molecular variation revealed little variation between seed source and NC recipient soil populations or between subpopulations within each region. Analysis of population data with a Bayesian-based statistical method previously developed for detecting migration in human populations suggested that six multilocus genotypes from the NC soil population had a statistically significant probability of being migrants from the northern source population. The one-way (unidirectional) migration of genotypes of R. solani AG-3 into NC on infested potato seed tubers from Canada, Maine, and Wisconsin provides a plausible explanation for the lack of genetic subdivision (differentiation) between populations of the pathogen in NC soils or between the northern source and the NC recipient soil populations.

          • EA Morehouse, TY James, AR Ganley, R Vilgalys, L Berger, PJ Murphy and JE Longcore.
          • (2003).
          • Multilocus sequence typing suggests the chytrid pathogen of amphibians is a recently emerged clone..
          • Mol Ecol
          • ,
          • 12
          • (2)
          • ,
          • 395-403.
          • [web]
          Publication Description

          Chytridiomycosis is a recently identified fungal disease associated with global population declines of frogs. Although the fungus, Batrachochytrium dendrobatidis, is considered an emerging pathogen, little is known about its population genetics, including the origin of the current epidemic and how this relates to the dispersal ability of the fungus. In this study, we use multilocus sequence typing to examine genetic diversity and relationships among 35 fungal strains from North America, Africa and Australia. Only five variable nucleotide positions were detected among 10 loci (5918 bp). This low level of genetic variation is consistent with the description of B. dendrobatidis as a recently emerged disease agent. Fixed (i.e. 100%) or nearly fixed frequencies of heterozygous genotypes at two loci suggested that B. dendrobatidis is diploid and primarily reproduces clonally. In contrast to the lack of nucleotide polymorphism, electrophoretic karyotyping of multiple strains demonstrated a number of chromosome length polymorphisms.

          • R Vilgalys.
          • (2003).
          • Taxonomic misidentification in public DNA databases.
          • New Phytologist
          • ,
          • 160
          • (1)
          • ,
          • 4-5.
          • [web]
          • A Pringle, JM Moncalvo and R Vilgalys.
          • (2003).
          • Revisiting the rDNA sequence diversity of a natural population of the arbuscular mycorrhizal fungus Acaulospora colossica.
          • Mycorrhiza
          • ,
          • 13
          • (4)
          • ,
          • 227-231.
          • [web]
          Publication Description

          In 1999, the diversity of a field population of the arbuscular mycorrhizal (AM) fungus Acaulospora colossica was characterized using DNA sequence data. Since 1999, AM fungal sequences have accumulated rapidly within public databases. Moreover, novel phylogenetic tools have been developed and can be used to interpret the data. A second analysis of those sequences collected in 1999 demonstrates that while the majority of the sequences are, in fact, sequences of A. colossica; a minority of the sequences still cannot be identified with confidence. Those sequences identified as A. colossica can be used to show that (1) the nuclear rDNA ITS regions are remarkably diverse, and (2) sequences isolated from different spores of the same site may be more closely related to each other than to sequences of other sites, so that the genetic diversity of an AM fungal field population may be spatially structured; however, identical sequences can also be recovered from different sites.

          • PC Ceresini, HD Shew, RJ Vilgalys and MA Cubeta.
          • (2002).
          • Genetic diversity of Rhizoctonia solani AG-3 from potato and tobacco in North Carolina..
          • Mycologia
          • ,
          • 94
          • (3)
          • ,
          • 437-449.
          • [web]
          Publication Description

          Anastomosis group 3 (AG-3) of Rhizoctonia solani (teleomorph = Thanatephorus cucumeris) is frequently associated with diseases of potato (AG-3 PT) and tobacco (AG-3 TB). Although isolates of R. solani AG-3 from these two Solanaceous hosts are somatically related based on anastomosis reaction and taxonomically related based on fatty acid, isozyme and DNA characters, considerable differences are evident in their biology, ecology, and epidemiology. However, genetic diversity among field populations of R. solani AG-3 PT and TB has not been documented. In this study, the genetic diversity of field populations of R. solani AG-3 PT and AG-3 TB in North Carolina was examined using somatic compatibility and amplified fragment length polymorphism (AFLP) criteria. A sample of 32 isolates from potato and 36 isolates from tobacco were paired in all possible combinations on PDA plus activated charcoal and examined for their resulting somatic interactions. Twenty-eight and eight distinct somatic compatibility groups (SCG) were identified in the AG-3 PT and AG-3 TB samples, respectively. AFLP analyses indicated that each of the 32 AG-3 PT isolates had a distinct AFLP phenotype, whereas 28 AFLP phenotypes were found among the 36 isolates of AG-3 TB. None of the AG-3 PT isolates were somatically compatible or shared a common AFLP phenotype with any AG-3 TB isolate. Clones (i.e., cases where two or more isolates were somatically compatible and shared the same AFLP phenotype) were identified only in the AG-3 TB population. Four clones from tobacco represented 22% of the total population. All eight SCG from tobacco were associated with more than one AFLP phenotype. Compatible somatic interactions between AG-3 PT isolates occurred only between certain isolates from the same field (two isolates in each of four different fields), and when this occurred AFLP phenotypes were similar but not identical.

          • PC Ceresini, HD Shew, RJ Vilgalys, UL Rosewich and MA Cubeta.
          • (2002).
          • Genetic structure of populations of Rhizoctonia solani AG-3 on potato in eastern North Carolina..
          • Mycologia
          • ,
          • 94
          • (3)
          • ,
          • 450-460.
          • [web]
          Publication Description

          A polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was developed to identify and differentiate genotypes of Rhizoctonia solani anastomosis group 3 subgroup PT (AG-3 PT), a fungal pathogen of potato. Polymorphic co-dominant single-locus PCR-RFLP markers were identified after sequencing of clones from a genomic library and digestion with restriction enzymes. Multilocus genotypes were determined by a combination of PCR product and digestion with a specific restriction enzyme for each of seven loci. A sample of 104 isolates from one commercial field in each of five counties in eastern North Carolina was analyzed, and evidence for high levels of gene flow between populations was revealed. When data were clone-corrected and samples pooled into one single North Carolina population, random associations of alleles were found for all loci or pairs of loci, indicating random mating. However, when all genotypes were analyzed, the observed genotypic diversity deviated from panmixia and alleles within and between loci were not randomly associated. These findings support a model of population structure for R. solani AG-3 PT on potato that includes both recombination and clonality.

          • J Xu, G Luo, RJ Vilgalys, ME Brandt and TG Mitchell.
          • (2002).
          • Multiple origins of hybrid strains of Cryptococcus neoformans with serotype AD..
          • Microbiology
          • ,
          • 148
          • (Pt 1)
          • ,
          • 203-212.
          • [web]
          Publication Description

          Cryptococcus neoformans is a major pathogen of humans throughout the world. Using commercial mAbs to capsular epitopes, strains of C. neoformans manifest five distinct serotypes--A, B, C, D and AD. Previous studies demonstrated significant divergence among serotypes A, B, C and D, which are thought to be haploid. In this study the origins and evolution of strains of serotype AD were investigated. A portion (537 bp) of the laccase gene was cloned and sequenced from 14 strains of serotype AD. Each strain contained two different alleles and sequences for both alleles were obtained. These sequences were compared to those from serotypes A, B, C and D. This analysis indicated that each of the 14 serotype AD strains contained two phylogenetically distinct haplotypes: one haplotype was highly similar to the serotype A group and the other to the serotype D group. To explain the origins of these serotype AD strains, genealogical analysis is consistent with at least three recent and independent hybridization events. The results demonstrate that the evolution of C. neoformans is continuing and dynamic.

          • U Peintner, E Horak, MM Moser and R Vilgalys.
          • (2002).
          • Phylogeny of Rozites, Cuphocybe and Rapacea inferred from ITS and LSU rDNA sequences.
          • Mycologia
          • ,
          • 94
          • (4)
          • ,
          • 620-629.
          Publication Description

          Phylogenetic relationships of Rozites, Cuphocybe, and Rapacea were assessed using molecular phylogenetic approaches. These three genera are placed in Cortinariaceae and have been regarded as closely related to Cortinarius. Rozites includes more than 20 species, which are characterized by having both a membranaceous partial veil in the form of a persistent annulus and a membranaceous universal veil. Cuphocye (4 species) lacks an annulus or cortina, but has pigmented veil fibrils or scales. The monotypic genus Rapacea accommodates a distinct taxon with pale, nearly smooth and thick-walled basidiospores. We analyzed 56 sequences of the internal transcribed spacer region (ITS1, ITS2, and the intervening 5.8S rRNA gene) for nine species of Rozites, three species of Cuphocybe, 28 species of Cortinarius, Rapacea mariae and Protoglossum luteum. Two species of Hebeloma were used as outgroup. Large subunit (LSU) rDNA sequences from selected taxa were also analyzed. The results clearly demonstrate that Rozites species are nested within the clade/Cortinarius, and that Rozites is polyphyletic, suggesting that membranaceous veils have evolved several times in the genus Cortinarius. Also Rapacea and Cuphocybe are nested within Cortinarius, making the latter genus paraphyletic. Based on phylogenetic studies, Rozites, Cuphocybe and Rapacea are artificial genera and do not reflect natural relationships.

          • U Peintner, M Moser and R Vilgalys.
          • (2002).
          • Thaxterogaster is a taxonomic synonym of Cortinarius: New combinations and new names.
          • Mycotaxon
          • ,
          • 81
          • ,
          • 177-184.
          Publication Description

          Results of our earlier molecular phylogenetic studies using sequences of the rDNA interna transcribed spacers (ITS) showed that the genus Thaxterogaster is polyphyletic, and nested within Cortinarius: the secotioid Thaxterogaster spp. have multiple origins within the subgenera Myxacium, Phlegmacium and Telamonia. In order to acknowledge these phylogenetic relationships, and the given morphological transitions, we propose to synonymize Thaxterogaster with Cortinarius. For the 54 currently recognized species of Thaxterogaster as well as for 2 varieties, 41 new combinations and 15 new names are proposed.

