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| Publications of Rytas Vilgalys :chronological combined listing:
%% Papers Published
@article{fds214146,
Author = {Henkel TW and Husbands D and Bonito GM and Vilgalys R and Smith
ME},
Title = {New species of Xerocomus (Boletales) from the Guiana Shield,
with notes on their mycorrhizal status and fruiting
occurrence},
Journal = {Mycologia},
Volume = {in press},
Year = {2012},
Abstract = {. (2013). Mycologia. In Press.},
Key = {fds214146}
}
@article{fds214147,
Author = {Hersh, M. and James Clark and Rytas Vilgalys},
Title = {Evaluating the impacts of multiple generalist fungal
pathogens on temperate tree seedling survival.},
Journal = {Ecology},
Volume = {93},
Pages = {511–520},
Year = {2012},
Abstract = {10..},
Key = {fds214147}
}
@article{fds214145,
Author = {Bonito, Gregory and Matthew E. Smith and Michael Nowak and Rosanne A.
Healy and Gonzalo Guevara and Efren Cázares and Akihiko Kinoshita and Eduardo R. Nouhra and Laura S. Domínguez and Leho Tedersoo and Claude Murat and Yun Wang and Baldomero, Arroyo Moreno and Donald H.
Pfister and Kazuhide Nara and Alessandra Zambonelli and James M.
Trappe and Rytas Vilgalys},
Title = {Historical biogeography and diversification of truffles in
the Tuberaceae and their newly identified Southern
hemisphere sister lineage},
Journal = {PLOS ONE (in press)},
Year = {2012},
Abstract = {2. Bonito, Gregory, Matthew E. Smith, Michael Nowak, Rosanne
A. Healy, Gonzalo Guevara, ,Efren Cázares, Akihiko
Kinoshita, Eduardo R. Nouhra, Laura S. Domínguez, Leho
Tedersoo, Claude Murat, Yun Wang, Baldomero, Arroyo Moreno,
Donald H. Pfister, Kazuhide Nara, Alessandra Zambonelli,
James M. Trappe, Rytas Vilgalys. Historical biogeography and
diversification of truffles in the Tuberaceae and their
newly identified Southern hemisphere sister lineage, PLOS
ONE in press},
Key = {fds214145}
}
@article{fds214148,
Author = {Husbands, Dillon R. and Terry W. Henkel and Gregory Bonito and Rytas
Vilgalys and Matthew E. Smith},
Title = {New species of Xerocomus (Boletales) from the Guiana Shield,
with notes on their mycorrhizal status and fruiting
occurrence},
Journal = {Mycologia},
Year = {2012},
Abstract = {13.. . 2012. .},
Key = {fds214148}
}
@article{fds214149,
Author = {Porter, T. M. and M. Rodriguez and B. Robbertse and R. Yoder and P. M.
Letcher and J. E. Longcore and J. W. Spatafora and R.
Vilgalys},
Title = {Chytrid transcriptome pyrosequencing: application to
phylogenetic systematics},
Journal = {submitted to Mol. Phylog. Evol.},
Year = {2012},
Abstract = {14.. .},
Key = {fds214149}
}
@article{fds214150,
Author = {Healy, R. A. and M. E. Smith and G. M. Bonito and D. H. P F I Ster and Z.-W. Ge and G. G. Guevara and G. W Illiam S and K. Stafford and L.
Kumar, T. Lee and C. Hobart and J. Trappe and R. Vilgalys And D. J.
Mclaughlin},
Title = {High diversity and widespread occurrence of mitotic spore
mats in ectomycorrhizal Pezizales},
Journal = {in press, Molecular Ecology},
Year = {2012},
Abstract = {15. . . in press, MOLECULAR ECOLOGY},
Key = {fds214150}
}
@article{fds214151,
Author = {Smith ME and Henkel TW and Uehling JK and Fremier AK and Clarke HD and Vilgalys R},
Title = {Ectomycorrhizal fungal community in a tropical forest
dominated by the Neotropical Dipterocarp, Pakaraimea
dipterocarpaceae},
Journal = {PLOS ONE (in press)},
Year = {2012},
Abstract = {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},
Key = {fds214151}
}
@article{fds214152,
Author = {Thaler, Andrew David and Cindy Lee Van Dover and Rytas
Vilgalys},
Title = {Ascomycete phylotypes recovered from a Gulf of Mexico
methane seep are identical to an uncultured deep-sea fungal
clade from the Pacific},
Journal = {Fungal Ecology},
Volume = {5},
Pages = {270–273},
Year = {2012},
Abstract = {17.. .},
Key = {fds214152}
}
@article{fds214153,
Author = {Uehling JK and Henkel TW and Aime MC and Vilgalys R and Smith
ME},
Title = {New species of Clavulina (Cantharellales, Basidiomycota)
with resupinate and effused basidiomata from the Guiana
Shield},
Journal = {Mycologia},
Volume = {103},
Pages = {883–94},
Year = {2012},
Abstract = {18. Uehling JK, Henkel TW, Aime MC, Vilgalys R, Smith ME.
(2012).},
Key = {fds214153}
}
@article{fds214154,
Author = {Uehling JK and Henkel TW and Aime MC and Vilgalys R and Smith
ME},
Title = {Four new species of Clavulina (Cantharellales,
Basidiomycota) from the Guiana Shield, and a key to the
lowland neotropical species.},
Journal = {Fungal Biology. In Press},
Year = {2012},
Abstract = {19.. (2013) F},
Key = {fds214154}
}
@article{fds214155,
Author = {Uehling JK and Henkel TW and Vilgalys R and Smith
ME},
Title = {Membranomyces species are common ectomycorrhizal symbionts
in Northern Hemisphere forests},
Journal = {Mycorrhiza (online)},
Year = {2012},
Abstract = {. (2012).},
Key = {fds214155}
}
@article{fds213972,
Author = {Dunbar J and Eichorst SA and Gallegos-Graves L and Silva S and Xie G and Hengartner NW and Evans RD and Hungate BA and Jackson RB and Megonigal
JP, Schadt CW and Vilgalys R and Zak DR and Kuske
CR.},
Title = {Common bacterial responses in six ecosystems exposed to 10
years of elevated atmospheric carbon dioxide.},
Journal = {Environmental Microbiology},
Volume = {14},
Pages = {1145-1158},
Year = {2012},
Key = {fds213972}
}
@article{fds213973,
Author = {Gryganskyi, A. P. and R. A. Humber and M E. Smith and J.
Miadlikowska, S. Wu and K. Voigt and G. Walther and I. M.
Anishchenko and R. Vilgalys.},
Title = {Molecular phylogeny of the Entomophthoromycota:},
Journal = {Molecular Phylogenetics and Evolution},
Volume = {65:},
Pages = {682–694.},
Year = {2012},
Key = {fds213973}
}
@article{fds213975,
Author = {Gryganskyi, Andrii P. and Richard A. Humber and Jason E. Stajich and Bradley Mullens and Iryna M. Anishchenko and Rytas
Vilgalys.},
Title = {Sequential utilization of hosts from different fly families
by the fungal pathogen Entomophthora muscae},
Journal = {PLOS ONE (submitted)},
Year = {2012},
Key = {fds213975}
}
@article{fds213976,
Author = {Guevara, Gonzalo and Gregory Bonito and James M. Trappe and Efren
Cázares, Gwendolyn Williams and Rosaria Ann Healy and Christopher
W Schadt and Rytas Vilgalys.},
Title = {New North American truffles (Tuber spp.) and their
ectomycorrhizal associations.},
Journal = {Mycologia},
Volume = {2012},
Year = {2012},
Key = {fds213976}
}
@article{fds213978,
Author = {Henkel TW and Aime MC and Chin MML and Miller SL and Vilgalys R and Smith
ME (2012)},
Title = {Ectomycorrhizal fungal sporocarp diversity and discovery of
new taxa in Dicymbe monodominant forests of the Guiana
Shield.},
Journal = {Biodiversity and Conservation.},
Volume = {21:},
Pages = {2195–2220},
Year = {2012},
Key = {fds213978}
}
@article{fds213970,
Author = {Bonito, G. and Timothy Brenneman and Rytas Vilgalys.},
Title = {Ectomycorrhizal fungal diversity in orchards of cultivated
pecan (Carya illinoinensis; Juglandaceae).
.},
Journal = {Mycorrhiza.},
Pages = {601-612},
Year = {2012},
Key = {fds213970}
}
@article{fds213974,
Author = {Gryganskyi, A. P. and R. A. Humber and M. E. Smith and K. Hodge and B.
