Journal ArticleDOI
The phylogenetic distribution of resupinate forms across the major clades of mushroom-forming fungi (Homobasidiomycetes)
TLDR
Phylogenetic relationships of resupinate Homobasidiomycetes (Corticiaceae s. lat. and others) were studied using ribosomal DNA sequences from a broad sample of res upinate and nonresupinate taxa to support monophyly of the eight major clades of Homob as well as independent lineages corresponding to the Gloeophyllum clade, corticioid clade and Jaapia argillacea.Abstract:
Phylogenetic relationships of resupinate Homobasidiomycetes (Corticiaceae s. lat. and others) were studied using ribosomal DNA (rDNA) sequences from a broad sample of resupinate and nonresupinate taxa. Two datasets were analysed using parsimony, a 'core' dataset of 142 species, each of which is represented by four rDNA regions (mitochondrial and nuclear large and small subunits), and a 'full' dataset of 656 species, most of which were represented only by nuclear large subunit rDNA sequences. Both datasets were analysed using traditional heuristic methods with bootstrapping, and the full dataset was also analysed with the Parsimony Ratchet, using equal character weights and six-parameter weighted parsimony. Analyses of both datasets supported monophyly of the eight major clades of Homobasidiomycetes recognised by Hibbett and Thorn, as well as independent lineages corresponding to the Gloeophyllum clade, corticioid clade and Jaapia argillacea. Analyses of the full dataset resolved two additional groups, the athelioid clade and trechisporoid clade (the latter may be nested in the polyporoid clade). Thus, there are at least 12 independent clades of Homobasidiomycetes. Higher- level relationships among the major clades are not resolved with confidence. Nevertheless, the euagarics clade, bolete clade, athelioid clade and Jaapia argillacea are consistently resolved as a monophyletic group, whereas the cantharelloid clade, gomphoid-phalloid clade and hymenochaetoid clade are placed at the base of the Homobasidiomycetes, which is consistent with the preponderance of imperforate parenthesomes in those groups. Resupinate forms occur in each of theread more
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A higher-level phylogenetic classification of the Fungi
David S. Hibbett,Manfred Binder,Joseph F. Bischoff,Meredith Blackwell,Paul F. Cannon,Ove E. Eriksson,Sabine M. Huhndorf,Timothy Y. James,Paul M. Kirk,Robert Lücking,H. Thorsten Lumbsch,François Lutzoni,P. Brandon Matheny,David J. McLaughlin,Martha J. Powell,Scott A. Redhead,Conrad L. Schoch,Joseph W. Spatafora,Joost A. Stalpers,Rytas Vilgalys,M. Catherine Aime,André Aptroot,Robert Bauer,Dominik Begerow,Gerald L. Benny,Lisa A. Castlebury,Pedro W. Crous,Yu-Cheng Dai,Walter Gams,David M. Geiser,Gareth W. Griffith,Cécile Gueidan,David L. Hawksworth,Geir Hestmark,Kentaro Hosaka,Richard A. Humber,Kevin D. Hyde,Joseph E. Ironside,Urmas Kõljalg,Cletus P. Kurtzman,Karl-Henrik Larsson,Robert W. Lichtwardt,Joyce E. Longcore,Jolanta Miadlikowska,Andrew N. Miller,Jean-Marc Moncalvo,Sharon E. Mozley-Standridge,Franz Oberwinkler,Erast Parmasto,Valérie Reeb,Jack D. Rogers,Claude Roux,Leif Ryvarden,José Paulo Sampaio,Arthur Schüssler,Junta Sugiyama,R. Greg Thorn,Leif Tibell,Wendy A. Untereiner,Christopher Walker,Zheng Wang,Alex Weir,Michael Weiss,Merlin M. White,Katarina Winka,Yi-Jian Yao,Ning Zhang +66 more
TL;DR: 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.