          • V Hofstetter, H Clémençon, R Vilgalys and JM Moncalvo.
          • (2002).
          • Phylogenetic analyses of the Lyophylleae (Agaricales, Basidiomycota) based on nuclear and mitochondrial rDNA sequences.
          • Mycological Research
          • ,
          • 106
          • (9)
          • ,
          • 1043-1059.
          • [web]
          Publication Description

          Current classifications of the Lyophylleae and the importance of siderophilous granulation in the basidia for the classification of agaricoid fungi were evaluated using parsimony analyses of sequence data from the nuclear ribosomal large subunit gene (nLSU), the internal transcribed spacer region of the nuclear ribosomal array (ITS), and the mitochondrial ribosomal small subunit gene (mtSSU). These three different data partitions were phylogenetically congruent on the basis of the Mickevich-Farris statistical test, but not from the ILD and the Templeton tests. Bootstrap supports for nodes in phylogenetic trees generated from combined nLSU, ITS, and mtSSU sequence data were generally higher than those in trees generated from individual data sets. This suggests a lack of major conflict in the phylogenetic signal among the different data sets. We conclude that the Mickevich-Farris test is more appropriate for estimating congruence and combinability between different sources of molecular data than the more widely used ILD and Templeton tests, at least when the different data sets have their respective resolution power at different depths in the phylogeny. Results of the combined analyses show that the Entolomataceae are a sister group to a clade composed of the Lyophylleae, Termitomyceteae, and Tricholomateae p.p. This implies that presence of siderophilous granulation in the basidia of agaric fungi has probably a single origin, and would have been lost in the Tricholomateae. Inclusion of the Termitomyceteae within the Lyophylleae suggests homology of the macro type granulation. Because the exact placement of Tricholomateae pro parte remains uncertain, it remains unclear whether the Lyophylleae (including Termitomyceteae) are monophyletic or paraphyletic. Within the Lyophylleae, genera Lyophyllum and Calocybe are shown to be artificial, as are Lyophyllum sections Lyophyllum, Difformia, and Tephrophana. Four main natural groups of Lyophylleae have been identified that should serve as a basis for developing a more natural classification system for these fungi.

          • U Peintner, E Horak, M Moser and R Vilgalys.
          • (2002).
          • Rozites, Cuphocybe and Rapacea are taxonomic synonyms of Cortinarius: New combinations and new names.
          • Mycotaxon
          • ,
          • 83
          • ,
          • 447-451.
          Publication Description

          Results of recent molecular phylogenetic studies using rDNA sequences of ITS and LSU showed that Rozites is nested within Cortinarius and polyphyletic. Rozites spp. were delimited from Cortinarius spp. by having both a membranaecous universal veil and a membranaceous partial veil in the form of a persistent annulus. However, molecular studies suggest that membranaceous veils have independently evolved several times in the genus Cortinarius. Cuphocybe and Rapacea are also nested within Cortinarius, making the latter genus paraphyletic. The morphological delimitation of all these genera is critical: Cuphocye spp. lack an annulus or cortina, but have pigmented veil fibrils or scales; the monotypic genus Rapacea accommodates a taxon macroscopically resembling Cortinarius spp., but with pale, nearly smooth and thick-walled basidiospores. In order to acknowledge the phylogenetic relationships and the given morphological transitions between these genera and Cortinarius, we recommend synonymizing Rozites, Cuphocybe and Rapacea with Cortinarius, making 16 new combinations and providing 10 new names, which became necessary due to homonyms.

          • TW Henkel, J Terborgh and RJ Vilgalys.
          • (2002).
          • Ectomycorrhizal fungi and their leguminous hosts in the Pakaraima Mountains of Guyana.
          • Mycological Research
          • ,
          • 106
          • (5)
          • ,
          • 515-531.
          • [web]
          Publication Description

          Ecologically important ectomycorrhizal (EM) associations are poorly known from equatorial rain forests of South America. Recent field studies in the Pakaraima Mountains of western Guyana revealed previously undocumented forests dominated by EM leguminous trees, with a rich assemblage of EM mycobionts. Along transects, basidiomes from 75 species or morphospecies of putatively EM fungi were spatially associated with leguminous host trees. These fungi belonged to the basidiomycete families Boletaceae, Amanitaceae, Russulaceae, Cortinariaceae, Cantharellaceae, Clavulinaceae, and Entolomataceae, all of which are poorly documented from the lowland neotropics. Ectomycorrhizas were confirmed on D. corymbosa, D. altsonii, and D. jenmanii (Caesalpiniaceae, tribe Amherstieae), and a fourth species, Aldina insignis (Papilionaceae). The tribe Amherstieae contains most of the EM leguminous species forming monodominant forests in Guineo-Congolian Africa. Dicymbe species constituted the first record of EM Amherstieae in the New World. A variety of other co-occurring caesalpiniaceous trees failed to exhibit ectomycorrhizas. Transect surveys indicated that D. corymbosa and D. altsonii were: (1) highly clumped and dominant at specific sites; (2) occurred on soils with widely varying chemical and textural characteristics; and (3) the most important hosts for EM fungi in the local landscape. Dicymbe species have life history attributes, including the ectomycorrhizal habit, which enhance their competitive abilities irrespective of soil conditions. The spatial restriction of EM fungal basidiomes indicated that discrete groves of EM trees harbour an important component of regional macromycete diversity.

          • SA Redhead, F Lutzoni, JM Moncalvo and R Vilgalys.
          • (2002).
          • Phylogeny of agarics: Partial systematics solutions for core Omphalinoid genera in the Agaricales (Euagarics).
          • Mycotaxon
          • ,
          • 83
          • ,
          • 19-57.
          Publication Description

          The taxonomy of species previously assigned to Omphalina sensu lato or Clitocybe is reevaluated in light of recent molecularly-based phylogenetic hypotheses. Nomenclatural complications involving generic and specific names, lectotypifications and changes to the Code are analysed. Lichenomphalia gen. nov. (type Hygrophorus hudsonianus, syn. Omphalina hudsoniana) is proposed for lichenized former omphalinas. Ampulloclitocybe gen. nov. (type Agaricus clavipes, syn. Clitocybe clavipes) is erected for its type species. Arrhenia is emended to include greyish species formerly included in Omphalina, but excluding reddish brown species related to Omphalina pyxidata, the conserved lectotype for Omphalina. The genera Cantharellula, Chrysomphalina, Gerronema, Glabrocyphella, Gliophorus, Haasiella, Hygrophorus, Hygrocybe, Pseudoarmillariella, and Rickenella, and the generic names Botrydina, Coriscium, Leptoglossum, Phaeotellus, Phytoconis, and Semiomphalina are discussed.

          • JM Moncalvo, R Vilgalys, SA Redhead, JE Johnson, TY James, MC Aime, V Hofstetter, SJW Verduin, E Larsson, TJ Baroni, RG Thorn, S Jacobsson, H Clémençon and OKM Jr.
          • (2002).
          • One hundred and seventeen clades of euagarics.
          • Molecular Phylogenetics and Evolution
          • ,
          • 23
          • (3)
          • ,
          • 357-400.
          • [web]
          Publication Description

          This study provides a first broad systematic treatment of the euagarics as they have recently emerged in phylogenetic systematics. The sample consists of 877 homobasidiomycete taxa and includes approximately one tenth (ca. 700 species) of the known number of species of gilled mushrooms that were traditionally classified in the order Agaricales. About 1000 nucleotide sequences at the 5′ end of the nuclear large ribosomal subunit gene (nLSU) were produced for each taxon. Phylogenetic analyses of nucleotide sequence data employed unequally weighted parsimony and bootstrap methods. Clades revealed by the analyses support the recognition of eight major groups of homobasidiomycetes that cut across traditional lines of classification, in agreement with other recent phylogenetic studies. Gilled fungi comprise the majority of species in the euagarics clade. However, the recognition of a mono-phyletic euagarics results in the exclusion from the clade of several groups of gilled fungi that have been traditionally classified in the Agaricales and necessitates the inclusion of several clavaroid, poroid, secotioid, gasteroid, and reduced forms that were traditionally classified in other basidiomycete orders. A total of 117 monophyletic groups (clades) of euagarics can be recognized on the basis on nLSU phylogeny. Though many clades correspond to traditional taxonomic groups, many do not. Newly discovered phylogenetic affinities include for instance relationships of the true puffballs (Lycoperdales) with Agaricaceae, of Panellus and the poroid fungi Dictyopanus and Favolaschia with Mycena, and of the reduced fungus Caripia with Gymnopus. Several clades are best supported by ecological, biochemical, or trophic habits rather than by morphological similarities. © 2002 Elsevier Science (USA). All rights reserved.

          • J Xu, G Luo, RJ Vilgalys, ME Brandt and TG Mitchell.
          • (2002).
          • Multiple origins of hybrid strains of Cryptococcus neoformans with serotype AD.
          • Microbiology
          • ,
          • 148
          • (1)
          • ,
          • 203-212.
          Publication Description

          Cryptococcus neoformans is a major pathogen of humans throughout the world. Using commercial mAbs to capsular epitopes, strains of C. neoformans manifest five distinct serotypes - A, B, C, D and AD. Previous studies demonstrated significant divergence among serotypes A, B, C and D, which are thought to be haploid. In this study the origins and evolution of strains of serotype AD were investigated. A portion (537 bp) of the laccase gene was cloned and sequenced from 14 strains of serotype AD. Each strain contained two different alleles and sequences for both alleles were obtained. These sequences were compared to those from serotypes A, B, C and D. This analysis indicated that each of the 14 serotype AD strains contained two phylogenetically distinct haplotypes: one haplotype was highly similar to the serotype A group and the other to the serotype D group. To explain the origins of these serotype AD strains, genealogical analysis is consistent with at least three recent and independent hybridization events. The results demonstrate that the evolution of C. neoformans is continuing and dynamic.

          • J Xu, C Onyewu, HJ Yoell, RY Ali, RJ Vilgalys and TG Mitchell.
          • (2001).
          • Dynamic and heterogeneous mutations to fluconazole resistance in Cryptococcus neoformans..
          • Antimicrob Agents Chemother
          • ,
          • 45
          • (2)
          • ,
          • 420-427.
          • [web]
          Publication Description

          Infections with the human pathogenic basidiomycetous yeast Cryptococcus neoformans are often treated with fluconazole. Resistance to this antifungal agent has been reported. This study investigated the patterns of mutation to fluconazole resistance in C. neoformans in vitro. The MIC of fluconazole was measured for 21 strains of C. neoformans. The MICs for these 21 strains differed (0.25 to 4.0 microg/ml), but the strains were selected for this study because they exhibited no growth on plates of yeast morphology agar (YMA) containing 8 microg of fluconazole per ml. To determine their mutation rates, six independent cultures from a single original colony were established for each of the 21 strains. Each culture was then spread densely on a YMA plate with 8 microg of fluconazole per ml. A random set of putative mutants was subcultured, and the MIC of fluconazole was determined for each mutant. The 21 strains evinced significant heterogeneity in their mutation rates. The MICs of the putative mutants ranged widely, from their original MIC to 64 microg of fluconazole per ml. However, for this set of 21 strains, there was no significant correlation between the original MIC for a strain and the mutation rate of that strain; the MIC for the mutant could not be predicted from the original MIC. These results suggest that dynamic and heterogeneous mutational processes are involved in generating fluconazole resistance in C. neoformans.