Huang, K. Voigt and R. Vilgalys},
Title = {Phylogenetic lineages in Entomophthoromycota.},
Journal = {Persoonia.},
Year = {2012},
Key = {fds213974}
}
@article{Smith:2011p14453,
Author = {Matthew E Smith and Terry W Henkel and M Catherine Aime and Alex K Fremier and Rytas Vilgalys},
Title = {Ectomycorrhizal fungal diversity and community structure on
three co-occurring leguminous canopy tree species in a
Neotropical rainforest},
Journal = {New Phytol},
Volume = {192},
Number = {3},
Pages = {699--712},
Organization = {Department of Biology, Duke University, Durham, NC 27708,
USA Department of Biological Sciences, Humboldt State
University, Arcata, CA 95521, USA Department of Plant
Pathology {\&} Crop Physiology, Louisiana State University
Agricultural Center, Baton Rou},
Institution = {Department of Biology, Duke University, Durham, NC 27708,
USA Department of Biological Sciences, Humboldt State
University, Arcata, CA 95521, USA Department of Plant
Pathology {\&} Crop Physiology, Louisiana State University
Agricultural Center, Baton Rou},
Year = {2011},
Month = {November},
url = {http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Retrieve&list_uids=21883231&dopt=abstractplus},
Abstract = {* 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.},
Language = {eng},
Doi = {10.1111/j.1469-8137.2011.03844.x},
Key = {Smith:2011p14453}
}
@article{Bonito:2011p13587,
Author = {Gregory Bonito and Timothy Brenneman and Rytas
Vilgalys},
Title = {Ectomycorrhizal fungal diversity in orchards of cultivated
pecan (Carya illinoinensis; Juglandaceae)},
Journal = {Mycorrhiza},
Volume = {21},
Number = {7},
Pages = {601--612},
Year = {2011},
Month = {October},
url = {http://dx.doi.org/10.1007/s00572-011-0368-0},
Doi = {10.1007/s00572-011-0368-0},
Key = {Bonito:2011p13587}
}
@article{Weber:2011p14454,
Author = {Carolyn F Weber and Donald R Zak and Bruce A Hungate and Robert B Jackson and Rytas Vilgalys and R David Evans and Christopher W Schadt and J Patrick Megonigal and Cheryl R
Kuske},
Title = {Responses of soil cellulolytic fungal communities to
elevated atmospheric CO(2) are complex and variable across
five ecosystems},
Journal = {Environmental microbiology},
Volume = {13},
Number = {10},
Pages = {2778--2793},
Organization = {Bioscience Division, Los Alamos National Laboratory, Los
Alamos, NM 87545, USA School of Natural Resources {\&}
Environment Department of Ecology and Evolutionary Biology,
University of Michigan, Ann Arbor, MI 48109, USA Department
of Biological Sciences},
Institution = {Bioscience Division, Los Alamos National Laboratory, Los
Alamos, NM 87545, USA School of Natural Resources {\&}
Environment Department of Ecology and Evolutionary Biology,
University of Michigan, Ann Arbor, MI 48109, USA Department
of Biological Sciences},
Year = {2011},
Month = {October},
url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02548.x/abstract},
Abstract = {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; < 0.001), with
few operational taxonomic units (OTUs) being shared across
ecosystems. Using a 114-member cbhI sequence database
compiled from known fungi, less than 1% of the environmental
sequences could be classified at the family level indicating
that cellulolytic fungi in situ are likely dominated by
novel fungi or known fungi that are not yet recognized as
cellulose degraders. Shifts in fungal cbhI composition and
richness that were correlated with elevated CO(2) exposure
varied across the ecosystems. In aspen plantation and desert
creosote bush soils, cbhI gene richness was significantly
higher after exposure to elevated CO(2) (550 µmol mol(-1)
) than under ambient CO(2) (360 µmol mol(-1) CO(2) ). In
contrast, while the richness was not altered, the relative
abundance of dominant OTUs in desert soil crusts was
significantly shifted. This suggests that responses are
complex, vary across different ecosystems and, in at least
one case, are OTU-specific. Collectively, our results
document the complexity of cellulolytic fungal communities
in multiple terrestrial ecosystems and the variability of
their responses to long-term exposure to elevated
atmospheric CO(2) .},
Language = {ENG},
Doi = {10.1111/j.1462-2920.2011.02548.x},
Key = {Weber:2011p14454}
}
@article{Gottel:2011p14452,
Author = {Neil R Gottel and Hector F Castro and Marilyn Kerley and Zamin Yang and Dale A Pelletier and Mircea Podar and Tatiana
Karpinets and Ed Uberbacher and Gerald A Tuskan and Rytas
Vilgalys and Mitchel J Doktycz and Christopher W
Schadt},
Title = {Distinct microbial communities within the endosphere and
rhizosphere of Populus deltoides roots across contrasting
soil types},
Journal = {Applied and Environmental Microbiology},
Volume = {77},
Number = {17},
Pages = {5934--44},
Organization = {Biosciences Division, Oak Ridge National Laboratory, Oak
Ridge, TN 37831-6038, USA.},
Institution = {Biosciences Division, Oak Ridge National Laboratory, Oak
Ridge, TN 37831-6038, USA.},
Year = {2011},
Month = {September},
url = {http://aem.asm.org/cgi/content/full/77/17/5934?view=long&pmid=21764952},
Abstract = {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.},
Language = {eng},
Doi = {10.1128/AEM.05255-11},
Key = {Gottel:2011p14452}
}
@article{Baroni:2011p14444,
Author = {T Y Baroni and V Hofstetter and D L Largent and R
Vilgalys},
Title = {Entocybe is proposed as a new genus in the Entolomataceae
(Agaricomycetes, Basidiomycota) based on morphological and
molecular evidence},
Journal = {North American Fungi},
Volume = {6},
Pages = {1--19},
Year = {2011},
Month = {September},
Key = {Baroni:2011p14444}
}
@article{Porter:2011p13586,
Author = {Teresita M Porter and Wallace Martin and Timothy Y James and Joyce E Longcore and Frank H Gleason and Peter H Adler and Peter M Letcher and Rytas Vilgalys},
Title = {Molecular phylogeny of the Blastocladiomycota (Fungi) based
on nuclear ribosomal DNA},
Journal = {Fungal Biology},
Volume = {115},
Number = {4-5},
Pages = {381--92},
Organization = {Duke University, Biology Department, Campus Box 90338,
Durham, NC 27708, USA. terri@evol.mcmaster.ca},
Institution = {Duke University, Biology Department, Campus Box 90338,
Durham, NC 27708, USA. terri@evol.mcmaster.ca},
Year = {2011},
Month = {January},
url = {http://www.sciencedirect.com/science/article/pii/S1878614611000250},
Keywords = {Insects, DNA: Fungal, Cell Nucleus, DNA: Ribosomal,
Blastocladiomycota, Larva, Animals, Evolution: Molecular,
Phylogeny},
Abstract = {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.},
Language = {eng},
Doi = {10.1016/j.funbio.2011.02.004},
Key = {Porter:2011p13586}
}
@article{Thaler:2011p14513,
Author = {A D Thaler and C Van Dover and R Vilgalys},
Title = {Ascomycete phylotypes recovered from a Gulf of Mexico
methane seep are identical to an uncultured deep-sea fungal
clade from the Pacific},
Journal = {Fungal Ecology},
Year = {2011},
Month = {January},
url = {http://www.sciencedirect.com/science/article/pii/S1754504811000729},
Abstract = {Abstract Deep-sea endemic fungi are one component of an
under-sampled invisible biosphere whose contribution to
benthic ecosystems is not yet understood. In the last
decade, molecular techniques have facilitated the discovery
of several new deep-sea ...},
Key = {Thaler:2011p14513}
}
@article{fds184664,
Author = {G Bonito and JM Trappe and P Rawlinson and R Vilgalys},
Title = {Improved resolution of major clades within Tuber and
taxonomy of species within the Tuber gibbosum
complex.},
Journal = {Mycologia},
Volume = {102},
Number = {5},
Pages = {1042-57},
Year = {2010},
Month = {November},
ISSN = {0027-5514},
url = {http://dx.doi.org/10.3852/09-213},
Keywords = {Ascomycota • California • DNA, Fungal • DNA,
Ribosomal • Ecosystem • Phylogeny • Poaceae
• Species Specificity • Spores, Fungal •
Trees • classification • genetics • genetics*
• isolation & purification • microbiology},
Abstract = {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.},
Language = {eng},
Doi = {10.3852/09-213},
Key = {fds184664}
}
@article{fds184663,
Author = {GM Bonito and AP Gryganskyi and JM Trappe and R Vilgalys},
Title = {A global meta-analysis of Tuber ITS rDNA sequences: species
diversity, host associations and long-distance
dispersal.},
Journal = {Molecular ecology},
Volume = {19},
Number = {22},
Pages = {4994-5008},
Year = {2010},
Month = {November},
ISSN = {1365-294X},
url = {http://dx.doi.org/10.1111/j.1365-294X.2010.04855.x},
Keywords = {DNA, Ribosomal • Fungi • Genes, Fungal •
Genetic Variation* • Host Specificity* • Introns
• Phylogeny • Sequence Analysis, DNA* •
Spores, Fungal • classification •
genetics*},
Abstract = {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.},
Language = {eng},
Doi = {10.1111/j.1365-294X.2010.04855.x},
Key = {fds184663}
}
@article{Bonito:2010p7410,
Author = {Gregory M Bonito and Andrii P Gryganskyi and James M Trappe and Rytas Vilgalys},
Title = {A global meta-analysis of Tuber ITS rDNA sequences: species
diversity, host associations and long-distance
dispersal},
Journal = {Mol Ecol},
Volume = {19},
Number = {22},
Pages = {4994--5008},
Organization = {Department of Biology, Duke University, Durham, NC
27708-0338, USA. gmb2@duke.edu},
