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Stud Mycol 64(1): 1-1510 2009
DOI: 10.3114/sim.2009.64.01
Copyright © 2009 CBS Fungal Biodiversity Centre
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A class-wide phylogenetic assessment of Dothideomycetes

C.L. Schoch1,*, P.W. Crous2, J.Z. Groenewald2, E.W.A. Boehm3, T.I. Burgess4, J. de Gruyter2,5, G.S. de Hoog2, L.J. Dixon6, M. Grube7, C. Gueidan2, Y. Harada8, S. Hatakeyama8, K. Hirayama8, T. Hosoya9, S.M. Huhndorf10, K.D. Hyde11,33, E.B.G. Jones12, J. Kohlmeyer13, Å. Kruys14, Y.M. Li33, R. Lücking10, H.T. Lumbsch10, L. Marvanová15, J.S. Mbatchou10,16, A.H. McVay17, A.N. Miller18, G.K. Mugambi10,19,27, L. Muggia7, M.P. Nelsen10,20, P. Nelson21, C A. Owensby17, A.J.L. Phillips22, S. Phongpaichit23, S.B. Pointing24, V. Pujade-Renaud25, H.A. Raja26, E. Rivas Plata10,27, B. Robbertse1, C. Ruibal28, J. Sakayaroj12, T. Sano8, L. Selbmann29, C.A. Shearer26, T. Shirouzu30, B. Slippers31, S. Suetrong12,23, K. Tanaka8, B. Volkmann-Kohlmeyer13, M.J. Wingfield31, A.R. Wood32, J.H.C. Woudenberg2, H. Yonezawa8, Y. Zhang24 and J.W. Spatafora17

1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, MSC 6510, Bethesda, Maryland 20892-6510, U.S.A.
2 CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, Netherlands
3 Department of Biological Sciences, Kean University, 1000 Morris Ave., Union, New Jersey 07083, U.S.A.
4 Biological Sciences, Murdoch University, Murdoch, 6150, Australia
5 Plant Protection Service, P.O. Box 9102, 6700 HC Wageningen, The Netherlands
6 USDA-ARS Systematic Mycology and Microbiology Laboratory, Beltsville, MD 20705, U.S.A.
7 Institute of Plant Sciences, Karl-Franzens-University of Graz, Austria
8 Faculty of Agriculture and Life Sciences, Hirosaki University, Bunkyo-cho 3, Hirosaki, Aomori 036-8561, Japan
9 National Museum of Nature and Science, Amakubo 4-1-1, Tsukuba, Ibaraki 305-0005, Japan
10 Department of Botany, The Field Museum, 1400 South Lake Shore Drive, Chicago, Illinois 60605-2496, U.S.A.
11 School 17 of Science, Mae Fah Luang University, Tasud, Muang, Chiang Rai 57100, Thailand
12 Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Paholyothin Road, Khlong 1, Khlong Luang, Pathum Thani, 12120, Thailand
13 Institute of Marine Sciences, University of North Carolina at Chapel Hill, Morehead City, North Carolina 28557, U.S.A.
14 Department of Systematic Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
15 Czech Collection of Mircroorganisms, Institute of Experimental Biology, Faculty of Science, Masaryk University, Tvrdého 14, Brno CZ-602 00, Czech Republic
16 College of Liberal Arts and Sciences, DePaul University, 1 E. Jackson Street, Chicago, Illinois 60604, U.S.A.
17 Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 U.S.A.
18 Illinois Natural History Survey, University of Illinois, 1816 South Oak St., Champaign, IL, 61820, U.S.A.
19 National Museums of Kenya, Botany Dept., P.O. Box 45166, 00100, Nairobi, Kenya
20 Committee on Evolutionary Biology, University of Chicago, 1025 E. 57th Street, Chicago, Illinois 60637, U.S.A.
21 University of Minnesota, Ecology, Evolution, and Behavior, 100 Ecology Building, St. Paul, MN 55108, U.S.A.
22 Centro de Recursos Microbiológicos, Departamento de Ciências da Vida, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829-516 Caparica, Portugal
23 Department of Microbiology, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
24 Division of Microbiology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P.R. China
25 CIRAD/PIAF, Université Blaise Pascal, Bâtiment Biologie Végétale Recherche, 24 avenue des Landais, BP 80026, 63177 Aubière, France
26 Department of Plant Biology, University of Illinois, 505 S. Goodwin Ave., Urbana, IL 61801, U.S.A.
27 Department of Biological Sciences, University of Illinois-Chicago, 845 West Taylor Street (MC 066), Chicago, Illinois 60607, U.S.A.
28 Departamento de Ingeniería y Ciencia de los Materiales, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid (UPM), José Gutiérrez Abascal 2, 28006 Madrid, Spain
29 DECOS, Università degli Studi della Tuscia, Largo dell'Università, Viterbo, Italy
30 Fungus/Mushroom Resource and Research Center, Tottori University, Minami 4-101, Koyama, Tottori, Tottori 680-8553 Japan
31 Forestry and Agricultural Biotechnology Institute (FABI), Centre of Excellence in Tree Health Biotechnology, Department of Genetics, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, 0002, South Africa
32 ARC – Plant Protection Research Institute, P. Bag X5017, Stellenbosch, 7599, South Africa
33 International Fungal Research Development Centre, The Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming, Yunnan, P.R. China

* Correspondence: Conrad L. Schoch, schoch2{at}ncbi.nlm.nih.gov

We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae is expanded to include the aquatic order Jahnulales. An ancestral reconstruction of basic nutritional modes supports numerous transitions from saprobic life histories to plant associated and lichenised modes and a transition from terrestrial to aquatic habitats are confirmed. Finally, 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.

Keywords Ascomycota / Pezizomycotina / Dothideomyceta / fungal evolution / lichens / multigene phylogeny / phylogenomics / plant pathogens / saprobes / Tree of Life




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