          • TY James, JM Moncalvo, S Li and R Vilgalys.
          • (2001).
          • Polymorphism at the ribosomal DNA spacers and its relation to breeding structure of the widespread mushroom Schizophyllum commune..
          • Genetics
          • ,
          • 157
          • (1)
          • ,
          • 149-161.
          Publication Description

          The common split-gilled mushroom Schizophyllum commune is found throughout the world on woody substrates. This study addresses the dispersal and population structure of this fungal species by studying the phylogeny and evolutionary dynamics of ribosomal DNA (rDNA) spacer regions. Extensive sampling (n = 195) of sequences of the intergenic spacer region (IGS1) revealed a large number of unique haplotypes (n = 143). The phylogeny of these IGS1 sequences revealed strong geographic patterns and supported three evolutionarily distinct lineages within the global population. The same three geographic lineages were found in phylogenetic analysis of both other rDNA spacer regions (IGS2 and ITS). However, nested clade analysis of the IGS1 phylogeny suggested the population structure of S. commune has undergone recent changes, such as a long distance colonization of western North America from Europe as well as a recent range expansion in the Caribbean. Among all spacer regions, variation in length and nucleotide sequence was observed between but not within the tandem rDNA repeats (arrays). This pattern is consistent with strong within-array and weak among-array homogenizing forces. We present evidence for the suppression of recombination between rDNA arrays on homologous chromosomes that may account for this pattern of concerted evolution.

          • GM Mueller, QX Wu, YQ Huang, SY Guo, R Aldana-Gomez and R Vilgalys.
          • (2001).
          • Assessing biogeographic relationships between North American and Chinese macrofungi.
          • Journal of Biogeography
          • ,
          • 28
          • (2)
          • ,
          • 271-281.
          • [web]
          Publication Description

          Aim: A close biogeographic relationship between the macrofungi of eastern North America and eastern Asia has been documented based on comparisons of species lists. In addition to having a similar species composition, the two regions are reported to share a number of species with putative disjunct distributions. This close biogeographic relationship, however, has rarely been tested within a phylogenetic context. In this paper we examine relationships within three genera, Armillaria, Xerula and Suillus (Fungi, Basidiomycetes, Agaricales) chosen as exemplars of different ecological guilds occupied by macrofungi (plant pathogens, saprobes, mutualists). Location: Fieldwork for this project centered in eastern North America, Central America, China and Australasia. Material from additional localities were obtained from cooperating herbaria and additional sequences were downloaded from GenBank. Methods: ITS sequence data were used to construct phylogenies for each genus. Results: Only one of four tested putative disjunct species, Xerula hispida Halling and Mueller, was supported. Material referable to X. furfuracea (Peck) Redhead, Ginns and Shoemaker from China and North America do not form a monophyletic group. Disjunct populations of Suillus spraguei (Berkeley & Curtis) Kuntze were shown to be paraphyletic. The morphological similarity of the Chinese material to the North American material is likely due to morphological stasis. Finally, morphologically identical material referable to Suillus americanus (Peck) Snell in Slipp and Snell from eastern North America and S. sibiricus (Singer) Singer from China, along with the morphologically similar western North American S. sibiricus, probably represent a single circumboreal taxon. Main conclusions: The resulting data, while not refuting the hypothesis that there exists a relatively close biogeographic relationship for macrofungi between eastern North America and eastern Asia, suggest that the relationship may not be as close as indicated by morphological data. These results are similar to emerging data from analyses of flowering plants displaying putative eastern North American/eastern Asian disjunct distribution patterns.

          • SA Redhead, R Vilgalys, JM Moncalvo, J Johnson and HJS Jr.
          • (2001).
          • Coprinus Pers. and the disposition of Coprinus species sensu lato.
          • Taxon
          • ,
          • 50
          • (1)
          • ,
          • 203-241.
          Publication Description

          Based upon molecular studies, the genus Coprinus Pers. is subdivided into Coprinus sensu stricto (Agaricaceae), and Coprinellus P. Karst., Coprinopsis P. Karst., and Parasola gen. nov. in the new family Psathyrellaceae. The nomenclatural history and typifications of names previously treated as synonyms of Coprinus are reviewed. It is demonstrated that taxonomic characters previously considered not to be generically significant gain importance when correlated with molecular evidence. Many new combinations are proposed. A key using anatomical features to molecularly (phylogenetically) recognised coprinoid genera is provided.

          • KW Hughes, RH Petersen, JE Johnson, JM Moncalvo, R Vilgalys, SA Redhead, T Thomas and LL McGhee.
          • (2001).
          • Infragenic phylogeny of Collybia s. str. based on sequences of ribosomal ITS and LSU regions.
          • Mycological Research
          • ,
          • 105
          • (2)
          • ,
          • 164-172.
          • [web]
          Publication Description

          Collybia, as understood by Antonin & Noordeloos, comprises four species: C. racemosa, C. tuberosa, C. cirrhata and C. cookei. Collybia tuberosa, C. cirrhata and C. cookei are morphologically similar and are primarily distinguished from each other by the presence or absence and the colour of sclerotia. All four share a common and unique habitat. Phylogenetic reconstructions using DNA sequences of the ribosomal ITS1-5.8S-ITS2 support four distinct clades, each corresponding to a morphological species, with the C. tuberosa, C. cirrhata and C. cookei clades forming a larger group. Analyses of ribosomal Large Subunit DNA sequences confirmed that Collybia tuberosa, C. cirrhata and C. cookei formed a monophyletic group. In both analyses, the C. racemosa sequence was highly divergent from those of the other three species of the complex and we propose a separate genus name, Dendrocollybia, for this species. Simple diagnostic RFLP patterns were identified for the four species and were used to validate morphological designations and distributions.

          • TY James, JM Moncalvo, S Li and R Vilgalys.
          • (2001).
          • The other fly room: J. T. Patterson and Texas genetics.
          • Genetics
          • ,
          • 157
          • (1)
          • ,
          • 1-5.
          • U Peintner, NL Bougher, MA Castellano, JM Moncalvo, MM Moser, JM Trappe and R Vilgalys.
          • (2001).
          • Multiple origins of sequestrate fungi related to Cortinarius (Cortinariaceae).
          • American Journal of Botany
          • ,
          • 88
          • (12)
          • ,
          • 2168-2179.
          Publication Description

          The aim of the present study was to investigate the phylogeny and evolution of sequestrate fungi (with gastroid or partially exposed basidiomes) in relation to their gilled relatives from the Cortinariaceae (Basidiomycetes). Phylogenetic analyses of 151 ITS sequences from 77 gilled species and 37 sequestrate taxa were performed using maximum parsimony and maximum likelihood methods. Results show that sequestrate basidiome forms occur in all three major ectomycorrhizal lineages of Cortinariaceae: the clades Cortinarius, Hebeloma/Hymenogaster/Naucoria, and Descolea. However, these forms do not appear within the saprobic outgroup Gymnopilus, indicating multiple origins of sequestrate forms from ectomycorrhizal ancestors. Additionally, within the Cortinarius clade sequestrate forms have multiple origins: emergent Cortinarius spp., Thaxterogaster, Quadrispora, Protoglossum, and two Hymenogaster spp. (H. remyi, H. sublilacinus) share common ancestors with Cortinarius spp., but these sequestrate genera are not closely related to each other (with exception of Thaxterogaster and Quadrispora). Hymenogaster sensu stricto, Setchelliogaster, and Descomyces were placed in the two other major clades. Thus, sequestrate taxa evolved independently many times within brown-spored Agaricales. Furthermore, emergent, secotioid, and gastroid forms have evolved independently from each other, and so are not necessarily intermediate forms. After their establishment, these apparently morphologically stable taxa show a tendency to radiate.

          • D Gonzalez, DE Carling, S Kuninaga, R Vilgalys and MA Cubetae.
          • (2001).
          • Ribosomal DNA systematics of Ceratobasidium and Thanatephorus with Rhizoctonia anamorphs.
          • Mycologia
          • ,
          • 93
          • (6)
          • ,
          • 1138-1150.
          Publication Description

          The phylogenetic relationships of anastomosis groups (AG) of Rhizoctonia associated with Ceratobasidium and Thanatephorus teleomorphs were determined by cladistic analyses of internal transcribed spacer (ITS) and 28S large subunit (LSU) regions of nuclear-encoded ribosomal DNA (rDNA). Combined analyses of ITS and LSU rDNA sequences from 41 isolates representing 28 AG of Ceratobasidium and Thanatephorus supported at least 12 monophyletic groupings within Ceratobasidium and Thanatephorus. There was strong support for separation of Ceratobasidium and Thanatephorus, however, six sequences representing different AG of Ceratobasidium grouped with certain sequences within the Thanatephorus clade. Phylogenetic analysis of ITS sequence data from 122 isolates revealed 31 genetically distinct groups from Thanatephorus (21 groups) and Ceratobasidium (10 groups) that corresponded well with previously recognized AG or AG subgroups. Although phylogenetic analysis of ITS sequences provided evidence that several AG of Ceratobasidium may be more closely related with some AG from Thanatephorus, these relationships were not as strongly supported by bootstrap analysis.

          • TY James and R Vilgalys.
          • (2001).
          • Abundance and diversity of Schizophyllum commune spore clouds in the Caribbean detected by selective sampling.
          • Molecular Ecology
          • ,
          • 10
          • (2)
          • ,
          • 471-479.
          • [web]
          Publication Description

          Selective spore trapping and molecular genotyping methods were employed to examine potential long-distance gene flow among Caribbean populations of the common mushroom Schizophyllum commune. Spore-trap samples from five locations were analysed using restriction fragment polymorphisms of five enzymatically amplified gene regions. Successful trappings suggested S. commune spores to be abundant in the air, with an estimated sedimentation rate of ≈ 18 spores/m2/h. High levels of genetic diversity characterized the spore-trap samples, with as many as 12 alleles observed at a single locus (chitin synthase) over all samples. In addition, spore-trap samples showed significant among sample heterogeneity including geographical population substructure. The ribosomal DNA (rDNA) intergenic spacer displayed the greatest allele frequency differences among samples, clearly separating the samples into those possessing only a South American-type allele and those segregating for both North and South American-type alleles. The molecular variation provided no clear evidence for dispersal over large, aquatic barriers within the Caribbean region, and instead suggested that spore-trapping experiments are primarily reflective of the local, established population.

          • U Kües, TY James, R Vilgalys and MP Challen.
          • (2001).
          • The chromosomal region containing pab-1, mip, and the A mating type locus of the secondarily homothallic homobasidiomycete Coprinus bilanatus.
          • Current Genetics
          • ,
          • 39
          • (1)
          • ,
          • 16-24.
          • [web]
          Publication Description

          In this paper we describe the cloning of the DNA region containing the A1 mating type genes of the secondarily homothallic mushroom Coprinus bilanatus and compare its organization to that of heterothallic homobasidiomycetes. As in other species, the C. bilanatus A factor contains several different genes that encode two different types of homeodomain transcription factor (HD1 and HD2); and some of these genes are active in the heterologous host C. cinereus. The HD1 and HD2 genes are distributed over two closely linked subloci, Aα and Aβ. A gene coding for a mitochondrial intermediate peptidase (mip) directly flanks the Aα sublocus. The pab-1 gene, required for para-aminobenzoic acid synthesis, is found 39 kb upstream of mip. The structural arrangement of this chromosomal region closely resembles the heterothallic C. cinereus. In contrast, the Aα and Aβ subloci of Schizophyllum commune are further separated, with pab-1 located between the two subloci, suggesting that a translocation event may have occurred during evolution.