Institution = {Department of Biology, Duke University, Durham, NC
27708-0338, USA. gmb2@duke.edu},
Year = {2010},
Month = {November},
url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2010.04855.x/abstract},
Abstract = {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.},
Language = {eng},
Doi = {10.1111/j.1365-294X.2010.04855.x},
Key = {Bonito:2010p7410}
}
@article{fds184666,
Author = {G Bonito and OS Isikhuemhen and R Vilgalys},
Title = {Identification of fungi associated with municipal compost
using DNA-based techniques.},
Journal = {Bioresource technology},
Volume = {101},
Number = {3},
Pages = {1021-7},
Year = {2010},
Month = {February},
ISSN = {1873-2976},
url = {http://dx.doi.org/10.1016/j.biortech.2009.08.109},
Keywords = {Aspergillus • Candida • DNA • DNA, Fungal
• DNA, Ribosomal • Electrophoresis, Polyacrylamide
Gel • Fungi • Humans • Neurospora •
Phylogeny • Sequence Analysis, DNA • Soil
Microbiology • Soil* • Temperature • Time
Factors • chemistry • chemistry* • genetics
• metabolism • metabolism* •
methods},
Abstract = {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.},
Language = {eng},
Doi = {10.1016/j.biortech.2009.08.109},
Key = {fds184666}
}
@article{fds184662,
Author = {AP Gryganskyi and SC Lee and AP Litvintseva and ME Smith and G Bonito and TM Porter and IM Anishchenko and J Heitman and R Vilgalys},
Title = {Structure, Function, and Phylogeny of the Mating Locus in
the Rhizopus oryzae Complex.},
Journal = {PloS one},
Volume = {5},
Number = {12},
Pages = {e15273},
Year = {2010},
ISSN = {1932-6203},
url = {http://dx.doi.org/10.1371/journal.pone.0015273},
Keywords = {Alleles • Crosses, Genetic • DNA Primers •
DNA, Fungal • DNA, Ribosomal • Genes, Fungal
• Genes, Mating Type, Fungal* • L-Lactate
Dehydrogenase • Likelihood Functions • Models,
Genetic • Phylogeny • Polymerase Chain Reaction
• Rhizopus • Sequence Analysis, DNA • Species
Specificity • genetics • genetics*},
Abstract = {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.},
Language = {eng},
Doi = {10.1371/journal.pone.0015273},
Key = {fds184662}
}
@article{fds184665,
Author = {DJ McLaughlin and DS Hibbett and F Lutzoni and JW Spatafora and R
Vilgalys},
Title = {The search for the fungal tree of life.},
Journal = {Trends in microbiology},
Volume = {17},
Number = {11},
Pages = {488-97},
Year = {2009},
Month = {November},
ISSN = {1878-4380},
url = {http://dx.doi.org/10.1016/j.tim.2009.08.001},
Keywords = {Evolution, Molecular* • Fungi • Phylogeny* •
classification* • cytology • genetics •
metabolism},
Abstract = {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.},
Language = {eng},
Doi = {10.1016/j.tim.2009.08.001},
Key = {fds184665}
}
@article{Parrent09,
Author = {J. L. Parrent and R. Vilgalys},
Title = {Expression of genes involved in symbiotic carbon and
nitrogen transport in Pinus taeda mycorrhizal roots exposed
to CO2 enrichment and nitrogen fertilization.},
Journal = {Mycorrhiza},
Volume = {19},
Number = {7},
Pages = {469-79},
Organization = {Biology Department, Duke University, P.O. Box 90338, Durham,
NC 27708-0338, USA. jparrent@umich.edu},
Institution = {Biology Department, Duke University, P.O. Box 90338, Durham,
NC 27708-0338, USA. jparrent@umich.edu},
Year = {2009},
Month = {September},
Keywords = {Biological Transport Carbon/*metabolism Carbon
Dioxide/*metabolism Fertilizers Fungi/genetics/*physiology
*Gene Expression Regulation, Plant Molecular Sequence Data
Mycorrhizae/genetics/*physiology Nitrogen/*metabolism
Phylogeny Pinus taeda/genetics/*physiology Plant
Proteins/genetics/metabolism Plant Roots/genetics/physiology
Plants/classification/genetics *Symbiosis},
Abstract = {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.},
Key = {Parrent09}
}
@article{James09,
Author = {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},
Title = {Rapid global expansion of the fungal disease
chytridiomycosis into declining and healthy amphibian
populations.},
Journal = {PLoS Pathog},
Volume = {5},
Number = {5},
Pages = {e1000458},
Organization = {Department of Biology, Duke University, Durham, NC, USA.
tyjames@umich.edu},
Institution = {Department of Biology, Duke University, Durham, NC, USA.
tyjames@umich.edu},
Year = {2009},
Month = {May},
Keywords = {Amphibians/*microbiology Animals Base Sequence
Chytridiomycota/*genetics DNA, Viral Disease Outbreaks
Genome, Mitochondrial Genotype Loss of Heterozygosity
Mycoses Polymorphism, Genetic Rana catesbeiana/microbiology
Recombination, Genetic},
Abstract = {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.},
Key = {James09}
}
@article{fds184667,
Author = {K Findley and M Rodriguez-Carres and B Metin and J Kroiss and A Fonseca and R Vilgalys and J Heitman},
Title = {Phylogeny and phenotypic characterization of pathogenic
Cryptococcus species and closely related saprobic taxa in
the Tremellales.},
Journal = {Eukaryotic cell},
Volume = {8},
Number = {3},
Pages = {353-61},
Year = {2009},
Month = {March},
ISSN = {1535-9786},
url = {http://dx.doi.org/10.1128/EC.00373-08},
Keywords = {Animals • Basidiomycota • Cryptococcosis •
Cryptococcus • DNA, Fungal • DNA, Ribosomal •
Humans • Insects • Molecular Sequence Data •
Mycological Typing Techniques • Phenotype •
Phylogeny* • Soil Microbiology • Virulence •
classification* • genetics • isolation &
purification • microbiology* •
pathogenicity*},
Abstract = {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.},
Language = {eng},
Doi = {10.1128/EC.00373-08},
Key = {fds184667}
}
@article{fds152948,
Author = {WH Hartman and CJ Richardson and R Vilgalys and GL
Bruland},
Title = {Environmental and anthropogenic controls over bacterial
communities in wetland soils.},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America, United States},
Volume = {105},
Number = {46},
Pages = {17842-7},
Year = {2008},
Month = {November},
ISSN = {1091-6490},
url = {http://dx.doi.org/10.1073/pnas.0808254105},
Keywords = {Bacteria • Fresh Water • Humans •
Hydrogen-Ion Concentration • Molecular Sequence Data
• North Carolina • Phylogeny • Principal
Component Analysis • RNA, Ribosomal, 16S • Soil
Microbiology* • Soil* • Wetlands* •
classification • genetics • genetics*},
Abstract = {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.},
Language = {eng},
Doi = {10.1073/pnas.0808254105},
Key = {fds152948}
}
@article{fds141084,
Author = {TM Porter and CW Schadt and L Rizvi and AP Martin and SK Schmidt and L
Scott-Denton, R Vilgalys and JM Moncalvo},
Title = {Widespread occurrence and phylogenetic placement of a soil
clone group adds a prominent new branch to the fungal tree
of life.},
Journal = {Molecular phylogenetics and evolution, United
States},
Volume = {46},
Number = {2},
Pages = {635-44},
Year = {2008},
Month = {February},
ISSN = {1055-7903},
url = {http://dx.doi.org/10.1016/j.ympev.2007.10.002},
Keywords = {Ascomycota • DNA, Ribosomal • Phylogeny* •
Soil Microbiology* • chemistry • classification*
• genetics},
Abstract = {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.},
Language = {eng},
Doi = {10.1016/j.ympev.2007.10.002},
Key = {fds141084}
}
@article{fds141098,
Author = {PB Matheny and JM Curtis and V Hofstetter and MC Aime and JM Moncalvo and ZW Ge and JC Slot and JF Ammirati and TJ Baroni and NL Bougher and KW
Hughes, DJ Lodge and RW Kerrigan and MT Seidl and DK Aanen and M
DeNitis, GM Daniele and DE Desjardin and BR Kropp and LL Norvell and A
Parker, EC Vellinga and R Vilgalys and DS Hibbett},
Title = {Major clades of Agaricales: a multilocus phylogenetic
overview.},
Journal = {Mycologia, United States},
Volume = {98},
Number = {6},
Pages = {982-95},
Year = {2007},
Month = {October},
ISSN = {0027-5514},
Keywords = {Agaricales • Cluster Analysis • DNA, Fungal •
DNA, Ribosomal • Ecology • Introns •
Mitochondrial Proton-Translocating ATPases • Molecular
Sequence Data • Mycorrhizae • Phylogeny* •
RNA, Ribosomal • RNA, Ribosomal, 18S • RNA,
Ribosomal, 5.8S • Sequence Analysis, DNA •
Sequence Homology • chemistry • classification*
• genetics • genetics* • physiology},
Abstract = {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.},
Language = {eng},
Key = {fds141098}
}
@article{fds141099,
Author = {JM Moncalvo and RH Nilsson and B Koster and SM Dunham and T Bernauer and PB
Matheny, TM Porter and S Margaritescu and M Weiss and S Garnica and E
Danell, G Langer and E Langer and E Larsson and KH Larsson and R
Vilgalys},
Title = {The cantharelloid clade: dealing with incongruent gene trees
and phylogenetic reconstruction methods.},
Journal = {Mycologia, United States},
Volume = {98},
Number = {6},
Pages = {937-48},
Year = {2007},
Month = {October},
ISSN = {0027-5514},
Keywords = {Basidiomycota • Computational Biology • DNA,
Fungal • DNA, Mitochondrial • DNA, Ribosomal
• Evolution, Molecular • Molecular Sequence Data
• Phylogeny* • RNA Polymerase II • RNA,
Ribosomal, 18S • RNA, Ribosomal, 28S • Sequence
Analysis, DNA • classification* • genetics •
genetics* • methods* • physiology},
Abstract = {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.},
Language = {eng},
Key = {fds141099}
}
@article{fds141100,
Author = {TY James and PM Letcher and JE Longcore and SE Mozley-Standridge and D
