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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. © 2009 CBS-KNAW Fungal Biodiversity Centre.

We present an expanded multigene phylogeny of the Dothideomycetes. The final data matrix consisted of four loci (nuc SSU rDNA, nuc LSU rDNA, TEF1, RPB2) for 96 taxa, representing five of the seven orders in the current classification of Dothideomycetes and several outgroup taxa representative of the major clades in the Pezizomycotina. The resulting phylogeny differentiated two main dothideomycete lineages comprising the pseudoparaphysate Pleosporales and aparaphysate Dothideales. We propose the subclasses Pleosporomycetidae (order Pleosporales) and Dothideomycetidae (orders Dothideales, Capnodiales and Myriangiales). Furthermore we provide strong molecular support for the placement of Mycosphaerellaceae and Piedraiaceae within the Capnodiales and introduce Davidiellaceae as a new family to accommodate species of Davidiella with Cladosporium anamorphs. Some taxa could not be placed with certainty (e.g. Hysteriales), but there was strong support for new groupings. The clade containing members of the genera Botryosphaeria and Guignardia resolved well but without support for any relationship to any other described orders and we hereby propose the new order Botryosphaeriales. These data also are consistent with the removal of Chaetothyriales and Coryneliales from the Dothideomycetes and strongly support their placement in the Eurotiomycetes.

Phylogenetic analysis of partial ribosomal DNA sequences was undertaken to assess the phylogenetic distribution of ophiostomatoid anamorphs with an emphasis on members of Leptographium and the generic limits of Ceratocystis sensu lato Ell. & Halst. Molecular data identified one group of Ophiostoma species with anamorphs assignable to Pesotum and Leptographium that appears to be monophyletic. This study also showed that, based on molecular characters, Pesotum pini (Hutchison & Reid) Okada and all Leptographium strains tested, including L. terebrantis Barras & Perry, L. lundbergii Lag. & Melin, and L. procerum (Kendr.) Wingf., could be placed among Ophiostoma species. With regard to the anamorphs of Ophiostoma, we determined that the separation of Leptographium from Pesotum, although convenient, is artificial. The partial ribosomal DNA sequences also confirm that Europhium should be considered a synonym of Ophiostoma. The phylogenetic position of species of Ceratocystis sensu lato with Chalara-like, Knoxdaviesia, and Gabarnaudia anamorphs is also discussed.