          • A Forche, J Xu, R Vilgalys and TG Mitchell.
          • (December, 2001).
          • Development and characterization of a genetic linkage map of Cryptococcus neoformans var. neoformans using amplified fragment length polymorphisms and other markers..
          • Fungal Genet Biol
          • ,
          • 31
          • (3)
          • ,
          • 189-203.
          • [web]
          Publication Description

          A segregating population of single basidiospore isolates from a sexual cross was used to generate the first moderately dense genetic linkage map of Cryptococcus neoformans var. neoformans (Serotype D). Polymorphic DNA markers were developed using amplified fragment length polymorphisms, random amplified polymorphic DNA, and gene-encoding sequences. These markers were used to analyze 100 meiotic progeny. All markers were tested for distorted segregation with a goodness of fit test. Of the total of 181 markers, 148 showed balanced (1:1) segregation ratios. Segregation distortion was observed for 33 markers. Based on all the markers, a linkage map was generated that consists of 14 major linkage groups with 127 markers, several small linkage groups, and 2 linkage groups that consist only of highly skewed markers. The genetic distance of the linkage map is 1356.3 cM. The estimated total haploid genome size for C. neoformans var. neoformans was calculated using Hulberts method and yielded a map size of 1917 cM. The number of major linkage groups correlates well with the proposed number of 13 chromosomes for C. neoformans var. neoformans. Several genes, including CAP64, CnLAC, and the mating-type locus, were mapped, and their associations were consistent with published data. To date, 6 linkage groups have been assigned to their corresponding chromosomes. This linkage map should provide a framework for the ongoing genome sequencing project and will be a useful tool for studying the genetics and pathogenicity of this important medical yeast.

          • J Xu, R Vilgalys and TG Mitchell.
          • (2000).
          • Multiple gene genealogies reveal recent dispersion and hybridization in the human pathogenic fungus Cryptococcus neoformans..
          • Mol Ecol
          • ,
          • 9
          • (10)
          • ,
          • 1471-1481.
          • [web]
          Publication Description

          Cryptococcus neoformans (= Filobasidiella neoformans) is a significant emerging fungal pathogen of humans. To understand the evolution of this pathogen, 34 strains were obtained from various locations around the world and fragments of four genes were sequenced from each. These strains represented all three varieties and five serotypes. The four sequenced genes are: (i) the mitochondrial large ribosomal subunit RNA; (ii) the internal transcribed spacer region of the nuclear rRNA, including ITS1, 5.8S rRNA subunit and ITS2; (iii) orotidine monophosphate pyrophosphorylase; and (iv) diphenol oxidase. Phylogenetic analyses indicated considerable divergence among lineages, which corresponded to the current classification of C. neoformans into three varieties. However, there is no apparent phylogeographic pattern. Significant incongruences were observed among gene genealogies. The analyses indicated that the major lineages in C. neoformans diverged tens of millions of years ago but have undergone recent dispersion and hybridization.

          • JM Moncalvo, FM Lutzoni, SA Rehner, J Johnson and R Vilgalys.
          • (2000).
          • Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences..
          • Syst Biol
          • ,
          • 49
          • (2)
          • ,
          • 278-305.
          • [web]
          Publication Description

          Phylogenetic relationships of mushrooms and their relatives within the order Agaricales were addressed by using nuclear large subunit ribosomal DNA sequences. Approximately 900 bases of the 5' end of the nucleus-encoded large subunit RNA gene were sequenced for 154 selected taxa representing most families within the Agaricales. Several phylogenetic methods were used, including weighted and equally weighted parsimony (MP), maximum likelihood (ML), and distance methods (NJ). The starting tree for branch swapping in the ML analyses was the tree with the highest ML score among previously produced MP and NJ trees. A high degree of consensus was observed between phylogenetic estimates obtained through MP and ML. NJ trees differed according to the distance model that was used; however, all NJ trees still supported most of the same terminal groupings as the MP and ML trees did. NJ trees were always significantly suboptimal when evaluated against the best MP and ML trees, by both parsimony and likelihood tests. Our analyses suggest that weighted MP and ML provide the best estimates of Agaricales phylogeny. Similar support was observed between bootstrapping and jackknifing methods for evaluation of tree robustness. Phylogenetic analyses revealed many groups of agaricoid fungi that are supported by moderate to high bootstrap or jackknife values or are consistent with morphology-based classification schemes. Analyses also support separate placement of the boletes and russules, which are basal to the main core group of gilled mushrooms (the Agaricineae of Singer). Examples of monophyletic groups include the families Amanitaceae, Coprinaceae (excluding Coprinus comatus and subfamily Panaeolideae), Agaricaceae (excluding the Cystodermateae), and Strophariaceae pro parte (Stropharia, Pholiota, and Hypholoma); the mycorrhizal species of Tricholoma (including Leucopaxillus, also mycorrhizal); Mycena and Resinomycena; Termitomyces, Podabrella, and Lyophyllum; and Pleurotus with Hohenbuehelia. Several groups revealed by these data to be nonmonophyletic include the families Tricholomataceae, Cortinariaceae, and Hygrophoraceae and the genera Clitocybe, Omphalina, and Marasmius. This study provides a framework for future systematics studies in the Agaricales and suggestions for analyzing large molecular data sets.

          • J Xu, RY Ali, DA Gregory, D Amick, SE Lambert, HJ Yoell, RJ Vilgalys and TG Mitchell.
          • (2000).
          • Uniparental mitochondrial transmission in sexual crosses in Cryptococcus neoformans..
          • Curr Microbiol
          • ,
          • 40
          • (4)
          • ,
          • 269-273.
          • [web]
          Publication Description

          Restriction fragment length polymorphism (RFLP) in the large ribosomal RNA region of the mitochondrial DNA (mtDNA) was developed as a genetic marker for investigating mitochondrial transmission in sexual crosses of the human pathogenic basidiomycetous yeast Cryptococcus neoformans. Strain JEC20 of C. neoformans var. neoformans (mat a) was mated with six strains of C. neoformans var. grubii (mat alpha). Successful mating was indicated by the formation of hyphae and basidiospores. These basidiospores were examined for mtDNA RFLP genotypes. All 570 basidiospores examined from the six crosses showed the mtDNA genotype of strain JEC20. The failure to recover the C. neoformans var. grubii mtDNA in any cross indicates that the C. neoformans var. grubii mtDNA is either selectively eliminated in the newly formed dikaryon or selectively excluded in the immediate dikaryotic hyphae of the newly formed dikaryon.

          • J Xu, AR Ramos, R Vilgalys and TG Mitchell.
          • (2000).
          • Clonal and spontaneous origins of fluconazole resistance in Candida albicans..
          • J Clin Microbiol
          • ,
          • 38
          • (3)
          • ,
          • 1214-1220.
          • [web]
          Publication Description

          The genotypes and susceptibilities to fluconazole of 78 strains of the human pathogenic yeast Candida albicans were compared. The strains comprised two sets of samples from Durham, N.C.: one from patients infected with the human immunodeficiency virus (HIV) and the other from healthy volunteers. For each strain, the MIC of fluconazole was determined by the standard National Committee for Clinical Laboratory Standards protocol. Genotypes were determined by PCR fingerprinting with five separate primers. The analysis revealed little evidence for genotypic clustering according to HIV status or body site. However, a small group of fluconazole-resistant strains isolated from patients infected with HIV formed a distinct cluster. In addition, two fluconazole-resistant strains were isolated from individuals who never took fluconazole, one from a patient infected with HIV and the other from a healthy person. The results suggest both clonal and spontaneous origins of fluconazole resistance in C. albicans.

          • OS Isikhuemhen, F Nerud and R Vilgalys.
          • (2000).
          • Cultivation studies on wild and hybrid strains of Pleurotus tuberregium (Fr.) Sing. on wheat straw substrate.
          • World Journal of Microbiology and Biotechnology
          • ,
          • 16
          • (5)
          • ,
          • 431-435.
          • [web]
          Publication Description

          Wild of strains Pleurotus tuberregium from Nigeria and the Australasian-Pacific regions and selected hybrids were studied to determine their growth and sclerotia production capacity on wheat straw substrate. Although the Australasian-Pacific strains showed faster growth rates, the wild strains from Nigeria performed better than the Australasian-Pacific strains in sclerotia yield. Under similar conditions, some hybrids had sclerotial yields that were higher than any wild strain. Our study showed the possibilities of using selected strains and the low cost methods adopted in this experiment, for the cultivation of sclerotia of P. tuberregium.

          • TY James, D Porter, CA Leander, R Vilgalys and JE Longcore.
          • (2000).
          • Molecular phylogenetics of the Chytridiomycota supports the utility of ultrastructural data in chytrid systematics.
          • Canadian Journal of Botany
          • ,
          • 78
          • (3)
          • ,
          • 336-350.
          Publication Description

          The chytrids (Chytridiomycota) are morphologically simple aquatic fungi that are unified by their possession of zoospores that typically have a single, posteriorly directed flagellum. This study addresses the systematics of the chytrids by generating a phylogeny of ribosomal DNA sequences coding for the small subunit gene of 54 chytrids, with emphasis on sampling the largest order, the Chytridiales. Selected chytrid sequences were also compared with sequences from Zygomycota, Ascomycota, and Basidiomycota to derive an overall fungal phylogeny. These analyses show that the Chytridiomycota is probably not a monophyletic group; the Blastocladiales cluster with the Zygomycota. Analyses did not resolve relationships among chytrid orders, or among clades within the Chytridiales, which suggests that the divergence times of these groups may be ancient. Four clades were well supported within the Chytridiales, and each of these clades was coincident with a group previously identified by possession of a common subtype of zoospore ultrastructure. In contrast, the analyses revealed homoplasy in several developmental and zoosporangial characters.

          • SA Redhead, KA Seifert, R Vilgalys and JM Moncalvo.
          • (2000).
          • Rhacophyllus and Zerovaemyces - Teleomorphs or anamorphs?.
          • Taxon
          • ,
          • 49
          • (4)
          • ,
          • 789-798.
          Publication Description

          Redhead, S. A., Seifert, K. A., Vilgalys, R. and Moncalvo, J.-M.: Rhacophyllus and Zerovaemyces - teleomorphs or anamorphs? - Taxon 49: 789-798. - ISSN 0040-0262. The originally monotypic genus Rhacophyllus was conceived for an agaric-like fungus that bore sheets of miniature sclerotium-like bodies (lysomeres) in place of lamellae. Subsequently it was demonstrated that a 'normal' Coprinus-like teleomorph exists as an alternative state (morph). Following this discovery, most authors have treated Rhacophyllus as an anamorph. Ontogenetic studies indicate that the Rhacophyllus state is a variation on basidiome production. Rhacophyllus apparently was rediscovered and redescribed as a new genus Zerovaemyces, for which a new family, Zerovaemycetaceae, and a new order, Loculomycetes, were also described, all as teleomorphs. Nomenclatural application of these names are analysed, and it is concluded that Rhacophyllus (and Zerovaemyces, Zerovaemycetaceae) are best considered to be nomina anamorphosium. These decisions affect the naming of other taxa newly resolved molecularly. An analogous second case of modified basidiomes involves the anamorph Decapitatus gen. nov., described here for the well-known gemmiferous state of Mycena citricolor, Decapitatus flavidus comb. nov. (= Stilbum flavidum).

