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. 2009:64:1-15S10.
doi: 10.3114/sim.2009.64.01.

A class-wide phylogenetic assessment of Dothideomycetes

C L Schoch  1 , P W Crous, J Z Groenewald, E W A Boehm, T I Burgess, J de Gruyter, G S de Hoog, L J Dixon, M Grube, C Gueidan, Y Harada, S Hatakeyama, K Hirayama, T Hosoya, S M Huhndorf, K D Hyde, E B G Jones, J Kohlmeyer, A Kruys, Y M Li, R Lücking, H T Lumbsch, L Marvanová, J S Mbatchou, A H McVay, A N Miller, G K Mugambi, L Muggia, M P Nelsen, P Nelson, C A Owensby, A J L Phillips, S Phongpaichit, S B Pointing, V Pujade-Renaud, H A Raja, E Rivas Plata, B Robbertse, C Ruibal, J Sakayaroj, T Sano, L Selbmann, C A Shearer, T Shirouzu, B Slippers, S Suetrong, K Tanaka, B Volkmann-Kohlmeyer, M J Wingfield, A R Wood, J H C Woudenberg, H Yonezawa, Y Zhang, J W Spatafora
Affiliations

A class-wide phylogenetic assessment of Dothideomycetes

C L Schoch et al. Stud Mycol. 2009.

Abstract

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; Dothideomyceta; Pezizomycotina; Tree of Life; fungal evolution; lichens; multigene phylogeny; phylogenomics; plant pathogens; saprobes.

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Figures

Fig. 1.
Fig. 1.
Dothidea sambuci. A–B. Appearance of ascomata on the host surface. C, F. Asci in cotton blue reagent. D. Vertical section through ascomata illustrating the mutilocule at the upper layer. E. Vertical section through ascomata in cotton blue reagent illustrating the locule. G–H. Ascospores in cotton blue reagent. Scale bars: B = 1000 μm; C = 500 μm; E = 100 μm; F–H = 10 μm.
Fig. 2A–C.
Fig. 2A–C.
Best scoring ML tree with RAxML and GARLI bootstrap values respectively above (green) and below (red) the nodes. Values below 50 % were removed and branches with more than 90 % bootstrap for both methods are thickened without values. Environmental sources relevant to the papers in this volume are indicated in the key (R-Rock; M-Marine; F-Freshwater; D-Dung; B-Bamboo). Nutritional characters are indicated by colour as per the key.
Fig. 2A–C.
Fig. 2A–C.
Best scoring ML tree with RAxML and GARLI bootstrap values respectively above (green) and below (red) the nodes. Values below 50 % were removed and branches with more than 90 % bootstrap for both methods are thickened without values. Environmental sources relevant to the papers in this volume are indicated in the key (R-Rock; M-Marine; F-Freshwater; D-Dung; B-Bamboo). Nutritional characters are indicated by colour as per the key.
Fig. 2A–C.
Fig. 2A–C.
Best scoring ML tree with RAxML and GARLI bootstrap values respectively above (green) and below (red) the nodes. Values below 50 % were removed and branches with more than 90 % bootstrap for both methods are thickened without values. Environmental sources relevant to the papers in this volume are indicated in the key (R-Rock; M-Marine; F-Freshwater; D-Dung; B-Bamboo). Nutritional characters are indicated by colour as per the key.
Fig. 3.
Fig. 3.
Simplified ancestral state reconstructions, showing potential transitions between character states. The same phylogeny as in Fig. 2A–C is shown, with the outgroups positioned at twelve o' clock and subsequent clades arranged in a clockwise manner. Characters were traced over 2 000 bootstrap trees and those that were recovered in the majority are coloured on the nodes. In the case of equivocal construction no colour was used (white). To simplify the figure, only clades with two or more neighbouring character states are shown.
Fig. 4.
Fig. 4.
Pie chart showing relative numbers of unique proteins per genome according to taxonomic classification.
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