• Publications of Rytas Vilgalys

      • Papers Published

          • Benitez, M, Hersh, M H and Vilgalys, R and Clark, J S.
          • (December, 2013).
          • Pathogen regulation of plant diversity via effective specialization.
          • Trends in Ecology and Evolution
          • ,
          • 28
          • ,
          • 705-711.
          • 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 Stajich, J E and Mullens, B and Anishchenko, I M and Vilgalys, R.
          • (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.
          • 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.
          • Husbands, D R and Henkel, T W and Bonito, G and Vilgalys, R and Smith, M E.
          • (2013).
          • New species of Xerocomus (Boletales) from the Guiana Shield, with notes on their mycorrhizal status and fruiting occurrence..
          • Mycologia
          • ,
          • 105
          • (2)
          • ,
          • 422--435.
          • Healy, R A and Smith, M E and Bonito, G M and Pfister, D H and Ge, Z W and Guevara, G G and Williams, G and Stafford, K and Kumar, L and Lee, T and Hobart, C and Trappe, J and Vilgalys, R and Mclaughlin, D J.
          • (2013).
          • High diversity and widespread occurrence of mitotic spore mats in ectomycorrhizal Pezizales..
          • Molecular Ecology
          • ,
          • 22
          • (6)
          • ,
          • 1717--1732.
          • Guevara, G and Bonito, G and Trappe, J M and Cazares, E and Williams, G and Healy, R A and Schadt, C and Vilgalys, R.
          • (2013).
          • New North American truffles (Tuber spp.) and their ectomycorrhizal associations..
          • Mycologia
          • ,
          • 105
          • (1)
          • ,
          • 194--209.
          • 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.
          • Bonito, G and Smith, M E and Nowak, M and Healy, R A and G, Gonzalo and Cazares, E and Kinoshita, A and Nouhra, E R and Dominguez, L S and Tedersoo, L and Murat, C and Wang, Y and Moreno, B A and Pfister, D H and Nara, K and Zambonelli, A and Trappe, J M and Vilgalys, R.
          • (2013).
          • Historical biogeography and diversification of truffles in the Tuberaceae and their newly identified southern hemisphere sister lineage..
          • PLoS ONE
          • ,
          • 8
          • (1)
          • ,
          • e52765.
          • Weber, C F and Vilgalys, R and Kuske, C R.
          • (2013).
          • Changes in Fungal Community Composition in Response to Elevated Atmospheric CO2 and Nitrogen Fertilization Varies with Soil Horizon.
          • Frontiers in Microbiology
          • ,
          • 4
          • ,
          • 1--14.
          • Shakya, M and Gottel, N and Castro, H and Yang, Z K and Gunter, L and Labbe, J and Muchero, W and Bonito, G and Vilgalys, R and Tuskan, G and Podar, M and Schadt, C W.
          • (2013).
          • A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature Populus deltoides Trees..
          • PLoS ONE
          • ,
          • 8
          • (10)
          • ,
          • e76382.
          • Golonka, A M and Vilgalys, Rytas.
          • (2013).
          • Nectar Inhabiting Yeasts in Virginian Populations of Silene latifolia (Caryophyllaceae) and Coflowering Species.
          • The American Midland Naturalist
          • .
          • Talbot JM, Bruns TD, Smith DP, Branco S, Glassman SI, Erlandson S, Vilgalys R, Peay KG.
          • (2013).
          • Independent roles of ectomycorrhizal and saprotrophic communities in soil organic matter decomposition..
          • Soil Biology & Biochemistry
          • ,
          • 57
          • ,
          • 282-291.
          • Hersh, M., James Clark, Rytas Vilgalys.
          • (2012).
          • Evaluating the impacts of multiple generalist fungal pathogens on temperate tree seedling survival..
          • Ecology
          • ,
          • 93
          • ,
          • 511–520.
          Publication Description

          10..

          • Smith ME, Henkel TW, Uehling JK, Fremier AK, Clarke HD, Vilgalys R.
          • (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

          • Thaler, A D , C L Van Dover, 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
          • ,
          • 270–273.
          Publication Description

          17.. .