          • RG Thorn, J-M Moncalvo, CA Reddy and R Vilgalys.
          • (2000).
          • Phylogenetic analyses and the distribution of nematophagy support a monophyletic Pleurotaceae within the polyphyletic pleurotoid-lentinoid fungi.
          • Mycologia
          • ,
          • 92
          • (2)
          • ,
          • 241-252.
          Publication Description

          Phylogenetic analyses based on partial sequences from nuclear 25S rDNA indicate a monophyletic Pleurotaceae, consisting of the monophyletic genera Pleurotus and Hohenbuehelia, within the polyphyletic pleurotoid-lentinoid fungi. The attack and consumption of nematodes (nematophagy) supports the monophyly of this family. Other pleurotoid-lentinoid fungi that have been studied are not nematophagous and, in phylogenetic analyses, occur within the euagaric, polyporoid and russuloid clades. The pleurotoid agarics Lampteromyces, Lentinula, Nothopanus, and Omphalotus form a clade together with Gymnopus dryophilus. A clade that corresponds to the Tricholomataceae includes the pleurotoid agarics Conchomyces, Hypsizygus, Phyllotopsis, and Resupinatus. Faerberia, Heliocybe, Lentinus, Neolentinus, and Panus are gilled polypores, and all deserve recognition at the generic level. The brown-rotters Heliocybe and Neolentinus form a distinct clade within the polypores together with the brown-rotting polypore, Gloeophyllum. The Pleurotaceae belong in the Agaricales, are not closely related to or synonymous with the Polyporaceae, and should be restricted to the genera Pleurotus and Hohenbuehelia. An isolate of Hohenbuehelia from Alberta, Canada produces adhesive knobs typical of Hohenbuehelia and its anamorph Nematoctonus, and also nonadhesive nematotoxic droplets characteristic of Pleurotus. This combination is unique within Hohenbuehelia and Pleurotus. Phylogenetic analyses place this species at the base of the genus Hohenbuehelia, indicating that nematotoxic droplets were probably present in the common ancestor of Pleurotus and Hohenbuehelia. In contrast, the gelatinized fruiting bodies of Hohenbuehelia and Resupinatus are independently derived. The tribe Resupinateae (Tricholomataceae) should be restricted to Resupinatus (including Asterotus) arid cyphelloid allies such as Stigmatolemma.

          • A Pringle, J-M Moncalvo and R Vilgalys.
          • (2000).
          • High levels of variation in ribosomal DNA sequences within and among spores of a natural population of the arbuscular mycorrhizal fungus Acaulospora colossica.
          • Mycologia
          • ,
          • 92
          • (2)
          • ,
          • 259-268.
          Publication Description

          Sequences of the nuclear rDNA ITS region were sampled from a natural population of an arbuscular mycorrhizal fungus, Acaulospora colossica. Genetic diversity was explored through three levels of sampling: within an individual (a single spore), between individuals of a single soil sample, and between individuals of different soil samples across a 36 m2 area. High levels of ITS sequence variation were discovered, and sequences from different spores and different soil samples were sometimes more similar than sequences of the same spore or soil sample. These results demonstrate a complex pattern of rDNA organization within a natural population of Glomalean fungi, and challenge ideas of individuality and collectivism in fungi.

          • OS Isikhuemhen, JM Moncalvo, F Nerud and R Vilgalys.
          • (2000).
          • Mating compatibility and phylogeography in Pleurotus tuberregium.
          • Mycological Research
          • ,
          • 104
          • (6)
          • ,
          • 732-737.
          • [web]
          Publication Description

          Genetic relationships were investigated among several populations of Pleurotus tuberregium from Nigeria, Papua New Guinea and New Caledonia. Intrastock mating compatibility studies using progeny from two collections demonstrated a tetrapolar mating system for P. tuberregium. Interstock matings among the geographically distinct populations were compatible. All isolates were found to be intersterile with tester strains of other Pleurotus species, showing that P. tuberregium represents a unique intersterility group in Pleurotus. Nucleotide sequences of the ITS region of the rDNA gene were determined for 30 isolates and used to infer phylogenetic structure of populations. Phylogenetic analysis shows that African and Australasian-Pacific isolates form at least two distinct evolutionary lineages. Higher genetic divergence was observed among ITS sequences from the Australasian-Pacific region than among African isolates, which suggests a possible origin of P. tuberregium in the Australasian-Pacific region.

          • JM Moncalvo, D Drehmel and R Vilgalys.
          • (2000).
          • Variation in modes and rates of evolution in nuclear and mitochondrial ribosomal DNA in the mushroom genus Amanita (Agaricales, Basidiomycota): Phylogenetic implications.
          • Molecular Phylogenetics and Evolution
          • ,
          • 16
          • (1)
          • ,
          • 48-63.
          • [web]
          Publication Description

          Modes and rates of molecular evolution, and congruence and combinability for phylogenetic reconstruction, of portions of the nuclear large ribosomal subunit (nLSU-rDNA) and mitochondrial small subunit (mtSSU-rDNA) genes were investigated in the mushroom genus Amanita. The AT content was higher in the mtSSU-rDNA than in the nLSU-rDNA. A transition bias in which AT substitutions were as frequent as transitions was present in the mtSSU-rDNA but not in the nLSU-rDNA. Among-sites rate variation in nucleotide substitutions at variable sites was present in the nLSU-rDNa but not in the mtSSU-rDNA. Likelihood ratio tests indicated very different models of evolution for the two molecules. A molecular clock could be rejected for both data sets. Rates of molecular evolution in the two molecules were uncoupled: faster evolutionary rates in the mtSSU-rDNA and nLSU-rDNA were not observed for the same taxa. In separate phylogenetic analyses, the nLSU-rDNA data set had higher phylogenetic resolution. The partition homogeneity test and statistical bootstrap support for branches indicated absence of conflict in the phylogenetic signal in the two data sets; however, tree topologies produced from the separate data sets were not congruent. Heterogeneity in modes and rates of evolution in the two molecules pose difficulties for a combined analysis of the two data sets: the use of equally weighted parsimony is not fully satisfactory when rate heterogeneity is present, and it is impractical to determine a model for maximum-likelihood analysis that fits simultaneously two heterogeneous data sets. Overall topologies produced from either the separated or the combined analyses using various tree reconstruction methods were identical for nearly all statistically significant branches. (C) 2000 Academic Press.

          • JG McEwen, JW Taylor, D Carter, J Xu, MS Felipe, R Vilgalys, TG Mitchell, T Kasuga, T White, T Bui and CM Soares.
          • (2000).
          • Molecular typing of pathogenic fungi..
          • Med Mycol
          • ,
          • 38 Suppl 1
          • ,
          • 189-197.
          • [web]
          Publication Description

          In this Round Table, the application of several methods of molecular typing were discussed in reference to four important pathogenic fungi: Coccidioides immitis, Histoplasma capsulatum, Candida albicans and Paracoccidioides brasiliensis. Among the different methods the following were discussed: restriction fragment length polymorphisms (RFLP), single nucleotide polymorphisms, random amplified polymorphic DNA (RAPD), polymerase chain reaction (PCR)-RFLP and microsatellites. By means of these methods, several important biological questions related to speciation, mode of reproduction and population genetics could be approached. The basic information obtained from this approach has implications in the understanding of these pathogenic fungi in relation to their behavior and the development of pathogenic features, such as resistance to antimicrobials and virulence factors used for colonization of mammalian hosts. The knowledge obtained from these studies could also be used for the development of innovative diagnostic methods, as well as for novel therapeutic approaches and production of vaccines.

          • G Schönian, A Forche, HJ Tietz, M Müller, Y Gräser, R Vilgalys, TG Mitchell and W Presber.
          • (2000).
          • [Genetic structure of geographically different populations of candida albicans]..
          • Mycoses
          • ,
          • 43 Suppl 2
          • ,
          • 51-56.
          • [web]
          Publication Description

          Codominant single-locus markers were developed by amplifying genomic DNA of C. albicans with pairs of random primers. Monomorphic PCR products were screened for polymorphisms by the SSCP technique. Sequencing confirmed that SSCP's were mostly due to single nucleotide substitutions in the polymorphic fragments. A total of 85 polymorphic loci were observed within 13 PCR fragments. Populations from Africa displayed less genotype variation than the populations from Europe and USA. Two genetically similar African C. albicans populations exhibiting an atypical biotype were strictly clonal and perhaps represent a geographically distributed clone. Analyses of "typical" C. albicans populations of different geographical origin provided however evidence for both clonality and recombination. Evidence for clonality was supported by the absence of segregation genotypes, and by deviation of genotypic frequencies from Hardy-Weinberg expectations. Tests for nonrandom association of alleles across loci revealed less evidence for linkage disequilibrium than expected for strictly clonal populations. Although all C. albicans populations tested were primarily clonal, evidence for recombination suggests that sexual reproduction or some other form of genetic exchange occurs in this species.

          • A Forche, G Schönian, Y Gräser, R Vilgalys and TG Mitchell.
          • (1999).
          • Genetic structure of typical and atypical populations of Candida albicans from Africa..
          • Fungal Genet Biol
          • ,
          • 28
          • (2)
          • ,
          • 107-125.
          • [web]
          Publication Description

          Atypical isolates of the pathogenic yeast Candida albicans have been reported with increasing frequency. To investigate the origin of a set of atypical isolates and their relationship to typical isolates, we employed a combination of molecular phylogenetic and population genetic analyses using rDNA sequencing, PCR fingerprinting, and analysis of co-dominant DNA nucleotide polymorphisms to characterize the population structure of one typical and two atypical populations of C. albicans from Angola and Madagascar. The extent of clonality and recombination was assessed in each population. The analyses revealed that the structure of all three populations of C. albicans was predominantly clonal but, as in previous studies, there was also evidence for recombination. Allele frequencies differed significantly between the typical and the atypical populations, suggesting very low levels of gene flow between them. However, allele frequencies were quite similar in the two atypical C. albicans populations, suggesting that they are closely related. Phylogenetic analysis of partial sequences encoding the nuclear 26S rDNA demonstrated that all three populations belong to a single monophyletic group, which includes the type strain of C. albicans.