Porter, MJ Powell and GW Griffith and R Vilgalys},
Title = {A molecular phylogeny of the flagellated fungi
(Chytridiomycota) and description of a new phylum
(Blastocladiomycota).},
Journal = {Mycologia, United States},
Volume = {98},
Number = {6},
Pages = {860-71},
Year = {2007},
Month = {October},
ISSN = {0027-5514},
Keywords = {Chytridiomycota • DNA, Fungal • DNA, Ribosomal
• Fungi • Microscopy, Electron, Transmission
• Phylogeny* • RNA, Ribosomal, 18S • RNA,
Ribosomal, 28S • RNA, Ribosomal, 5.8S • Sequence
Analysis, DNA • chemistry • classification* •
genetics • genetics* • ultrastructure},
Abstract = {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.},
Language = {eng},
Key = {fds141100}
}
@article{fds141088,
Author = {PB Matheny and JM Curtis and V Hofstetter and MC Aime and JM Moncalvo and ZW Ge and JC Slot and JF Ammirati and TJ Baroni and NL Bougher and KW
Hughes, DJ Lodge and RW Kerrigan and MT Seidl and DK Aanen and M
DeNitis, GM Daniele and DE Desjardin and BR Kropp and LL Norvell and A
Parker, EC Vellinga and R Vilgalys and DS Hibbett},
Title = {Major clades of Agaricales: a multilocus phylogenetic
overview.},
Journal = {Mycologia, United States},
Volume = {98},
Number = {6},
Pages = {982-95},
Year = {2007},
Month = {October},
ISSN = {0027-5514},
Keywords = {Agaricales • Cluster Analysis • DNA, Fungal •
DNA, Ribosomal • Ecology • Introns •
Mitochondrial Proton-Translocating ATPases • Molecular
Sequence Data • Mycorrhizae • Phylogeny* •
RNA, Ribosomal • RNA, Ribosomal, 18S • RNA,
Ribosomal, 5.8S • Sequence Analysis, DNA •
Sequence Homology • chemistry • classification*
• genetics • genetics* • physiology},
Abstract = {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.},
Language = {eng},
Key = {fds141088}
}
@article{fds141089,
Author = {JM Moncalvo and RH Nilsson and B Koster and SM Dunham and T Bernauer and PB
Matheny, TM Porter and S Margaritescu and M Weiss and S Garnica and E
Danell, G Langer and E Langer and E Larsson and KH Larsson and R
Vilgalys},
Title = {The cantharelloid clade: dealing with incongruent gene trees
and phylogenetic reconstruction methods.},
Journal = {Mycologia, United States},
Volume = {98},
Number = {6},
Pages = {937-48},
Year = {2007},
Month = {October},
ISSN = {0027-5514},
Keywords = {Basidiomycota • Computational Biology • DNA,
Fungal • DNA, Mitochondrial • DNA, Ribosomal
• Evolution, Molecular • Molecular Sequence Data
• Phylogeny* • RNA Polymerase II • RNA,
Ribosomal, 18S • RNA, Ribosomal, 28S • Sequence
Analysis, DNA • classification* • genetics •
genetics* • methods* • physiology},
Abstract = {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.},
Language = {eng},
Key = {fds141089}
}
@article{fds141090,
Author = {TY James and PM Letcher and JE Longcore and SE Mozley-Standridge and D
Porter, MJ Powell and GW Griffith and R Vilgalys},
Title = {A molecular phylogeny of the flagellated fungi
(Chytridiomycota) and description of a new phylum
(Blastocladiomycota).},
Journal = {Mycologia, United States},
Volume = {98},
Number = {6},
Pages = {860-71},
Year = {2007},
Month = {October},
ISSN = {0027-5514},
Keywords = {Chytridiomycota • DNA, Fungal • DNA, Ribosomal
• Fungi • Microscopy, Electron, Transmission
• Phylogeny* • RNA, Ribosomal, 18S • RNA,
Ribosomal, 28S • RNA, Ribosomal, 5.8S • Sequence
Analysis, DNA • chemistry • classification* •
genetics • genetics* • ultrastructure},
Abstract = {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.},
Language = {eng},
Key = {fds141090}
}
@article{fds141092,
Author = {AE Arnold and DA Henk and RL Eells and F Lutzoni and R
Vilgalys},
Title = {Diversity and phylogenetic affinities of foliar fungal
endophytes in loblolly pine inferred by culturing and
environmental PCR.},
Journal = {Mycologia, United States},
Volume = {99},
Number = {2},
Pages = {185-206},
Year = {2007},
Month = {September},
ISSN = {0027-5514},
Keywords = {Biodiversity* • DNA, Fungal • DNA, Ribosomal
• DNA, Ribosomal Spacer • Fungi • North
Carolina • Phylogeny • Pinus taeda • Plant
Leaves • Polymerase Chain Reaction • Sequence
Analysis, DNA • Symbiosis* • chemistry •
classification* • genetics • growth & development
• isolation & purification* • microbiology*},
Abstract = {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.},
Language = {eng},
Key = {fds141092}
}
@article{fds141086,
Author = {AE Arnold and DA Henk and RL Eells and F Lutzoni and R
Vilgalys},
Title = {Diversity and phylogenetic affinities of foliar fungal
endophytes in loblolly pine inferred by culturing and
environmental PCR.},
Journal = {Mycologia, United States},
Volume = {99},
Number = {2},
Pages = {185-206},
Year = {2007},
Month = {September},
ISSN = {0027-5514},
Keywords = {Biodiversity* • DNA, Fungal • DNA, Ribosomal
• DNA, Ribosomal Spacer • Fungi • North
Carolina • Phylogeny • Pinus taeda • Plant
Leaves • Polymerase Chain Reaction • Sequence
Analysis, DNA • Symbiosis* • chemistry •
classification* • genetics • growth & development
• isolation & purification* • microbiology*},
Abstract = {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.},
Language = {eng},
Key = {fds141086}
}
@article{fds141087,
Author = {DS Hibbett and M Binder and JF Bischoff and M Blackwell and PF Cannon and OE Eriksson and S Huhndorf and T James and PM Kirk and R Lücking and H
Thorsten Lumbsch and F Lutzoni and PB Matheny and DJ McLaughlin and MJ
Powell, S Redhead and CL Schoch and JW Spatafora and JA Stalpers and R
Vilgalys, MC Aime and A Aptroot and R Bauer and D Begerow and GL Benny and LA Castlebury and PW Crous and YC Dai and W Gams and DM Geiser and GW
Griffith, C Gueidan and DL Hawksworth and G Hestmark and K Hosaka and RA
Humber, KD Hyde and JE Ironside and U Kõljalg and CP Kurtzman and KH
Larsson, R Lichtwardt and J Longcore and J Miadlikowska and A Miller and JM Moncalvo and S Mozley-Standridge and F Oberwinkler and E Parmasto and V Reeb and JD Rogers and C Roux and L Ryvarden and JP Sampaio and A
Schüssler, J Sugiyama and RG Thorn and L Tibell and WA Untereiner and C
Walker, Z Wang and A Weir and M Weiss and MM White and K Winka and YJ Yao and N Zhang},
Title = {A higher-level phylogenetic classification of the
Fungi.},
Journal = {Mycological research, England},
Volume = {111},
Number = {Pt 5},
Pages = {509-47},
Year = {2007},
Month = {May},
ISSN = {0953-7562},
url = {http://dx.doi.org/10.1016/j.mycres.2007.03.004},
Keywords = {Evolution, Molecular • Fungi • Phylogeny •
Terminology as Topic • classification* •
genetics*},
Abstract = {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.},
Language = {eng},
Doi = {10.1016/j.mycres.2007.03.004},
Key = {fds141087}
}
@article{fds141095,
Author = {Henk DA and Vilgalys R},
Title = {Molecular phylogeny suggests a single origin of insect
symbiosis in the Pucciniomycetes with support for some
relationships within the genus Septobasidium},
Journal = {American Journal of Botany},
Volume = {94},
Pages = {1515-1526},
Year = {2007},
ISSN = {000249831000008},
Key = {fds141095}
}
@article{fds141093,
Author = {JL Parrent and R Vilgalys},
Title = {Biomass and compositional responses of ectomycorrhizal
fungal hyphae to elevated CO2 and nitrogen
fertilization.},
Journal = {The New phytologist, England},
Volume = {176},
Number = {1},
Pages = {164-74},
Year = {2007},
ISSN = {0028-646X},
url = {http://dx.doi.org/10.1111/j.1469-8137.2007.02155.x},
Keywords = {Biodiversity • Biomass* • Carbon • Carbon
Dioxide • Fertilizers • Hyphae • Mycorrhizae
• Nitrogen • Pinus taeda • Population
Dynamics • classification • drug effects* •
growth & development • metabolism • microbiology
• pharmacology*},
Abstract = {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.},
Language = {eng},
Doi = {10.1111/j.1469-8137.2007.02155.x},
Key = {fds141093}
}
@article{fds152950,
Author = {PC Ceresini and HD Shew and TY James and RJ Vilgalys and MA
Cubeta},
Title = {Phylogeography of the Solanaceae-infecting Basidiomycota
fungus Rhizoctonia solani AG-3 based on sequence analysis of
two nuclear DNA loci.},
Journal = {BMC evolutionary biology, England},
Volume = {7},
Pages = {163},
Year = {2007},
ISSN = {1471-2148},
url = {http://dx.doi.org/10.1186/1471-2148-7-163},
Keywords = {Cloning, Molecular • DNA, Fungal • Evolution,
Molecular • Genetic Variation* • Genotype •
Haplotypes • Likelihood Functions • Mycological
Typing Techniques • Phylogeny* • Polymerase Chain
Reaction • Rhizoctonia • Sequence Analysis, DNA
• Solanaceae • Species Specificity • Tobacco
• classification • genetics • genetics*
• microbiology • microbiology*},
Abstract = {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 < 0.05) but not for locus pP42F (Phi ST =
0.034, not significant). Results based on NCA of the pP89
locus suggest that historical restricted gene flow is a
plausible explanation for the geographical association of
clades. Coalescent-based simulations of genealogical
relationships between populations of R. solani AG-3 from
potato and tobacco were used to estimate the amount and
directionality of historical migration patterns in time, and
the ages of mutations of populations. Low rates of
historical movement of genes were observed between the
potato and tobacco populations of R. solani AG-3.
