The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits
Conrad L. Schoch,Gi-Ho Sung,Francesc López-Giráldez,Jeffrey P. Townsend,Jolanta Miadlikowska,Valérie Hofstetter,Barbara Robbertse,P. Brandon Matheny,P. Brandon Matheny,Frank Kauff,Zheng Wang,Cécile Gueidan,Rachael M. Andrie,Kristin M. Trippe,Linda M. Ciufetti,Anja Amtoft Wynns,Emily Fraker,Brendan P. Hodkinson,Gregory Bonito,Johannes Z. Groenewald,Mahdi Arzanlou,Mahdi Arzanlou,G. Sybren de Hoog,Pedro W. Crous,David Hewitt,Donald H. Pfister,Kristin R. Peterson,Marieka Gryzenhout,Michael J. Wingfield,André Aptroot,Sung-Oui Suh,Meredith Blackwell,David M. Hillis,Gareth W. Griffith,Lisa A. Castlebury,Amy Y. Rossman,H. Thorsten Lumbsch,Robert Lücking,Burkhard Büdel,Alexandra Rauhut,Paul Diederich,Damien Ertz,David M. Geiser,Kentaro Hosaka,Patrik Inderbitzin,Jan Kohlmeyer,Brigitte Volkmann-Kohlmeyer,Lizel Mostert,Kerry O'Donnell,Harrie J. M. Sipman,Jack D. Rogers,R. A. Shoemaker,Junta Sugiyama,Richard C. Summerbell,Wendy A. Untereiner,Peter R. Johnston,Soili Stenroos,Alga Zuccaro,Paul S. Dyer,Peter D. Crittenden,Mariette S. Cole,Karen Hansen,James M. Trappe,Rebecca Yahr,Franois Lutzoni,Joseph W. Spatafora +65 more
TLDR
A 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi, and a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions support a terrestrial, saprobic ecology as ancestral are presented.Abstract:
We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.read more
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Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
Conrad L. Schoch,Keith A. Seifert,Sabine M. Huhndorf,Vincent Robert,John L. Spouge,C. André Lévesque,Wen Chen,Elena Bolchacova,Kerstin Voigt,Pedro W. Crous,Andrew N. Miller,Michael J. Wingfield,M. Catherine Aime,Kwang Deuk An,Feng-Yan Bai,Robert W. Barreto,Dominik Begerow,Marie Josée Bergeron,Meredith Blackwell,Teun Boekhout,Teun Boekhout,Mesfin Bogale,Nattawut Boonyuen,Ana Rosa Burgaz,Bart Buyck,Lei Cai,Qing Cai,Gianluigi Cardinali,Priscila Chaverri,Brian J. Coppins,Ana Crespo,Paloma Cubas,Craig Cummings,Ulrike Damm,Z. Wilhelm de Beer,G. Sybren de Hoog,Ruth Del-Prado,Bryn T. M. Dentinger,Bryn T. M. Dentinger,Javier Diéguez-Uribeondo,Pradeep K. Divakar,Brian Douglas,Margarita Dueñas,Tuan A. Duong,Ursula Eberhardt,Joan E. Edwards,Mostafa S. Elshahed,Katerina Fliegerova,Manohar R. Furtado,Miguel A. García,Zai-Wei Ge,Gareth W. Griffith,K. Griffiths,Johannes Z. Groenewald,Marizeth Groenewald,Martin Grube,Marieka Gryzenhout,Liang-Dong Guo,Ferry Hagen,Sarah Hambleton,Richard C. Hamelin,Karen Hansen,Paul Harrold,Gregory Heller,Cesar S. Herrera,Kazuyuki Hirayama,Yuuri Hirooka,Hsiao Man Ho,Kerstin Hoffmann,Valérie Hofstetter,Filip Högnabba,Peter M. Hollingsworth,Seung-Beom Hong,Kentaro Hosaka,Jos Houbraken,Karen W. Hughes,Seppo Huhtinen,Kevin D. Hyde,Kevin D. Hyde,Timothy Y. James,Eric M. Johnson,Joan E. Johnson,Peter R. Johnston,E. B. Gareth Jones,Laura J. Kelly,Laura J. Kelly,Paul M. Kirk,Dániel G. Knapp,Urmas Kõljalg,Gábor M. Kovács,Cletus P. Kurtzman,Sara Landvik,Steven D. Leavitt,Audra S. Liggenstoffer,Kare Liimatainen,Lorenzo Lombard,J. Jennifer Luangsa-ard,H. Thorsten Lumbsch,Harinad Maganti,Sajeewa S. N. Maharachchikumbura,María P. Martín,Tom W. May,Alistair R. McTaggart,Andrew S. Methven,Wiel Meyer,Jean-Marc Moncalvo,Suchada Mongkolsamrit,László Nagy,R. Henrik Nilsson,Tuula Niskanen,Ildikó Nyilasi,Gen Okada,Izumi Okane,Ibai Olariaga,Jürgen Otte,Tamás Papp,Duckchul Park,Tamás Petkovits,Raquel Pino-Bodas,W. Quaedvlieg,Huzefa A. Raja,Dirk Redecker,Tara L. Rintoul,Constantino Ruibal,Jullie M. Sarmiento-Ramírez,Imke Schmitt,Imke Schmitt,Arthur Schüßler,Carol A. Shearer,Kozue Sotome,Franck O.P. Stefani,Soili Stenroos,B. Stielow,Herbert Stockinger,Satinee Suetrong,Sung-Oui Suh,Gi-Ho Sung,Motofumi Suzuki,Kazuaki Tanaka,Leho Tedersoo,M. Teresa Telleria,Eric D. Tretter,Wendy A. Untereiner,Hector Urbina,Csaba Vágvölgyi,Agathe Vialle,Thuy Duong Vu,Grit Walther,Qi Ming Wang,Yan Wang,Bevan S. Weir,Michael Weiß,Merlin M. White,Jianping Xu,Rebecca Yahr,Zhu L. Yang,Andrey Yurkov,Juan Carlos Zamora,Ning Zhang,Wen Ying Zhuang,David Schindel +160 more
TL;DR: Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation.