          • J Xu, R Vilgalys and TG Mitchell.
          • (1999).
          • Lack of genetic differentiation between two geographically diverse samples of Candida albicans isolated from patients infected with human immunodeficiency virus..
          • J Bacteriol
          • ,
          • 181
          • (4)
          • ,
          • 1369-1373.
          • [web]
          Publication Description

          The patterns of genetic variation of samples of Candida albicans isolated from patients infected with human immunodeficiency virus in Durham, N.C., and Vitória, Brazil, were compared. Genotypes for 126 strains were obtained at 16 polymorphic restriction sites distributed on nine PCR fragments. The results indicated evidence of clonality both within and between these two geographically diverse samples. The samples are genetically very similar, with little evidence of genetic differentiation.

          • J Xu, TG Mitchell and R Vilgalys.
          • (1999).
          • PCR-restriction fragment length polymorphism (RFLP) analyses reveal both extensive clonality and local genetic differences in Candida albicans..
          • Mol Ecol
          • ,
          • 8
          • (1)
          • ,
          • 59-73.
          • [web]
          Publication Description

          Using a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method to obtain genotypes for the diploid pathogenic yeast, Candida albicans, we analysed 204 C. albicans isolates from three populations of the Duke University community: two from clinical sources [one from patients infected with human immunodeficiency virus (HIV) and the other from patients without HIV infection], and the third from healthy student volunteers. The results indicated: (i) extensive evidence for clonality within and between populations of C. albicans; and (ii) greater genotypic and gene diversities in the nonclinical population than those derived from clinical specimens, regardless of HIV status. The two clinical populations were genetically more similar to each other than either was to the population consisting of isolates from healthy people. Within each population sample there was a general lack of heterozygotes, and random associations of alleles within and between loci were found in less than 50% of the loci or pairs of loci. These findings were consistent between the two sets of samples analysed: those including all isolates and those including only clone-corrected isolates. Possible mechanisms are presented to explain the observed patterns of genetic variation within and between C. albicans populations.

          • TJ Baroni, NW Legon, R Vilgalys and DJ Lodge.
          • (1999).
          • Calocybe cyanea - A rare and beautiful agaric is discovered in Puerto Rico.
          • Mycologist
          • ,
          • 13
          • (1)
          • ,
          • 7-10.
          Publication Description

          A rare find of Calocybe cyanea from Puerto Rico is described and illustrated. A discussion of all species of Calocybe found in the Caribbean is provided. Since nearly one-half of the described species of Calocybe can be found in the Neotropics (nine out of the 20 or so known taxa), a key to the species of Calocybe which are found in the Neotropics is included.

          • Y Gräser, ME Fari, R Vilgalys, AFA Kuijpers, GSD Hoog, W Presber and HJ Tietz.
          • (1999).
          • Phylogeny and taxonomy of the family Arthrodermataceae (dermatophytes) using sequence analysis of the ribosomal ITS region.
          • Medical Mycology
          • ,
          • 37
          • (2)
          • ,
          • 105-114.
          • [web]
          Publication Description

          The internal transcribed spacer (ITS) region, covering the ITS1, ITS2 and 5.8S ribosomal DNA was used to evaluate phylogenetic relationships within the fungal family Arthrodermataceae. Sequences of variable length, ranging between 522 and 684 base pairs were aligned. An unrooted consensus tree based on parsimony analysis showed Trichophyton to be polyphyletic, and Microsporum to be paraphyletic. Non-monophyly of these two genera is in conflict with traditional classification. But this relation is not strongly supported by bootstrap analysis. Phylogenetic analysis showed that the two known members of the genus Epidermophyton grouped widely apart from each other. Within Trichophyton, our results suggest a separation of human pathogenic species and primarily geophilic species. Bootstrap support for these two groups is fairly high and both groups are recognized by current taxonomy. Three lineages were revealed within the T. mentagrophytes species complex. Microsporum canis, M. audouinii and M. equinum were found to be closely related. The topology of the tree was robust to various methods of analysis (parsimony and distance) and a different weighting scheme. Weighting of transversions over transitions did not improve the status of poorly supported branches of the tree.

          • JSH Jr and R Vilgalys.
          • (1999).
          • Phylogenetic Relationships in the Mushroom Genus Coprinus and Dark-Spored Allies Based on Sequence Data from the Nuclear Gene Coding for the Large Ribosomal Subunit RNA: Divergent Domains, Outgroups, and Monophyly.
          • Molecular Phylogenetics and Evolution
          • ,
          • 13
          • (1)
          • ,
          • 1-19.
          • [web]
          Publication Description

          Phylogenetic relationships were investigated in the mushroom genus Coprinus based on sequence data from the nuclear encoded large-subunit rDNA gene. Forty-seven species of Coprinus and 19 additional species from the families Coprinaceae, Strophariaceae, Bolbitiaceae, Agaricaceae, Podaxaceae, and Montagneaceae were studied. A total of 1360 sites was sequenced across seven divergent domains and intervening sequences. A total of 302 phylogenetically informative characters was found. Ninety-eight percent of the average divergence between taxa was located within the divergent domains, with domains D2 and D8 being most divergent and domains D7 and D10 the least divergent. An empirical test of phylogenetic signal among divergent domains also showed that domains D2 and D3 had the lowest levels of homoplasy. Two equally most parsimonious trees were resolved using Wagner parsimony. A character-state weighted analysis produced 12 equally most parsimonious trees similar to those generated by Wagner parsimony. Phylogenetic analyses employing topological constraints suggest that none of the major taxonomic systems proposed for subgeneric classification is able to completely reflect phylogenetic relationships in Coprinus. A strict consensus integration of the two Wagner trees demonstrates the problematic nature of choosing outgroups within dark-spored mushrooms. The genus Coprinus is found to be polyphyletic and is separated into three distinct clades. Most Coprinus taxa belong to the first two clades, which together form a larger monophyletic group with Lacrymaria and Psathyrella in basal positions. A third clade contains members of Coprinus section Comati as well as the genus Leucocoprinus, Podaxis pistillaris, Montagnea arenaria, and Agaricus pocillator. This third clade is separated from the other species of Coprinus by members of the families Strophariaceae and Bolbitiaceae and the genus Panaeolus. © 1999 Academic Press.

          • D Drehmel, JM Moncalvo and R Vilgalys.
          • (1999).
          • Molecular phylogeny of Amanita based on large-subunit ribosomal DNA sequences: Implications for taxonomy and character evolution.
          • Mycologia
          • ,
          • 91
          • (4)
          • ,
          • 610-618.
          Publication Description

          Phylogenetic relationships in the genus Amanita were investigated using sequence data from the nuclear-encoded large subunit ribosomal DNA. Exemplar taxa were selected to represent the all sections from the current classifications of Singer, Bas and Jenkins. Phylogenetic analysis of the nuc-LSU region supports the taxonomic distinction of subgenera Amanita and Lepidella, as well as all nine sections previously recognized by Singer (R. Singer, 1986, The Agaricales in Modern Taxonomy, 4th ed.) including sections Amanita, Amidellae, Caesareae, Lepidella, Mappae, Phalloideae, Ovigerae, Vaginatae, Validae. Phylogenetic analyses among these nine terminal groups reveal several higher-level relationships which are also supported by morphological and biochemical characters. A phylogenetic classification is proposed which recognizes two subgenera (Amanita, Lepidella), four sections (Amanita, Vaginate, Phalloideae, Lepidella), seven subsections (Amanita, Ovigerae, Amidellae, Caesareae, Phalloideae, Vaginatae, Validae), and two series (Mappae, Validae).

          • TY James, D Porter, JL Hamrick and R Vilgalys.
          • (1999).
          • Evidence for limited intercontinental gene flow in the cosmopolitan mushroom, Schizophyllum commune.
          • Evolution
          • ,
          • 53
          • (6)
          • ,
          • 1665-1677.
          Publication Description

          The genetic structure of populations of Schizophyllum commune was inferred from electrophoretic variation among 136 individuals at 11 polymorphic allozyme loci to determine the extent of geographic differentiation in this widespread mushroom species. The majority of the genetic variation was contained within populations; however, considerable genetic differentiation was observed among populations (global G(ST) = 0.214). Clustering analysis demonstrated that genetic distance was correlated with geographic distance and that a large component of the genetic variation was due to allele frequency differences among populations from the eastern and western hemispheres. Our results also suggest that populations are large and geographically widespread. The lack of fixed genetic differences among intercontinental populations at any of the allozyme loci suggests that long-distance spore dispersal may counter the effects of genetic drift in this cosmopolitan species. These results are contrasted with a previous description of the same collection, in which the mating allele distribution of the species displayed no population substructure at any geographic scale (Raper et al. 1958). Broader implications of this study are that both species and mating allele distributions may not be correlated with long-distance gene flow in basidiomycete fungi.

          • J Xu, R Vilgalys and TG Mitchell.
          • (1998).
          • Colony size can be used to determine the MIC of fluconazole for pathogenic yeasts..
          • J Clin Microbiol
          • ,
          • 36
          • (8)
          • ,
          • 2383-2385.
          • [web]
          Publication Description

          This report describes a new statistical method for estimating the MIC of fluconazole for yeasts pathogenic to humans. This method is based on comparison of the colony sizes on solid media containing different concentrations of fluconazole. By this method, the MICs of fluconazole for 10 yeast strains were comparable to results obtained by the standard method recommended by the National Committee for Clinical Laboratory Standards. This method is simple to perform and easy to interpret. The turnaround time is faster than other methods. The method should be applicable to the determination MICs of other antifungal drugs for yeasts.

          • J Johnson and R Vilgalys.
          • (1998).
          • Phylogenetic systematics of Lepiota sensu lato based on nuclear large subunit rDNA evidence.
          • Mycologia
          • ,
          • 90
          • (6)
          • ,
          • 971-979.
          Publication Description

          Taxonomic circumscription and segregation of the genus Lepiota has been problematic. Phylogenetic relationships were investigated for lepiotoid and closely related taxa using DNA sequence data. Our analysis reflects a broad sampling across eight segregate genera used by Singer: Lepiota s:s., Cystolepiota, Leucocoprinus, Leucoagaricus, Macrolepiota, Chlorophyllum, Cystoderma, and Ripartitella (Agaricaceae, Agaricales, Basidiomycota). Related fungi were evaluated from the dark-spored genera Agaricus and Coprinus and representative secotioid and attine fungi, along with more distantly related fungi. DNA sequences were compared for the 5' end region of the nuclear encoded large subunit ribosomal RNA gene (25-28S rDNA) from 55 ingroup and outgroup taxa. Results from parsimony analysis are consistent with the exclusion of the tribe Cystodermateae (Cystoderma and Ripartitella) from the family Agaricaceae, and the retention of the tribes Lepioteae and Leucocoprineae. Lepiotoid segregate genera remain poorly resolved using this molecule. Parsimony analysis indicates that both Agaricus and Coprinus section Comati are nested within the lepiotoid fungi. The support for Coprinus section Comati to be within the Agaricaceae presents interesting taxonomic problems involving nomeclatural precedence and usage of commonly known groups including Agaricus, Coprinus, and Lepiota.