CONCLUSION: The two sisters populations of the basidiomycete
fungus R. solani AG-3 from potato and tobacco represent two
genetically distinct and historically divergent lineages
that have probably evolved within the range of their
particular related Solanaceae hosts as sympatric
species.},
Language = {eng},
Doi = {10.1186/1471-2148-7-163},
Key = {fds152950}
}
@article{fds152951,
Author = {TY James and F Kauff and CL Schoch and PB Matheny and V Hofstetter and CJ
Cox, G Celio and C Gueidan and E Fraker and J Miadlikowska and HT
Lumbsch, A Rauhut and V Reeb and AE Arnold and A Amtoft and JE Stajich and K Hosaka and GH Sung and D Johnson and B O'Rourke and M Crockett and M
Binder, JM Curtis and JC Slot and Z Wang and AW Wilson and A Schüssler and JE Longcore and K O'Donnell and S Mozley-Standridge and D Porter and PM
Letcher, MJ Powell and JW Taylor and MM White and GW Griffith and DR
Davies, RA Humber and JB Morton and J Sugiyama and AY Rossman and JD
Rogers, DH Pfister and D Hewitt and K Hansen and S Hambleton and RA
Shoemaker, J Kohlmeyer and B Volkmann-Kohlmeyer and RA Spotts and M
Serdani, PW Crous and KW Hughes and K Matsuura and E Langer and G
Langer, WA Untereiner and R Lücking and B Büdel and DM Geiser and A
Aptroot, P Diederich and I Schmitt and M Schultz and R Yahr and DS
Hibbett, F Lutzoni and DJ McLaughlin and JW Spatafora and R
Vilgalys},
Title = {Reconstructing the early evolution of Fungi using a six-gene
phylogeny.},
Journal = {Nature, England},
Volume = {443},
Number = {7113},
Pages = {818-22},
Year = {2006},
Month = {October},
ISSN = {1476-4687},
url = {http://dx.doi.org/10.1038/nature05110},
Keywords = {Chytridiomycota • Evolution, Molecular* • Fungi
• Genes, Fungal • Microsporidia • Phylogeny*
• classification • genetics •
genetics*},
Abstract = {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.},
Language = {eng},
Doi = {10.1038/nature05110},
Key = {fds152951}
}
@article{fds152952,
Author = {JL Parrent and WF Morris and R Vilgalys},
Title = {CO2-enrichment and nutrient availability alter
ectomycorrhizal fungal communities.},
Journal = {Ecology, United States},
Volume = {87},
Number = {9},
Pages = {2278-87},
Year = {2006},
Month = {September},
ISSN = {0012-9658},
Keywords = {Biodiversity • Carbon Dioxide • DNA Primers •
DNA, Ribosomal Spacer • Ecology • Mycorrhizae
• Nitrogen • Phosphorus • Pinus taeda •
Plant Roots • Symbiosis • Trees • chemistry
• classification • genetics • growth &
development • isolation & purification •
metabolism • metabolism* • physiology •
physiology*},
Abstract = {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.},
Language = {eng},
Key = {fds152952}
}
@article{fds152954,
Author = {D González and MA Cubeta and R Vilgalys},
Title = {Phylogenetic utility of indels within ribosomal DNA and
beta-tubulin sequences from fungi in the Rhizoctonia solani
species complex.},
Journal = {Molecular phylogenetics and evolution, United
States},
Volume = {40},
Number = {2},
Pages = {459-70},
Year = {2006},
Month = {August},
ISSN = {1055-7903},
url = {http://dx.doi.org/10.1016/j.ympev.2006.03.022},
Keywords = {Base Sequence • DNA, Ribosomal • Phylogeny* •
Rhizoctonia • Sequence Alignment • Transcription,
Genetic • Tubulin • genetics •
genetics*},
Abstract = {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.},
Language = {eng},
Doi = {10.1016/j.ympev.2006.03.022},
Key = {fds152954}
}
@article{fds152956,
Author = {AP Litvintseva and R Thakur and R Vilgalys and TG
Mitchell},
Title = {Multilocus sequence typing reveals three genetic
subpopulations of Cryptococcus neoformans var. grubii
(serotype A), including a unique population in
Botswana.},
Journal = {Genetics, United States},
Volume = {172},
Number = {4},
Pages = {2223-38},
Year = {2006},
Month = {April},
ISSN = {0016-6731},
url = {http://dx.doi.org/10.1534/genetics.105.046672},
Keywords = {Botswana • Cryptococcosis • Cryptococcus
neoformans • DNA • DNA, Fungal • Genes,
Fungal • Genes, Mating Type, Fungal* • Genotype
• Humans • Models, Genetic • Phylogeny •
Polymorphism, Genetic • Sequence Analysis, DNA •
Species Specificity • genetics* • metabolism
• microbiology},
Abstract = {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.},
Language = {eng},
Doi = {10.1534/genetics.105.046672},
Key = {fds152956}
}
@article{fds152955,
Author = {TY James and P Srivilai and U Kües and R Vilgalys},
Title = {Evolution of the bipolar mating system of the mushroom
Coprinellus disseminatus from its tetrapolar ancestors
involves loss of mating-type-specific pheromone receptor
function.},
Journal = {Genetics, United States},
Volume = {172},
Number = {3},
Pages = {1877-91},
Year = {2006},
Month = {March},
ISSN = {0016-6731},
url = {http://dx.doi.org/10.1534/genetics.105.051128},
Keywords = {Agaricales • Alleles • Evolution, Molecular*
• Genes, Mating Type, Fungal* • Mitogen-Activated
Protein Kinase Kinases • Polymorphism, Genetic •
Polyploidy* • Protein Kinases • Receptors,
Pheromone • Saccharomyces cerevisiae Proteins •
Sequence Homology, Nucleic Acid • deficiency •
genetics • genetics* • physiology},
Abstract = {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.},
Language = {eng},
Doi = {10.1534/genetics.105.051128},
Key = {fds152955}
}
@article{fds52708,
Author = {James TY and Kauff F and Schoch CL and Matheny PB and Hofstetter V and Cox
CJ, Celio G and Gueidan C and Fraker E and Miadlikowska J and Lumbsch
HT, Rauhut A and Reeb V and Arnold AE and Amtoft A and Stajich JE and Hosaka K and Sung GH and Johnson D and O'Rourke B and Crockett M and Binder
M, Curtis JM and Slot JC and Wang Z and Wilson AW and Schussler A and Longcore JE and O'Donnell K and Mozley-Standridge S and Porter D and Letcher PM and Powell MJ and Taylor JW and White MM and Griffith GW and Davies DR and Humber RA and Morton JB and Sugiyama J and Rossman AY and Rogers JD and Pfister DH and Hewitt D and Hansen K and Hambleton S and Shoemaker RA and Kohlmeyer J and Volkmann-Kohlmeyer B and Spotts RA and Serdani M and Crous PW and Hughes KW and Matsuura K and Langer E and Langer
G, Untereiner WA and Lucking R and Budel B and Geiser DM and Aptroot A and Diederich P and Schmitt I and Schultz M and Yahr R and Hibbett DS and Lutzoni F and McLaughlin DJ and Spatafora JW and Vilgalys
R},
Title = {Reconstructing the early evolution of Fungi using a six-gene
phylogeny},
Journal = {Nature},
Volume = {443},
Pages = {818-822},
Year = {2006},
Key = {fds52708}
}
@article{fds52711,
Author = {Gonzalez D and Cubeta MA and Vilgalys R},
Title = {Phylogenetic utility of indels within ribosomal DNA and
beta-tubulin sequences from fungi in the Rhizoctonia solani
species complex},
Journal = {Molecular Phylogenetics and Evolution},
Volume = {40},
Pages = {459-470},
Year = {2006},
Key = {fds52711}
}
@article{fds52710,
Author = {Yahr R and Vilgalys R and DePriest PT},
Title = {Geographic variation in algal partners of Cladonia subtenuis
(Cladoniaceae) highlights the dynamic nature of a lichen
symbiosis},
Journal = {New Phytologist},
Volume = {171},
Pages = {847-860},
Year = {2006},
Key = {fds52710}
}
@article{fds52707,
Author = {Parrent, J. L. and W. F. Morris. and R. Vilgalys},
Title = {CO2-enrichment and nutrient availability alter
ectomycorrhizal fungal communities},
Journal = {Ecology},
Volume = {87},
Pages = {2278-2287},
Year = {2006},
Key = {fds52707}
}
@article{fds52709,
Author = {James TY and Srivilai P and Kues U and Vilgalys R},
Title = {Evolution of the bipolar mating system of the mushroom
Coprinellus disseminatus from its tetrapolar ancestors
involves loss of mating-type-specific pheromone receptor
function},
Journal = {Genetics},
Volume = {172},
Pages = {1877-1891},
Year = {2006},
Key = {fds52709}
}
@article{fds52712,
Author = {Litvintseva, A. P. and Thakur, R. and Vilgalys, R. and Mitchell, T.