          • Uehling JK, Henkel TW, Aime MC, Vilgalys R, Smith ME.
          • (2012).
          • New species of Clavulina (Cantharellales, Basidiomycota) with resupinate and effused basidiomata from the Guiana Shield.
          • Mycologia
          • ,
          • 103
          • ,
          • 883–94.
          Publication Description

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

          • Uehling JK, Henkel TW, Aime MC, Vilgalys R, Smith ME.
          • (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

          • Uehling JK, Henkel TW, Vilgalys R, Smith ME.
          • (2012).
          • Membranomyces species are common ectomycorrhizal symbionts in Northern Hemisphere forests.
          • Mycorrhiza (online)
          • .
          Publication Description

          . (2012).

          • Dunbar J, Eichorst SA, Gallegos-Graves L, Silva S, Xie G, Hengartner NW, Evans RD, Hungate BA, Jackson RB, Megonigal JP, Schadt CW, Vilgalys R, Zak DR, Kuske CR..
          • (2012).
          • Common bacterial responses in six ecosystems exposed to 10 years of elevated atmospheric carbon dioxide..
          • Environmental Microbiology
          • ,
          • 14
          • ,
          • 1145-1158.
          • Henkel TW, Aime MC, Chin MML, Miller SL, Vilgalys R, Smith ME (2012).
          • (2012).
          • Ectomycorrhizal fungal sporocarp diversity and discovery of new taxa in Dicymbe monodominant forests of the Guiana Shield..
          • Biodiversity and Conservation.
          • ,
          • 21:
          • ,
          • 2195–2220.
          • Bonito, G., Timothy Brenneman and Rytas Vilgalys..
          • (2012).
          • Ectomycorrhizal fungal diversity in orchards of cultivated pecan (Carya illinoinensis; Juglandaceae). ..
          • Mycorrhiza.
          • ,
          • 601-612.
          • Gryganskyi, A. P., R. A. Humber, M. E. Smith, K. Hodge, B. Huang, K. Voigt, R. Vilgalys.
          • (2012).
          • Phylogenetic lineages in Entomophthoromycota..
          • Persoonia.
          • .
          • M E Smith and T W Henkel and M C Aime and A K Fremier and R Vilgalys.
          • (2011).
          • Ectomycorrhizal fungal diversity and community structure on three co-occurring leguminous canopy tree species in a Neotropical rainforest.
          • New Phytol
          • ,
          • 192
          • (3)
          • ,
          • 699--712.
          • [web]
          Publication Description

          * 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.

          • G Bonito and T Brenneman and R Vilgalys.
          • (2011).
          • Ectomycorrhizal fungal diversity in orchards of cultivated pecan (Carya illinoinensis; Juglandaceae).
          • Mycorrhiza
          • ,
          • 21
          • (7)
          • ,
          • 601--612.
          • [web]
          • C F Weber and D R Zak and B A Hungate and R B Jackson and R Vilgalys and R D Evans and C W Schadt and J P Megonigal and C R 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 10 677 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; 

          • N R Gottel and H F Castro and M Kerley and Z Yang and D A Pelletier and M Podar and T Karpinets and E Uberbacher and G A Tuskan and R Vilgalys and M J Doktycz and C W 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--44.
          • [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.

          • T Y Baroni and V Hofstetter and D L 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
          • ,
          • 1--19.
          • T M Porter and W Martin and T Y James and J E Longcore and F H Gleason and P H Adler and P M Letcher and R Vilgalys.
          • (2011).
          • Molecular phylogeny of the Blastocladiomycota (Fungi) based on nuclear ribosomal DNA.
          • Fungal Biology
          • ,
          • 115
          • (4-5)
          • ,
          • 381--92.
          • [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.

          • G Bonito, JM Trappe, P Rawlinson, R Vilgalys.
          • (2010).
          • Improved resolution of major clades within Tuber and taxonomy of species within the Tuber gibbosum complex..
          • Mycologia
          • ,
          • 102
          • (5)
          • ,
          • 1042-57.
          • [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.

          • GM Bonito, AP Gryganskyi, JM Trappe, 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.

          • G Bonito, OS Isikhuemhen, R Vilgalys.
          • (2010).
          • Identification of fungi associated with municipal compost using DNA-based techniques..
          • Bioresource technology
          • ,
          • 101
          • (3)
          • ,
          • 1021-7.
          • [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 410day-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.