          • JM McPartland, RJ Vilgalys and MA Cubeta.
          • (1997).
          • Mushroom poisoning..
          • Am Fam Physician
          • ,
          • 55
          • (5)
          • ,
          • 1797-1812.
          • [web]
          Publication Description

          The majority of cases of mushroom poisoning occur in children and involve benign gastrointestinal irritants. Critical poisonings most frequently occur in adults who ingest Amanita phalloides or other mushrooms containing amanitin. Critical versus noncritical poisonings can be diagnosed with a high degree of confidence by the patient's history and initial symptoms. The most promising new medical treatment for Amanita mushroom poisoning is silibinin. In suspected cases of mushroom poisoning, it is important to obtain specimens of the ingested mushrooms, if possible, since treatment is specific to the species.

          • MA Cubeta and R Vilgalys.
          • (1997).
          • Population biology of the Rhizoctonia solani complex.
          • Phytopathology
          • ,
          • 87
          • (4)
          • ,
          • 480-483.
          • LA Lewis, BD Mishler and R Vilgalys.
          • (1997).
          • Phylogenetic Relationships of the Liverworts (Hepaticae), a Basal Embryophyte Lineage, Inferred from Nucleotide Sequence Data of the Chloroplast GenerbcL.
          • Molecular Phylogenetics and Evolution
          • ,
          • 7
          • (3)
          • ,
          • 377-393.
          • [web]
          Publication Description

          Sequence data from the chloroplast-encoded generbcL were obtained for 24 liverworts, a basal group of embryophytes. Maximum likelihood and parsimony analyses of these data, along with data from other major green plant lineages, confirm hypotheses based on morphological data, such as the paraphyly of bryophytes, and the basal position of liverworts. Molecular data corroborate the deep separation between the complex thalloid and leafy/simple thalloid liverworts implied by morphological data, but the monophyly of liverworts could not be rejected. The effects of accounting for site-to-site rate heterogeneity in these data were examined using maximum likelihood methods. Comparison of trees obtained with and without rate heterogeneity showed that simply allowing for heterogeneity had a greater improvement on likelihood score than optimization of transition/transversion bias. Incorporation of site-to-site rate heterogeneity in the larger analysis, however, did not necessarily change which topology was favored. Properties ofrbcL sequences from the two liverwort groups were compared. Significantly different substitution rates were found between leafy/simple thalloid and complex thalloid liverwort taxa, with rates ofrbcL sequence evolution in leafy/simple thalloid taxa being higher and more indicative of those of vascular plants, and with those of complex thalloid taxa (such asMarchantia) being slower. Codon usage inrbcL in complex thalloid liverworts was biased toward NNU and NNA, compared to the leafy/simple thalloid liverworts. Although base composition and relative substitution rates differed between the two groups, no significant differences were detected within each of the two groups of liverworts. The signal present in first and second codon sites versus third codon sites was compared. While the third codon positions inrbcL across this taxon sampling are highly variable (with only 15 constant sites of 439), the trees obtained were in general agreement with trees from the entire data set and with trees obtained from independent sources of data. The presence of signal in third codon positions across greater than 400 MY of plant evolution means that definitions of saturation based on pair-wise comparisons of sequences inadequately assess phylogenetic signal. © 1997 Academic Press.

          • Y Gräser, M Volovsek, J Arrington, G Schönian, W Presber, TG Mitchell and R Vilgalys.
          • (1996).
          • Molecular markers reveal that population structure of the human pathogen Candida albicans exhibits both clonality and recombination..
          • Proc Natl Acad Sci U S A
          • ,
          • 93
          • (22)
          • ,
          • 12473-12477.
          • [web]
          Publication Description

          The life history of Candida albicans presents an enigma: this species is thought to be exclusively asexual, yet strains show extensive phenotypic variation. To address the population genetics of C. albicans, we developed a genetic typing method for codominant single-locus markers by screening randomly amplified DNA for single-strand conformation polymorphisms. DNA fragments amplified by arbitrary primers were initially screened for single-strand conformation polymorphisms and later sequenced using locus-specific primers. A total of 12 single base mutations and insertions were detected from six out of eight PCR fragments. Patterns of sequence-level polymorphism observed for individual strains detected considerable heterozygosity at the DNA sequence level, supporting the view that most C. albicans strains are diploid. Population genetic analyses of 52 natural isolates from Duke University Medical Center provide evidence for both clonality and recombination in C. albicans. Evidence for clonality is supported by the presence of several overrepresented genotypes, as well as by deviation of genotypic frequencies from random (Hardy-Weinberg) expectations. However, tests for nonrandom association of alleles across loci reveal less evidence for linkage disequilibrium than expected for strictly clonal populations. Although C. albicans populations are primarily clonal, evidence for recombination suggests that sexual reproduction or some other form of genetic exchange occurs in this species.

          • AD Yoder, R Vilgalys and M Ruvolo.
          • (1996).
          • Molecular evolutionary dynamics of cytochrome b in strepsirrhine primates: The phylogenetic significance of third-position transversions.
          • Molecular Biology and Evolution
          • ,
          • 13
          • (10)
          • ,
          • 1339-1350.
          Publication Description

          DNA sequences of the complete cytochrome b gene are shown to contain robust phylogenetic signal for the strepsirrhine primates (i.e., lemurs and lorises). The phylogeny derived from these data conforms to other molecular studies of strepsirrhine relationships despite the fact that uncorrected nucleotide distances are high for nearly all intrastrepsirrhine comparisons, with most in the 15%-20% range. Cytochrome b sequences support the hypothesis that Malagasy lemuriforms and Afro-Asian lorisiforms each comprise clades that share a sister-group relationship. A study (Adkins and Honeycutt 1994) of the cytochrome c oxidase subunit II (COII) gene placed one Malagasy primate (Daubentonia) at the base of the strepsirrhine clade, thereby suggesting a diphyletic Lemuriformes. The reanalysis of COII third-position transversions, either alone or in combination with cytochrome b third- position transversions, however, yields a tree that is congruent with phylogenetic hypotheses derived from cytochrome b and other genetic data sets.

          • AD Yoder, M Cartmill, M Ruvolo, K Smith and R Vilgalys.
          • (1996).
          • Ancient single origin for Malagasy primates.
          • Proceedings of the National Academy of Sciences of the United States of America
          • ,
          • 93
          • (10)
          • ,
          • 5122-5126.
          • [web]
          Publication Description

          We report new evidence that bears decisively on a long-standing controversy in primate systematics. DNA sequence data for the complete cytochrome b gene, combined with an expanded morphological data set, confirm the results of a previous study and again indicate that all extant Malagasy lemurs originated from a single common ancestor. These results, as well as those from other genetic studies, call for a revision of primate classifications in which the dwarf and mouse lemurs are placed within the Afro-Asian lorisiforms. The phylogenetic results, in agreement with paleocontinental data, indicate an African origin for the common ancestor of lemurs and lorises (the Strepsirrhini). The molecular data further suggest the surprising conclusion that lemurs began evolving independently by the early Eocene at the latest. This indicates that the Malagasy primate lineage is more ancient than generally thought and places the split between the two strepsirrhine lineages well before the appearance of known Eocene fossil primates. We conclude that primate origins were marked by rapid speciation and diversification sometime before the late Paleocene.

          • G Haase, JW Spatafora, TG Mitchell and R Vilgalys.
          • (1995).
          • Analysis of genes coding for small-subunit rRNA sequences in studying phylogenetics of dematiaceous fungal pathogens [2].
          • Journal of Clinical Microbiology
          • ,
          • 34
          • (8)
          • ,
          • 2049-2050.
          • [web]
          Publication Description

          Because of their ability to display yeast-like growth forms in various environmental conditions, dematiaceous (melanized) hyphomycetes of the form-genera Exophiala, Rhinocladiella, and Wangiella have been informally termed "black yeasts." Cladistic analysis of 1,050 bp of the genes coding for small-subunit rRNA (SSU rDNA) supported a close relationship among species of these black yeasts with other dematiaceous hyphomycetes in the form-genera Fonsecaea, Phialophora, and Ramichloridium. The conventional categories of these fungi based on asexual states are not supported by phylogenetic analysis of SSU rDNA sequences. Isolates exhibiting annellidic modes of blastic conidiogenesis (e.g., Exophiala spp.) were not monophyletic and were placed as sister taxa to isolates that produce phialides or sympodulae. The results indicated very close relationships between isolates of Wangiella dermatitidis and Exophiala mansonii and between Rhinocladiella aquaspersa and Exophiala jeanselmei. This clade of dematiaceous hyphomycetes was a sister group to a clade comprising members of two orders of cleistothecial ascomycetes, Eurotiales and Onygenales. The etiological agents of chromoblastomycosis were found to be a closely related group (clade), while the agents of phaeohyphomycosis displayed a broader distribution on the SSU rDNA tree.

          • JW Spatafora, TG Mitchell and R Vilgalys.
          • (1995).
          • Analysis of genes coding for small-subunit rRNA sequences in studying phylogenetics of dematiaceous fungal pathogens..
          • J Clin Microbiol
          • ,
          • 33
          • (5)
          • ,
          • 1322-1326.
          • [web]
          Publication Description

          Because of their ability to display yeast-like growth forms in various environmental conditions, dematiaceous (melanized) hyphomycetes of the form-genera Exophiala, Rhinocladiella, and Wangiella have been informally termed "black yeasts." Cladistic analysis of 1,050 bp of the genes coding for small-subunit rRNA (SSU rDNA) supported a close relationship among species of these black yeasts with other dematiaceous hyphomycetes in the form-genera Fonsecaea, Phialophora, and Ramichloridium. The conventional categories of these fungi based on asexual states are not supported by phylogenetic analysis of SSU rDNA sequences. Isolates exhibiting annellidic modes of blastic conidiogenesis (e.g., Exophiala spp.) were not monophyletic and were placed as sister taxa to isolates that produce phialides or sympodulae. The results indicated very close relationships between isolates of Wangiella dermatitidis and Exophiala mansonii and between Rhinocladiella aquaspersa and Exophiala jeanselmei. This clade of dematiaceous hyphomycetes was a sister group to a clade comprising members of two orders of cleistothecial ascomycetes, Eurotiales and Onygenales. The etiological agents of chromoblastomycosis were found to be a closely related group (clade), while the agents of phaeohyphomycosis displayed a broader distribution on the SSU rDNA tree.