G.},
Title = {Multilocus sequence typing reveals three genetic
subpopulations of Cryptococcus neoformans var. grubii
(serotype A), Including a Unique Population in
Botswana},
Journal = {Genetics},
Volume = {172},
Pages = {2223-2238},
Year = {2006},
Key = {fds52712}
}
@article{fds152953,
Author = {R Yahr and R Vilgalys and PT DePriest},
Title = {Geographic variation in algal partners of Cladonia subtenuis
(Cladoniaceae) highlights the dynamic nature of a lichen
symbiosis.},
Journal = {The New phytologist, England},
Volume = {171},
Number = {4},
Pages = {847-60},
Year = {2006},
ISSN = {0028-646X},
url = {http://dx.doi.org/10.1111/j.1469-8137.2006.01792.x},
Keywords = {Algae • Ascomycota • Demography • Ecosystem*
• Genetic Variation • Geography • Lichens
• Phylogeny • Symbiosis • genetics •
genetics* • metabolism* • physiology*},
Abstract = {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.},
Language = {eng},
Doi = {10.1111/j.1469-8137.2006.01792.x},
Key = {fds152953}
}
@article{fds152957,
Author = {HE O'Brien and JL Parrent and JA Jackson and JM Moncalvo and R
Vilgalys},
Title = {Fungal community analysis by large-scale sequencing of
environmental samples.},
Journal = {Applied and environmental microbiology, United
States},
Volume = {71},
Number = {9},
Pages = {5544-50},
Year = {2005},
Month = {September},
ISSN = {0099-2240},
url = {http://dx.doi.org/10.1128/AEM.71.9.5544-5550.2005},
Keywords = {Computational Biology • DNA, Ribosomal Spacer •
Ecosystem* • Fungi • Genes, rRNA • Genetic
Variation • Molecular Sequence Data • Phylogeny
• Pinus taeda • Polymerase Chain Reaction •
Sequence Analysis, DNA* • Soil Microbiology* •
Trees • analysis* • classification* •
genetics},
Abstract = {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.},
Language = {eng},
Doi = {10.1128/AEM.71.9.5544-5550.2005},
Key = {fds152957}
}
@article{fds152959,
Author = {N Fierer and JA Jackson and R Vilgalys and RB Jackson},
Title = {Assessment of soil microbial community structure by use of
taxon-specific quantitative PCR assays.},
Journal = {Applied and environmental microbiology, United
States},
Volume = {71},
Number = {7},
Pages = {4117-20},
Year = {2005},
Month = {July},
ISSN = {0099-2240},
url = {http://dx.doi.org/10.1128/AEM.71.7.4117-4120.2005},
Keywords = {Bacteria • DNA Primers • DNA, Bacterial •
DNA, Fungal • Ecosystem* • Fungi • Polymerase
Chain Reaction • Sensitivity and Specificity •
Soil Microbiology* • Species Specificity •
analysis • classification* • genetics •
isolation & purification • methods*},
Abstract = {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.},
Language = {eng},
Doi = {10.1128/AEM.71.7.4117-4120.2005},
Key = {fds152959}
}
@article{fds152958,
Author = {M Didukh and R Vilgalys and SP Wasser and OS Isikhuemhen and E
Nevo},
Title = {Notes on Agaricus section Duploannulati using molecular and
morphological data.},
Journal = {Mycological research, England},
Volume = {109},
Number = {Pt 6},
Pages = {729-40},
Year = {2005},
Month = {June},
ISSN = {0953-7562},
Keywords = {Agaricus • Brazil • DNA Transposable Elements
• DNA, Fungal • DNA, Ribosomal • Europe
• Israel • Molecular Sequence Data •
Phylogeny • Species Specificity • United States
• classification* • genetics},
Abstract = {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.},
Language = {eng},
Key = {fds152958}
}
@article{fds152960,
Author = {AP Litvintseva and L Kestenbaum and R Vilgalys and TG
Mitchell},
Title = {Comparative analysis of environmental and clinical
populations of Cryptococcus neoformans.},
Journal = {Journal of clinical microbiology, United
States},
Volume = {43},
Number = {2},
Pages = {556-64},
Year = {2005},
Month = {February},
ISSN = {0095-1137},
url = {http://dx.doi.org/10.1128/JCM.43.2.556-564.2005},
Keywords = {Animals • California • Columbidae •
Cryptococcosis • Cryptococcus neoformans •
Environmental Microbiology* • Feces • Humans
• North Carolina • Serotyping • Texas •
Trees • classification* • genetics* •
isolation & purification • microbiology •
microbiology*},
Abstract = {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.},
Language = {eng},
Doi = {10.1128/JCM.43.2.556-564.2005},
Key = {fds152960}
}
@article{fds44637,
Author = {Litvintseva, A. P. and L. Kestenbaum and R. Vilgalys and T. G.
Mitchell},
Title = {Comparative analysis of environmental and clinical
populations of Cryptococcus neoformans},
Journal = {J Clin Microbiol},
Volume = {43},
Pages = {556-64},
Year = {2005},
Key = {fds44637}
}
@article{fds44649,
Author = {Wallenstein, M.D. and R. J. Vilgalys},
Title = {Quantitative analyses of nitrogen cycling genes in
soils},
Journal = {Pedobiologia},
Volume = {49},
Pages = {665-672},
Year = {2005},
Key = {fds44649}
}
@article{fds44650,
Author = {Fierer, N. and J. A. Jackson and R. Vilgalys and R. B.