          • AP Gryganskyi, SC Lee, AP Litvintseva, ME Smith, G Bonito, TM Porter, IM Anishchenko, J Heitman, 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 (+/-) 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 (-) 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.

          • DJ McLaughlin, DS Hibbett, F Lutzoni, JW Spatafora, R Vilgalys.
          • (2009).
          • The search for the fungal tree of life..
          • Trends in microbiology
          • ,
          • 17
          • (11)
          • ,
          • 488-97.
          • [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.

          • J. L. 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)
          • ,
          • 469-79.
          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.

          • T. Y. James and A. P. Litvintseva and R. Vilgalys and J. A. Morgan and J. W. Taylor and M. C. Fisher and L. Berger and C. Weldon and L. du Preez and J. E. Longcore.
          • (2009).
          • Rapid global expansion of the fungal disease chytridiomycosis into declining and healthy amphibian populations..
          • PLoS Pathog
          • ,
          • 5
          • (5)
          • ,
          • e1000458.
          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.

          • K Findley, M Rodriguez-Carres, B Metin, J Kroiss, A Fonseca, R Vilgalys, J Heitman.
          • (2009).
          • Phylogeny and phenotypic characterization of pathogenic Cryptococcus species and closely related saprobic taxa in the Tremellales..
          • Eukaryotic cell
          • ,
          • 8
          • (3)
          • ,
          • 353-61.
          • [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.

          • WH Hartman, CJ Richardson, R Vilgalys, GL Bruland.
          • (2008).
          • Environmental and anthropogenic controls over bacterial communities in wetland soils..
          • Proceedings of the National Academy of Sciences of the United States of America, United States
          • ,
          • 105
          • (46)
          • ,
          • 17842-7.
          • [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, 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, United States
          • ,
          • 46
          • (2)
          • ,
          • 635-44.
          • [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 2.4kbp 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.

          • 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.

          • 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.

          • DS Hibbett, M Binder, JF Bischoff, M Blackwell, PF Cannon, OE Eriksson, S Huhndorf, T James, PM Kirk, R Lücking, H Thorsten 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, N Zhang.
          • (2007).
          • A higher-level phylogenetic classification of the Fungi..
          • Mycological research, England
          • ,
          • 111
          • (Pt 5)
          • ,
          • 509-47.
          • [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.

          • Henk DA, Vilgalys R.
          • (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
          • ,
          • 1515-1526.
          • JL Parrent, R Vilgalys.
          • (2007).
          • Biomass and compositional responses of ectomycorrhizal fungal hyphae to elevated CO2 and nitrogen fertilization..
          • The New phytologist, England
          • ,
          • 176
          • (1)
          • ,
          • 164-74.
          • [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 CO(2) can have large effects on plant nutrient acquisition and carbon movement through forests. Here, the effects of CO(2) 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 CO(2) plots relative to control plots, but individual taxa responded to both CO(2) 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 CO(2) enrichment and N fertilization.

          • PC Ceresini, HD Shew, TY James, RJ Vilgalys, MA Cubeta.
          • (2007).
          • Phylogeography of the Solanaceae-infecting Basidiomycota fungus Rhizoctonia solani AG-3 based on sequence analysis of two nuclear DNA loci..
          • BMC evolutionary biology, England
          • ,
          • 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

          • 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, R Vilgalys.
          • (2006).
          • Reconstructing the early evolution of Fungi using a six-gene phylogeny..
          • Nature, England
          • ,
          • 443
          • (7113)
          • ,
          • 818-22.
          • [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.

          • 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.