          • R Vilgalys and SB Lin.
          • (1994).
          • Assessment of species distributions in Pleurotus based on trapping of airborne basidiospores.
          • Mycologia
          • ,
          • 86
          • (2)
          • ,
          • 270-274.
          • R Vilgalys and MA Cubeta.
          • (1994).
          • Molecular systematics and population biology of Rhizoctonia.
          • Annual Review of Phytopathology
          • ,
          • 32
          • ,
          • 135-155.
          • R Vilgalys and BL Sun.
          • (1994).
          • Erratum: Ancient and recent patterns of geographic speciation in the oyster mushroom Pleurotus revealed by phylogenetic analysis of ribosomal DNA sequences (Proceedings of the National Academy of Sciences of the United States of America (May 10, 1994) 91 (4599-4603)).
          • Proceedings of the National Academy of Sciences of the United States of America
          • ,
          • 91
          • (16)
          • ,
          • 7832-.
          • [web]
          • R Vilgalys and BL Sun.
          • (1994).
          • Ancient and recent patterns of geographic speciation in the oyster mushroom Pleurotus revealed by phylogenetic analysis of ribosomal DNA sequences.
          • Proceedings of the National Academy of Sciences of the United States of America
          • ,
          • 91
          • (10)
          • ,
          • 4599-4603.
          Publication Description

          Evidence from molecular systematic studies suggests that many mushroom species may be quite ancient. Gene phylogenies were developed to examine the relationship between reproductive isolation, genetic divergence, and biogeography in oyster mushrooms (Pleurotus). Sequence data were obtained for two regions of DNA from populations belonging to eight intersterility groups (biological species). Phylogenetic analysis of sequences from the 5' portion of the nuclear encoded large subunit rDNA demonstrates an ancient origin for four intersterility groups of broad geographic distribution (world-wide), with a more recent radiation of several intersterility groups that are restricted to the Northern Hemisphere. An expanded analysis using sequence data from the more variable rDNA internal transcribed spacer region also reveals a phylogenetically based pattern of genetic divergence associated with allopatric speciation among populations from different continents in the Northern Hemisphere. The ability of rDNA sequences to resolve phylogenetic relationships among geographically isolated populations within intersterility groups illustrates the importance of biogeography for understanding speciation in Pleurotus. Patterns of geographic distribution among intersterility groups suggest that several species lineages evolved quite early, with recently evolved groups restricted to the Northern Hemisphere and older lineages occurring throughout the world. Based on phylogenetic evidence, analysis of historical biogeography using area cladograms shows that multiple dispersal and vicariance events are responsible for patterns of speciation observed.

          • W Meyer, TG Mitchell, EZ Freedman and R Vilgalys.
          • (1993).
          • Hybridization probes for conventional DNA fingerprinting used as single primers in the polymerase chain reaction to distinguish strains of Cryptococcus neoformans..
          • J Clin Microbiol
          • ,
          • 31
          • (9)
          • ,
          • 2274-2280.
          • [web]
          Publication Description

          In conventional DNA fingerprinting, hypervariable and repetitive sequences (minisatellite or microsatellite DNA) are detected with hybridization probes. As demonstrated here, these probes can be used as single primers in the polymerase chain reaction (PCR) to generate individual fingerprints. Several conventional DNA fingerprinting probes were used to prime the PCR, yielding distinctive, hypervariable multifragment profiles for different strains of Cryptococcus neoformans. PCR fingerprinting with the oligonucleotide primers (GTG)5, (GACA)4, and the phage M13 core sequence (GAGGGTGGXGGXTCT), but not with (CA)8 or (CT)8, generated DNA polymorphisms with all 42 strains of C. neoformans investigated. PCR fingerprints produced by priming with (GTG)5, (GACA)4, or the M13 core sequence differentiated the two varieties of C. neoformans, C. neoformans var. neoformans (serotypes A and D) and C. neoformans var. gattii (serotypes B and C). Furthermore, strains of serotypes A, D, and B or C could be distinguished from each other by specific PCR fingerprint patterns. These primers, which also successfully amplified hypervariable DNA segments from other species, provide a convenient method of identification at the species or individual level. Amplification of polymorphic DNA patterns by PCR with these primers offers several advantages over classical DNA fingerprinting techniques, appears to be more reliable than other PCR-based methods for detecting polymorphic DNA, such as analysis of random-amplified polymorphic DNA, and should be applicable to many other organisms.

          • R Vilgalys, A Smith, BL Sun and OKM Jr.
          • (1993).
          • Intersterility groups in the Pleurotus ostreatus complex from the continental United States and adjacent Canada.
          • Canadian Journal of Botany
          • ,
          • 71
          • (1)
          • ,
          • 113-128.
          Publication Description

          Mating compatibility studies using strains from 17 North American collections in the Pleurotus ostreatus complex reveal three intersterile species of oyster mushrooms. All three species differ from one another in morphology, growth characteristics, geographic distributions, and host ranges. Other than mating compatibility tests, however, no single type of character was completely reliable for distinguishing these species. -from Authors

          • JM Moncalvo, SA Rehner and R Vilgalys.
          • (1993).
          • Systematics of Lyophyllum section difformia based on evidence from culture studies and ribosomal DNA sequences.
          • Mycologia
          • ,
          • 85
          • (5)
          • ,
          • 788-794.
          • E Kay and R Vilgalys.
          • (1992).
          • Spatial distribution and genetic relationships among individuals in a natural population of the oyster mushroom Pleurotus ostreatus.
          • Mycologia
          • ,
          • 84
          • (2)
          • ,
          • 173-182.
          Publication Description

          Spatial distribution of 60 heterokaryons in a natural population of Pleurotus ostreatus was examined through study of their somatic incompatibility interactions and analysis of mating compatibility factors. Results implicate basidiospore dispersal as a primary mechanism for dikaryon establishment. -from Authors

          • TD Barns, R Vilgalys, SM Barns, D Gonzalez, DS Hibbett, DJ Lane, L Simon, S Stickel, TM Szaro, WG Weisburg and ML Sogin.
          • (1992).
          • Evolutionary relationships within the fungi: Analyses of nuclear small subunit rRNA sequences.
          • Molecular Phylogenetics and Evolution
          • ,
          • 1
          • (3)
          • ,
          • 231-241.
          Publication Description

          Nucleotide sequences of the small subunit ribosomal RNA (18S) gene were used to investigate evolutionary relationships within the Fungi. The inferred tree topologies are in general agreement with traditional classifications in the following ways: (1) the Chytridiomycota and Zygomycota appear to be basal groups within the Fungi. (2) The Ascomycota and Basidiomycota are a derived monophyletic group. (3) Relationships within the Ascomycota are concordant with traditional orders and divide the hemi- and euascomycetes into distinct lineages. (4) The Basidiomycota is divided between the holobasidiomycetes and phragmobasidiomycetes. Conflicts with traditional classification were limited to weakly supported branches of the tree. Strongly supported relationships were robust to minor changes in alignment, method of analysis, and various weighting schemes. Weighting, either of transversions or by site, did not convincingly improve the status of poorly supported portions of the tree. The rate of variation at particular sites does not appear to be independent of lineage, suggesting that covariation of sites may be an important phenomenon in these genes. © 1992.

          • DS Hibbett and R Vilgalys.
          • (1991).
          • Evolutionary relationships of Lentinus to the Polyporaceae: evidence from restriction analysis of enzymatically amplified ribosomal DNA.
          • Mycologia
          • ,
          • 83
          • (4)
          • ,
          • 425-439.
          Publication Description

          Results suggest that Lentinus tigrinus is more closely related ot the Polyporaceae than to the Tricholomataceae. Morphological characters (dimitic hyphae and hyphal pegs) also support this hypothesis. The other species of Lentinus appear to be intermediate between the Polyporaceae and Tricholomataceae and could not be clearly assigned to either family. Lentinus is probably paraphyletic and, therefore, lamellae have arisen repeatedly by convergent evolution. -from Authors

          • R Vilgalys.
          • (1991).
          • Speciation and species concepts in the Collybia dryophila complex.
          • Mycologia
          • ,
          • 83
          • (6)
          • ,
          • 758-773.
          Publication Description

          All members of the C. dryophila complex have a heterothallic tetrapolar mating system. Several intercompatible groups are broadly distributed over several continents including North America, Europe and Asia. Limitations of the biological species concept are discussed, and a phylogenetic based species concept is proposed, which provides information about evolutionary relationships among allopatric mating groups based on combined data from mating compatibility, morphology and macromolecules. -from Author

          • R Vilgalys and M Hester.
          • (1990).
          • Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species.
          • Journal of Bacteriology
          • ,
          • 172
          • (8)
          • ,
          • 4238-4246.
          Publication Description

          Detailed restriction analyses of many samples often require substantial amounts of time and effort for DNA extraction, restriction digests, Southern blotting, and hybridization. We describe a novel approach that uses the polymerase chain reaction (PCR) for rapid simplified restriction typing and mapping of DNA from many different isolates. DNA fragments up to 2 kilobase pairs in length were efficiently amplified from crude DNA samples of several pathogenic Cryptococcus species, including C. neoformans, C. albidus, C. laurentii, and C. uniguttulatus. Digestion and electrophoresis of the PCR products by using frequent-cutting restriction enzymes produced complex restriction phenotypes (fingerprints) that were often unique for each strain or species. We used the PCR to amplify and analyze restriction pattern variation within three major portions of the ribosomal DNA (rDNA) repeats from these fungi. Detailed mapping of many restriction sites within the rDNA locus was determined by fingerprint analysis of progressively larger PCR fragments sharing a common primer site at one end. As judged by PCR fingerprints, the rDNA of 19 C. neoformans isolates showed no variation for four restriction enzymes that we surveyed. Other Cryptococcus spp. showed varying levels of restriction pattern variation within their rDNAs and were shown to be genetically distinct from C. neoformans. The PCR primers used in this study have also been successfully applied for amplification of rDNAs from other pathogenic and nonpathogenic fungi, including Candida spp., and ought to have wide applicability for clinical detection and other studies.

          • R Vilgalys and D Gonzalez.
          • (1990).
          • Organization of ribosomal DNA in the basidiomycete Thanatephorus praticola.
          • Current Genetics
          • ,
          • 18
          • (3)
          • ,
          • 277-280.
          Publication Description

          The plant pathogenic fungus Thanatephorus practicola (=Rhizoctonia solani AG4) was found to share a similar pattern of rDNA organization with other members of the Basidiomycotina. The 8.8 kb rDNA repeat unit from T. praticola contains coding regions for the 5S RNA as well as the major 17S-25S transcript. Major rDNA length variation between intraspecific strains was not observed. The number of rDNA repeat units in the genome was estimated to be 59.

      • Book Chapters

          • Idnurm, A., T. Y. James, and R. Vilgalys.
          • (2007).
          • Sex in the rest: mysterious mating in the Chytridiomycota and Zygomycota.
          • In Joe Heitman, Jim Kronstad, John Taylor, and Lorna Casselton eds (Eds.),
          • Sex in fungi: molecular determination and evolutionary implications
          • ASM Press, Washington, D.C..
          • James, T. Y. and R. Vilgalys.
          • (2006).
          • Amphibian chytridiomycosis as an emerging infectious disease of wildlife: what can we learn from the earliest diverging fungi?.
          • In J. Heitman, S.G. Filler, J.E. Edwards, Jr, and A.P. Mitchell (Eds.),
          • Molecular principles of fungal pathogenesis
          • ASM Press, Washington, D.C..

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