Jackson},
Title = {Assessment of Soil Microbial Community Structure by Use of
Taxon-Specific Quantitative PCR Assays},
Journal = {Appl. Env. Microbiol.},
Volume = {71},
Pages = {4117-4120},
Year = {2005},
Key = {fds44650}
}
@article{fds44652,
Author = {James, T. Y. and R. Vilgalys},
Title = {Chytrid fungi as agents of amphibian decline- what can we
learn from the earliest diverging fungi?},
Booktitle = {Fungal Molecular principles of fungal pathogenesis, ASM
Press. Joe Heitman, Scott Filler, and Aaron
Mitchell-eds},
Year = {2005},
Key = {fds44652}
}
@article{fds30117,
Author = {S Diezmann and CJ Cox and G Schonian and R Vilgalys and TG
Mitchell},
Title = {Phylogeny and evolution of medical species of Candida and
related taxa: a multigenic analysis.},
Journal = {J Clin Microbiol, United States},
Volume = {42},
Number = {12},
Pages = {5624-5635},
Year = {2004},
Month = {December},
ISSN = {0095-1137},
url = {http://dx.doi.org/10.1128/JCM.42.12.5624-5635.2004},
Keywords = {Bayes Theorem • Candida • Candidiasis • DNA,
Ribosomal • Evolution, Molecular* • Fungal
Proteins • Humans • Monte Carlo Method •
Phylogeny* • RNA, Ribosomal, 16S • RNA, Ribosomal,
18S • Saccharomycetales • analysis •
classification* • genetics • genetics* •
microbiology* • pathogenicity},
Abstract = {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.},
Language = {eng},
Doi = {10.1128/JCM.42.12.5624-5635.2004},
Key = {fds30117}
}
@article{fds30118,
Author = {R Yahr and R Vilgalys and PT Depriest},
Title = {Strong fungal specificity and selectivity for algal
symbionts in Florida scrub Cladonia lichens.},
Journal = {Mol Ecol, England},
Volume = {13},
Number = {11},
Pages = {3367-3378},
Year = {2004},
Month = {November},
ISSN = {0962-1083},
url = {http://dx.doi.org/10.1111/j.1365-294X.2004.02350.x},
Keywords = {Biological Evolution • Environment • Eukaryota
• Florida • Fungi • Lichens • Phylogeny
• Quercus • Rosmarinus • Symbiosis* •
classification • genetics* • metabolism},
Abstract = {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.},
Language = {eng},
Doi = {10.1111/j.1365-294X.2004.02350.x},
Key = {fds30118}
}
@article{fds30120,
Author = {TY James, SR Liou and R Vilgalys},
Title = {The genetic structure and diversity of the A and B
mating-type genes from the tropical oyster mushroom,
Pleurotus djamor.},
Journal = {Fungal Genet Biol, United States},
Volume = {41},
Number = {8},
Pages = {813-825},
Year = {2004},
Month = {August},
ISSN = {1087-1845},
url = {http://dx.doi.org/10.1016/j.fgb.2004.04.005},
Keywords = {Amino Acid Sequence • Chromosome Mapping • Gene
Library • Genes, Fungal* • Genes, Mating Type,
Fungal* • Genetic Variation* • Molecular Sequence
Data • Phylogeny • Pleurotus • Receptors,
Pheromone • Sequence Homology, Amino Acid •
Transcription Factors • classification • genetics
• genetics* • physiology},
Abstract = {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.},
Language = {eng},
Doi = {10.1016/j.fgb.2004.04.005},
Key = {fds30120}
}
@article{fds30119,
Author = {RE Marra and JC Huang and E Fung and K Nielsen and J Heitman and R Vilgalys and TG Mitchell},
Title = {A genetic linkage map of Cryptococcus neoformans variety
neoformans serotype D (Filobasidiella neoformans).},
Journal = {Genetics, United States},
Volume = {167},
Number = {2},
Pages = {619-631},
Year = {2004},
Month = {June},
ISSN = {0016-6731},
url = {http://dx.doi.org/10.1534/genetics.103.023408},
Keywords = {Chromosome Mapping* • Chromosomes, Fungal •
Cryptococcus neoformans • Genetic Markers •
Karyotyping • Lod Score • Polymorphism, Genetic
• Restriction Mapping • classification* •
genetics • genetics*},
Abstract = {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 < 0.05) segregation distortion. At a minimum
LOD score of 6.0 and a maximum recombination frequency of
0.30, 20 linkage groups were resolved, resulting in a map
length of approximately 1500 cM. Average marker density is
5.4 cM (range 1-28.7 cM). Hybridization of selected markers
to blots of electrophoretic karyotypes unambiguously
assigned all linkage groups to chromosomes and led us to
conclude that the C. neoformans genome is approximately 20.2
Mb, comprising 14 chromosomes ranging in size from 0.8 to
2.3 Mb, with a ratio of approximately 13.2 kb/cM averaged
across the genome. However, only 2 of 12 ungrouped markers
hybridized to chromosome 10. The hybridizations revealed at
least one possible reciprocal translocation involving
chromosomes 8, 9, and 12. This map has been critical to
genome sequence assembly and will be essential for future
studies of quantitative trait inheritance.},
Language = {eng},
Doi = {10.1534/genetics.103.023408},
Key = {fds30119}
}
@article{fds30121,
Author = {GI Zervakis and JM Moncalvo and R Vilgalys},
Title = {Molecular phylogeny, biogeography and speciation of the
mushroom species Pleurotus cystidiosus and allied
taxa.},
Journal = {Microbiology, England},
Volume = {150},
Number = {Pt 3},
Pages = {715-726},
Year = {2004},
Month = {March},
ISSN = {1350-0872},
Keywords = {Base Sequence • DNA, Fungal • DNA, Ribosomal
Spacer • Genetic Variation • Molecular Sequence
Data • Phylogeny • Pleurotus • Sequence
Homology, Nucleic Acid • Species Specificity •
classification* • genetics • genetics*},
Abstract = {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.},
Language = {eng},
Key = {fds30121}
}
@article{fds30122,
Author = {TY James and U Kües and SA Rehner and R Vilgalys},
Title = {Evolution of the gene encoding mitochondrial intermediate
peptidase and its cosegregation with the A mating-type locus
of mushroom fungi.},
Journal = {Fungal Genet Biol, United States},
Volume = {41},
Number = {3},
Pages = {381-390},
Year = {2004},
Month = {March},
ISSN = {1087-1845},
url = {http://dx.doi.org/10.1016/j.fgb.2003.11.008},
Keywords = {Agaricales • Base Sequence • DNA Primers •
DNA, Fungal • Genetic Variation •
Metalloendopeptidases • Peptides • Phylogeny
• classification • enzymology* • genetics
• genetics* • isolation & purification},
Abstract = {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 (
< 1 kbp) to the A mating-type locus of two model mushroom
species. In this study, the cosegregation of MIP and the A
mating-type locus was studied by genotyping progeny of seven
additional mushroom species using PCR and genetic crosses.
No evidence of any recombination between MIP and the A
mating-type locus was detected among all seven species.
Phylogenetic analysis of MIP sequences from diverse mushroom
species agrees with the current organismal phylogeny,
suggesting the sequences are generally orthologous.},
Language = {eng},
Doi = {10.1016/j.fgb.2003.11.008},
Key = {fds30122}
}
@article{fds30123,
Author = {AP Litvintseva and RE Marra and K Nielsen and J Heitman and R Vilgalys and TG Mitchell},
Title = {Evidence of sexual recombination among Cryptococcus
neoformans serotype A isolates in sub-Saharan
Africa.},
Journal = {Eukaryot Cell, United States},
Volume = {2},
Number = {6},
Pages = {1162-8},
Year = {2003},
Month = {December},
ISSN = {1535-9778},
Keywords = {AIDS-Related Opportunistic Infections • Africa South of
the Sahara • Alleles • Botswana • Clone Cells
• Cryptococcosis • Cryptococcus neoformans •
DNA, Fungal • Flow Cytometry • Genes, Fungal*
• Genes, Mating Type, Fungal* • Genetic Markers
• Genetic Variation • Genetics, Population •
Humans • Polymorphism, Restriction Fragment Length
• Recombination, Genetic* • Sequence Analysis, DNA
• Serotyping • cytology • genetics •
genetics* • isolation & purification •
microbiology • pathogenicity},
Abstract = {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.},
Language = {eng},
Key = {fds30123}
}
@article{fds30124,
Author = {A Pringle and JM Moncalvo and R Vilgalys},
Title = {Revisiting the rDNA sequence diversity of a natural
population of the arbuscular mycorrhizal fungus Acaulospora
colossica.},
Journal = {Mycorrhiza, Germany},
Volume = {13},
Number = {4},
Pages = {227-31},
Year = {2003},
Month = {August},
ISSN = {0940-6360},
url = {http://dx.doi.org/10.1007/s00572-003-0249-2},
Keywords = {DNA, Fungal • DNA, Ribosomal • Fungi •
Mycorrhizae • Phylogeny • genetics*},
Abstract = {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.},
Language = {eng},
Doi = {10.1007/s00572-003-0249-2},
Key = {fds30124}
}
@article{fds152949,
Author = {PC Ceresini and HD Shew and RJ Vilgalys and LR Gale and MA
Cubeta},
Title = {Detecting Migrants in Populations of Rhizoctonia solani
Anastomosis Group 3 from Potato in North Carolina Using
Multilocus Genotype Probabilities.},
Journal = {Phytopathology, United States},
Volume = {93},
Number = {5},
Pages = {610-5},
Year = {2003},
Month = {May},
ISSN = {0031-949X},
url = {http://dx.doi.org/10.1094/PHYTO.2003.93.5.610},
Abstract = {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.},
Language = {eng},
Doi = {10.1094/PHYTO.2003.93.5.610},
Key = {fds152949}
}
@article{fds30125,
Author = {EA Morehouse and TY James and AR Ganley and R Vilgalys and L Berger and PJ
Murphy, JE Longcore},
Title = {Multilocus sequence typing suggests the chytrid pathogen of
amphibians is a recently emerged clone.},
Journal = {Mol Ecol, England},
Volume = {12},
Number = {2},
Pages = {395-403},
Year = {2003},
Month = {February},
ISSN = {0962-1083},
Keywords = {Amphibians • Animal Diseases • Animals •