          • 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.
          • Gonzalez D, Cubeta MA, Vilgalys R.
          • (2006).
          • Phylogenetic utility of indels within ribosomal DNA and beta-tubulin sequences from fungi in the Rhizoctonia solani species complex.
          • Molecular Phylogenetics and Evolution
          • ,
          • 40
          • ,
          • 459-470.
          • Yahr R, Vilgalys R, DePriest PT.
          • (2006).
          • Geographic variation in algal partners of Cladonia subtenuis (Cladoniaceae) highlights the dynamic nature of a lichen symbiosis.
          • New Phytologist
          • ,
          • 171
          • ,
          • 847-860.
          • Parrent, J. L., W. F. Morris., R. Vilgalys.
          • (2006).
          • CO2-enrichment and nutrient availability alter ectomycorrhizal fungal communities.
          • Ecology
          • ,
          • 87
          • ,
          • 2278-2287.
          • James TY, Srivilai P, Kues U, Vilgalys R.
          • (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
          • ,
          • 1877-1891.
          • Litvintseva, A. P., Thakur, R., Vilgalys, R., Mitchell, T. G..
          • (2006).
          • Multilocus sequence typing reveals three genetic subpopulations of Cryptococcus neoformans var. grubii (serotype A), Including a Unique Population in Botswana.
          • Genetics
          • ,
          • 172
          • ,
          • 2223-2238.
          • 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, R Vilgalys.
          • (2005).
          • Fungal community analysis by large-scale sequencing of environmental samples..
          • Applied and environmental microbiology, United States
          • ,
          • 71
          • (9)
          • ,
          • 5544-50.
          • [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.

          • M Didukh, R Vilgalys, SP Wasser, OS Isikhuemhen, E Nevo.
          • (2005).
          • Notes on Agaricus section Duploannulati using molecular and morphological data..
          • Mycological research, England
          • ,
          • 109
          • (Pt 6)
          • ,
          • 729-40.
          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.

          • Litvintseva, A. P., L. Kestenbaum, R. Vilgalys, and T. G. Mitchell.
          • (2005).
          • Comparative analysis of environmental and clinical populations of Cryptococcus neoformans.
          • J Clin Microbiol
          • ,
          • 43
          • ,
          • 556-64.
          • Wallenstein, M.D. and R. J. Vilgalys.
          • (2005).
          • Quantitative analyses of nitrogen cycling genes in soils.
          • Pedobiologia
          • ,
          • 49
          • ,
          • 665-672.
          • Fierer, N., J. A. Jackson, R. Vilgalys, and R. B. Jackson.
          • (2005).
          • Assessment of Soil Microbial Community Structure by Use of Taxon-Specific Quantitative PCR Assays.
          • Appl. Env. Microbiol.
          • ,
          • 71
          • ,
          • 4117-4120.
          • 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
          • .
          • S Diezmann, CJ Cox, G Schonian, R Vilgalys & TG Mitchell.
          • (2004).
          • Phylogeny and evolution of medical species of Candida and related taxa: a multigenic analysis..
          • J Clin Microbiol, United States
          • ,
          • 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.

          • R Yahr, R Vilgalys & PT Depriest.
          • (2004).
          • Strong fungal specificity and selectivity for algal symbionts in Florida scrub Cladonia lichens..
          • Mol Ecol, England
          • ,
          • 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.

          • TY James, SR Liou & R Vilgalys.
          • (2004).
          • The genetic structure and diversity of the A and B mating-type genes from the tropical oyster mushroom, Pleurotus djamor..
          • Fungal Genet Biol, United States
          • ,
          • 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.

          • RE Marra, JC Huang, E Fung, K Nielsen, J Heitman, R Vilgalys & TG Mitchell.
          • (2004).
          • A genetic linkage map of Cryptococcus neoformans variety neoformans serotype D (Filobasidiella neoformans)..
          • Genetics, United States
          • ,
          • 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 & R Vilgalys.
          • (2004).
          • Molecular phylogeny, biogeography and speciation of the mushroom species Pleurotus cystidiosus and allied taxa..
          • Microbiology, England
          • ,
          • 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.

          • TY James, U Kües, SA Rehner & R Vilgalys.
          • (2004).
          • Evolution of the gene encoding mitochondrial intermediate peptidase and its cosegregation with the A mating-type locus of mushroom fungi..
          • Fungal Genet Biol, United States
          • ,
          • 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 (

          • AP Litvintseva, RE Marra, K Nielsen, J Heitman, R Vilgalys, TG Mitchell.
          • (2003).
          • Evidence of sexual recombination among Cryptococcus neoformans serotype A isolates in sub-Saharan Africa..
          • Eukaryot Cell, United States
          • ,
          • 2
          • (6)
          • ,
          • 1162-8.
          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.