Journal ArticleDOI
Reconstructing the early evolution of Fungi using a six-gene phylogeny
Timothy Y. James,Frank Kauff,Conrad L. Schoch,P. Brandon Matheny,Valérie Hofstetter,Cymon J. Cox,Cymon J. Cox,Gail Celio,Cécile Gueidan,Emily Fraker,Jolanta Miadlikowska,H. Thorsten Lumbsch,Alexandra Rauhut,Valérie Reeb,A. Elizabeth Arnold,A. Elizabeth Arnold,Anja Amtoft,Jason E. Stajich,Kentaro Hosaka,Kentaro Hosaka,Gi-Ho Sung,Desiree Johnson,Ben O'Rourke,Michael Crockett,Manfred Binder,Judd M. Curtis,Jason C. Slot,Zheng Wang,Zheng Wang,Andrew W. Wilson,Arthur Schüßler,Joyce E. Longcore,Kerry O'Donnell,Sharon E. Mozley-Standridge,David Porter,Peter M. Letcher,Martha J. Powell,John W. Taylor,Merlin M. White,Gareth W. Griffith,David R. Davies,Richard A. Humber,Joseph B. Morton,Junta Sugiyama,Amy Y. Rossman,Jack D. Rogers,Donald H. Pfister,David Hewitt,Karen Hansen,Sarah Hambleton,R. A. Shoemaker,Jan Kohlmeyer,Brigitte Volkmann-Kohlmeyer,Robert A. Spotts,Maryna Serdani,Pedro W. Crous,Karen W. Hughes,Kenji Matsuura,Ewald Langer,Gitta Langer,Wendy A. Untereiner,Robert Lücking,Burkhard Büdel,David M. Geiser,André Aptroot,Paul Diederich,Imke Schmitt,Imke Schmitt,Matthias Schultz,Rebecca Yahr,Rebecca Yahr,David S. Hibbett,François Lutzoni,David J. McLaughlin,Joseph W. Spatafora,Rytas Vilgalys +75 more
TL;DR: It is indicated that there may have been at least four independent losses of the flagellum in the kingdom Fungi, and 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.
Journal ArticleDOI
Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification
TL;DR: The present study estimates the intraspecific ITS variability in all fungi presently available to the mycological community through the international sequence databases and cautions against simplified approaches to automated ITS-based species delimitation and reiterate the need for taxonomic expertise in the translation of sequence data into species names.
Journal ArticleDOI
The Plant Cell Wall–Decomposing Machinery Underlies the Functional Diversity of Forest Fungi
Daniel C. Eastwood,Dimitrios Floudas,Manfred Binder,Andrzej Majcherczyk,Patrick Schneider,Andrea Aerts,Fred O. Asiegbu,Scott E. Baker,Kerrie Barry,Mika Bendiksby,Melanie Blumentritt,Pedro M. Coutinho,Dan Cullen,Ronald P. de Vries,Allen C. Gathman,Barry Goodell,Barry Goodell,Bernard Henrissat,Katarina Ihrmark,Håvard Kauserud,Annegret Kohler,Kurt LaButti,Alla Lapidus,José Luis Lavín,Yong-Hwan Lee,Erika Lindquist,Walt W. Lilly,Susan Lucas,Emmanuelle Morin,Claude Murat,José A. Oguiza,Jongsun Park,Antonio G. Pisabarro,Robert Riley,Anna Rosling,Asaf Salamov,Olaf Schmidt,Jeremy Schmutz,Inger Skrede,Jan Stenlid,Ad Wiebenga,Xinfeng Xie,Ursula Kües,David S. Hibbett,Dirk Hoffmeister,Nils Högberg,Francis Martin,Igor V. Grigoriev,S.C. Watkinson +48 more
TL;DR: Fungal nutritional mode diversification suggests that the boreal forest biome originated via genetic coevolution of above- and below-ground biota through convergent evolution and divergence among fungal decomposers.
References
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Book
PCR protocols : A guide to methods and applications
TL;DR: Basic Methodology: M.A. Innis and D.F. Frohman, RACE: Rapid Amplification of cDNA Ends, and RNA Processing: Apo-B.R. Kwok, Procedure to Minimuze PCR-Product Carry-Over.