Chromosomes, Fungal • Chytridiomycota • Clone
Cells • Genetic Variation* • Genetics, Population*
• Heterozygote • Molecular Sequence Data •
Nucleotides • Polymorphism, Genetic •
Reproduction, Asexual • United States • genetics
• genetics* • microbiology •
microbiology*},
Abstract = {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.},
Language = {eng},
Key = {fds30125}
}
@article{fds30127,
Author = {JM Moncalvo and R Vilgalys and SA Redhead and JE Johnson and TY James and M
Catherine Aime and V Hofstetter and SJ Verduin and E Larsson and TJ
Baroni, R Greg Thorn and S Jacobsson and H Clémençon and OK
Miller},
Title = {One hundred and seventeen clades of euagarics.},
Journal = {Mol Phylogenet Evol, United States},
Volume = {23},
Number = {3},
Pages = {357-400},
Year = {2002},
Month = {June},
ISSN = {1055-7903},
url = {http://dx.doi.org/10.1016/S1055-7903(02)00027-1},
Keywords = {Basidiomycota • Biological Evolution • DNA,
Ribosomal • Ecology • Phylogeny* •
classification* • genetics • physiology*},
Abstract = {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.},
Language = {eng},
Doi = {10.1016/S1055-7903(02)00027-1},
Key = {fds30127}
}
@article{fds30128,
Author = {J Xu and G Luo and RJ Vilgalys and ME Brandt and TG Mitchell},
Title = {Multiple origins of hybrid strains of Cryptococcus
neoformans with serotype AD.},
Journal = {Microbiology, England},
Volume = {148},
Number = {Pt 1},
Pages = {203-12},
Year = {2002},
Month = {January},
ISSN = {1350-0872},
Keywords = {Base Sequence • Cloning, Molecular • Crosses,
Genetic* • Cryptococcus neoformans • Evolution,
Molecular* • Genetic Variation • Humans •
Laccase • Molecular Sequence Data •
Oxidoreductases • Phylogeny • Sequence Analysis,
DNA • Serotyping • classification* •
genetics* • growth & development},
Abstract = {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.},
Language = {eng},
Key = {fds30128}
}
@article{fds30132,
Author = {A Forche and J Xu and R Vilgalys and TG Mitchell},
Title = {Development and characterization of a genetic linkage map of
Cryptococcus neoformans var. neoformans using amplified
fragment length polymorphisms and other markers.},
Journal = {Fungal Genet Biol, United States},
Volume = {31},
Number = {3},
Pages = {189-203},
Year = {2001},
Month = {December},
ISSN = {1087-1845},
url = {http://dx.doi.org/10.1006/fgbi.2000.1240},
Keywords = {Chromosome Mapping • Cryptococcus neoformans •
Genetic Linkage* • Genetic Markers • Genome,
Fungal* • Karyotyping • Meiosis • Random
Amplified Polymorphic DNA Technique • classification
• genetics* • methods*},
Abstract = {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.},
Language = {eng},
Doi = {10.1006/fgbi.2000.1240},
Key = {fds30132}
}
@article{fds30129,
Author = {U Kües and TY James and R Vilgalys and MP Challen},
Title = {The chromosomal region containing pab-1, mip, and the A
mating type locus of the secondarily homothallic
homobasidiomycete Coprinus bilanatus.},
Journal = {Curr Genet, United States},
Volume = {39},
Number = {1},
Pages = {16-24},
Year = {2001},
Month = {February},
ISSN = {0172-8083},
Keywords = {Amino Acid Sequence • Cloning, Molecular •
Coprinus • Genes, Fungal* • Genes, Homeobox •
Genes, Mating Type, Fungal* • Homeodomain Proteins
• Metalloendopeptidases • Molecular Sequence Data
• Phenotype • Transformation, Genetic •
biosynthesis • enzymology • genetics* •
growth & development},
Abstract = {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.},
Language = {eng},
Key = {fds30129}
}
@article{fds30130,
Author = {TY James and R Vilgalys},
Title = {Abundance and diversity of Schizophyllum commune spore
clouds in the Caribbean detected by selective
sampling.},
Journal = {Mol Ecol, England},
Volume = {10},
Number = {2},
Pages = {471-479},
Year = {2001},
Month = {February},
ISSN = {0962-1083},
Keywords = {Caribbean Region • DNA, Fungal • DNA, Ribosomal
Spacer • Gene Frequency • Genetic Variation •
Phylogeny • Polymorphism, Restriction Fragment Length
• Schizophyllum • Spores, Fungal • genetics
• genetics* • isolation & purification •
physiology},
Abstract = {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.},
Language = {eng},
Key = {fds30130}
}
@article{fds30134,
Author = {J Xu and C Onyewu and HJ Yoell and RY Ali and RJ Vilgalys and TG
Mitchell},
Title = {Dynamic and heterogeneous mutations to fluconazole
resistance in Cryptococcus neoformans.},
Journal = {Antimicrob Agents Chemother, United States},
Volume = {45},
Number = {2},
Pages = {420-7},
Year = {2001},
Month = {February},
ISSN = {0066-4804},
url = {http://dx.doi.org/10.1128/AAC.45.2.420-427.2001},
Keywords = {Antifungal Agents • Cryptococcus neoformans • DNA
Fingerprinting • Drug Resistance, Microbial •
Fluconazole • Genotype • Microbial Sensitivity
Tests • Mutation • Nucleic Acid Amplification
Techniques • drug effects • genetics* •
pharmacology*},
Abstract = {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.},
Language = {eng},
Doi = {10.1128/AAC.45.2.420-427.2001},
Key = {fds30134}
}
@article{fds30135,
Author = {TY James and JM Moncalvo and S Li and R Vilgalys},
Title = {Polymorphism at the ribosomal DNA spacers and its relation
to breeding structure of the widespread mushroom
Schizophyllum commune.},
Journal = {Genetics, United States},
Volume = {157},
Number = {1},
Pages = {149-61},
Year = {2001},
Month = {January},
ISSN = {0016-6731},
Keywords = {Base Sequence • DNA Primers • DNA, Fungal •
DNA, Ribosomal Spacer • Ecosystem • Evolution,
Molecular • Genetic Variation • Molecular Sequence
Data • Phylogeny • Polymorphism, Genetic •
Recombination, Genetic • Schizophyllum •
Selection, Genetic • genetics • genetics* •
isolation & purification},
Abstract = {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.},
Language = {eng},
Key = {fds30135}
}
@article{fds30136,
Author = {J Xu and R Vilgalys and TG Mitchell},
Title = {Multiple gene genealogies reveal recent dispersion and
hybridization in the human pathogenic fungus Cryptococcus
neoformans.},
Journal = {Mol Ecol, ENGLAND},
Volume = {9},
Number = {10},
Pages = {1471-1481},
Year = {2000},
Month = {October},
ISSN = {0962-1083},
Keywords = {Catechol Oxidase • Cryptococcus neoformans • DNA,
Ribosomal Spacer • Evolution, Molecular* • Genetic
Variation* • Humans • Molecular Sequence Data
• Orotate Phosphoribosyltransferase • Phylogeny*
• RNA, Ribosomal • Time Factors •
classification • genetics • genetics*},
Abstract = {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.},
Language = {eng},
Key = {fds30136}
}
@article{fds30126,
Author = {JM Moncalvo and FM Lutzoni and SA Rehner and J Johnson and R
Vilgalys},
Title = {Phylogenetic relationships of agaric fungi based on nuclear
large subunit ribosomal DNA sequences.},
Journal = {Syst Biol, England},
Volume = {49},
Number = {2},
Pages = {278-305},
Year = {2000},
Month = {June},
ISSN = {1063-5157},
Keywords = {Agaricales • Base Sequence • Biological Evolution
• Classification • DNA, Fungal • DNA,
Ribosomal • Genetic Variation • Phylogeny* •
classification* • genetics* • methods},
Abstract = {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.},
Language = {eng},
Key = {fds30126}
}
@article{fds30131,
Author = {G Schönian and A Forche and HJ Tietz and M Müller and Y Gräser and R Vilgalys and TG Mitchell and W Presber},
Title = {[Genetic structure of geographically different populations
of candida albicans]},
Journal = {Mycoses, Germany},
Volume = {43 Suppl 2},
Pages = {51-6},
Year = {2000},
ISSN = {0933-7407},
Keywords = {Africa • Candida albicans • DNA, Fungal •
Europe • Genetic Variation* • Genotype •
Polymerase Chain Reaction • Polymorphism, Genetic
• United States • genetics •
genetics*},
Abstract = {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.},
Language = {ger},
Key = {fds30131}
}
@article{fds30133,
Author = {JG McEwen and JW Taylor and D Carter and J Xu and MS Felipe and R Vilgalys and TG Mitchell and T Kasuga and T White and T Bui and CM
Soares},
Title = {Molecular typing of pathogenic fungi.},
Journal = {Med Mycol, England},
Volume = {38 Suppl 1},
Pages = {189-97},
Year = {2000},
ISSN = {1369-3786},
Keywords = {Genetic Techniques • Humans • Mitosporic Fungi
• Mycological Typing Techniques • Mycoses •
classification* • genetics • microbiology* •
pathogenicity},
Abstract = {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.},
Language = {eng},
Key = {fds30133}
}
%% Book Chapters
@article{fds141403,
Author = {Idnurm, A. and T. Y. James and R. Vilgalys},
Title = {Sex in the rest: mysterious mating in the Chytridiomycota
and Zygomycota},
Booktitle = {Sex in fungi: molecular determination and evolutionary
implications},
Publisher = {ASM Press, Washington, D.C.},
Editor = {Joe Heitman and Jim Kronstad and John Taylor and Lorna Casselton},
Year = {2007},
Key = {fds141403}
}
@article{fds52721,
Author = {James, T. Y. and R. Vilgalys},
Title = {Amphibian chytridiomycosis as an emerging infectious disease
of wildlife: what can we learn from the earliest diverging
fungi?},
Booktitle = {Molecular principles of fungal pathogenesis},
Publisher = {ASM Press, Washington, D.C.},
Editor = {J. Heitman and S.G. Filler and J.E. Edwards, Jr and A.P.
Mitchell},
Year = {2006},
Key = {fds52721}
}
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