          • A Pringle, JM Moncalvo, R Vilgalys.
          • (2003).
          • Revisiting the rDNA sequence diversity of a natural population of the arbuscular mycorrhizal fungus Acaulospora colossica..
          • Mycorrhiza, Germany
          • ,
          • 13
          • (4)
          • ,
          • 227-31.
          • [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, LR Gale, MA Cubeta.
          • (2003).
          • Detecting Migrants in Populations of Rhizoctonia solani Anastomosis Group 3 from Potato in North Carolina Using Multilocus Genotype Probabilities..
          • Phytopathology, United States
          • ,
          • 93
          • (5)
          • ,
          • 610-5.
          • [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, JE Longcore.
          • (2003).
          • Multilocus sequence typing suggests the chytrid pathogen of amphibians is a recently emerged clone..
          • Mol Ecol, England
          • ,
          • 12
          • (2)
          • ,
          • 395-403.
          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.

          • JM Moncalvo, R Vilgalys, SA Redhead, JE Johnson, TY James, M Catherine Aime, V Hofstetter, SJ Verduin, E Larsson, TJ Baroni, R Greg Thorn, S Jacobsson, H Clémençon, OK Miller.
          • (2002).
          • One hundred and seventeen clades of euagarics..
          • Mol Phylogenet Evol, United States
          • ,
          • 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 monophyletic 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.

          • J Xu, G Luo, RJ Vilgalys, ME Brandt, TG Mitchell.
          • (2002).
          • Multiple origins of hybrid strains of Cryptococcus neoformans with serotype AD..
          • Microbiology, England
          • ,
          • 148
          • (Pt 1)
          • ,
          • 203-12.
          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.

          • A Forche, J Xu, R Vilgalys & 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, United States
          • ,
          • 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.

          • U Kües, TY James, R Vilgalys & MP Challen.
          • (2001).
          • The chromosomal region containing pab-1, mip, and the A mating type locus of the secondarily homothallic homobasidiomycete Coprinus bilanatus..
          • Curr Genet, United States
          • ,
          • 39
          • (1)
          • ,
          • 16-24.
          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, Aalpha and Abeta. A gene coding for a mitochondrial intermediate peptidase (mip) directly flanks the Aalpha 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 Aalpha and Abeta 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.

          • TY James & R Vilgalys.
          • (2001).
          • Abundance and diversity of Schizophyllum commune spore clouds in the Caribbean detected by selective sampling..
          • Mol Ecol, England
          • ,
          • 10
          • (2)
          • ,
          • 471-479.
          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 approximately 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.

          • J Xu, C Onyewu, HJ Yoell, RY Ali, RJ Vilgalys, TG Mitchell.
          • (2001).
          • Dynamic and heterogeneous mutations to fluconazole resistance in Cryptococcus neoformans..
          • Antimicrob Agents Chemother, United States
          • ,
          • 45
          • (2)
          • ,
          • 420-7.
          • [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, R Vilgalys.
          • (2001).
          • Polymorphism at the ribosomal DNA spacers and its relation to breeding structure of the widespread mushroom Schizophyllum commune..
          • Genetics, United States
          • ,
          • 157
          • (1)
          • ,
          • 149-61.
          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.

          • J Xu, R Vilgalys, TG Mitchell.
          • (2000).
          • Multiple gene genealogies reveal recent dispersion and hybridization in the human pathogenic fungus Cryptococcus neoformans..
          • Mol Ecol, ENGLAND
          • ,
          • 9
          • (10)
          • ,
          • 1471-1481.
          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, R Vilgalys.
          • (2000).
          • Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences..
          • Syst Biol, England
          • ,
          • 49
          • (2)
          • ,
          • 278-305.
          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.

          • G Schönian, A Forche, HJ Tietz, M Müller, Y Gräser, R Vilgalys, TG Mitchell, W Presber.
          • (2000).
          • [Genetic structure of geographically different populations of candida albicans].
          • Mycoses, Germany
          • ,
          • 43 Suppl 2
          • ,
          • 51-6.
          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.

          • JG McEwen, JW Taylor, D Carter, J Xu, MS Felipe, R Vilgalys, TG Mitchell, T Kasuga, T White, T Bui, CM Soares.
          • (2000).
          • Molecular typing of pathogenic fungi..
          • Med Mycol, England
          • ,
          • 38 Suppl 1
          • ,
          • 189-97.
          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.

      • 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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