Journal ArticleDOI
Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea
Joelle Amselem,Christina A. Cuomo,Jan A. L. van Kan,Muriel Viaud,Ernesto P. Benito,Arnaud Couloux,Pedro M. Coutinho,Ronald P. de Vries,Paul S. Dyer,Sabine Fillinger,Elisabeth Fournier,Elisabeth Fournier,Lilian Gout,Matthias Hahn,Linda M. Kohn,Nicolas Lapalu,Kim M. Plummer,Jean-Marc Pradier,Emmanuel Quévillon,Emmanuel Quévillon,Amir Sharon,Adeline Simon,Arjen ten Have,Bettina Tudzynski,Paul Tudzynski,Patrick Wincker,Marion Andrew,Véronique Anthouard,Ross E. Beever,Rolland Beffa,Isabelle Benoit,Ourdia Bouzid,Baptiste Brault,Zehua Chen,Mathias Choquer,Mathias Choquer,Jérôme Collemare,Jérôme Collemare,Pascale Cotton,Etienne Danchin,Corinne Da Silva,Angélique Gautier,Corinne Giraud,Tatiana Giraud,Celedonio González,Sandrine Grossetete,Ulrich Güldener,Bernard Henrissat,Barbara J. Howlett,Chinnappa D. Kodira,Matthias Kretschmer,Anne Lappartient,Michaela Leroch,Caroline Levis,Evan Mauceli,Cécile Neuvéglise,Birgitt Oeser,Matthew D. Pearson,Julie Poulain,Nathalie Poussereau,Hadi Quesneville,Christine Rascle,Julia Schumacher,Béatrice Segurens,Adrienne Sexton,Evelyn Silva,Catherine Sirven,Darren M. Soanes,Nicholas J. Talbot,Matthew D. Templeton,Chandri Yandava,Oded Yarden,Qiandong Zeng,Jeffrey A. Rollins,Marc-Henri Lebrun,Marc-Henri Lebrun,Marty Dickman +76 more
TL;DR: Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea, and shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating.
Journal ArticleDOI
Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi
Robin A. Ohm,Nicolas Feau,Bernard Henrissat,Conrad L. Schoch,Benjamin A. Horwitz,Kerrie Barry,Bradford Condon,Alex Copeland,Braham Dhillon,Fabian Glaser,Cedar N. Hesse,Idit Kosti,Kurt LaButti,Erika Lindquist,Susan Lucas,Asaf Salamov,Rosie E. Bradshaw,Lynda M. Ciuffetti,Richard C. Hamelin,Richard C. Hamelin,Gert H. J. Kema,Christopher B. Lawrence,James A. Scott,Joseph W. Spatafora,B. Gillian Turgeon,Pierre J. G. M. de Wit,Shaobin Zhong,Stephen B. Goodwin,Igor V. Grigoriev +28 more
TL;DR: The Dothideomycetes are one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts as mentioned in this paper.
Journal ArticleDOI
A class-wide phylogenetic assessment of Dothideomycetes
Conrad L. Schoch,Pedro W. Crous,Johannes Z. Groenewald,Eric W.A. Boehm,Treena I. Burgess,J. de Gruyter,G.S. de Hoog,L. J. Dixon,Martin Grube,Cécile Gueidan,Yukio Harada,Satoshi Hatakeyama,Kazuyuki Hirayama,Tsuyoshi Hosoya,Sabine M. Huhndorf,Kevin D. Hyde,E. B. G. Jones,Jan Kohlmeyer,Åsa Kruys,Y. M. Li,Robert Lücking,H. T. Lumbsch,Ludmila Marvanová,Joelle Mbatchou,A. H.. McVay,Andrew N. Miller,G. K. Mugambi,Lucia Muggia,Matthew P. Nelsen,P. Nelson,C. A. Owensby,Alan J. L. Phillips,Souwalak Phongpaichit,Stephen B. Pointing,V. Pujade-Renaud,Huzefa A. Raja,E. Rivas Plata,Barbara Robbertse,Constantino Ruibal,Jariya Sakayaroj,Teruo Sano,Laura Selbmann,Carol A. Shearer,Takashi Shirouzu,Bernard Slippers,S. Suetrong,S. Suetrong,Kazuaki Tanaka,Brigitte Volkmann-Kohlmeyer,Michael J. Wingfield,Alan R. Wood,J.H.C. Woudenberg,H. Yonezawa,Ying Zhang,Joseph W. Spatafora +54 more
TL;DR: A genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon.
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