Genome-scale phylogeny and comparative genomics of the fungal order Sordariales.

The order Sordariales is taxonomically diverse, and harbours many species with different lifestyles and large economic importance. Despite its importance, a robust genome-scale phylogeny, and associated comparative genomic analysis of the order is lacking. In this study, we examined whole-genome data from 99 Sordariales, including 52 newly sequenced genomes, and seven outgroup taxa. We inferred a comprehensive phylogeny that resolved several contentious relationships amongst families in the order, and cleared-up intrafamily relationships within the Podosporaceae. Extensive comparative genomics showed that genomes from the three largest families in the dataset (Chaetomiaceae, Podosporaceae and Sordariaceae) differ greatly in GC content, genome size, gene number, repeat percentage, evolutionary rate, and genome content affected by repeat-induced point mutations (RIP). All genomic traits showed phylogenetic signal, and ancestral state reconstruction revealed that the variation of the properties stems primarily from within-family evolution. Together, the results provide a thorough framework for understanding genome evolution in this important group of fungi.

The taxonomy of the model filamentous fungus Podospora anserina.

The filamentous fungus Podospora anserina has been used as a model organism for more than 100 years and has proved to be an invaluable resource in numerous areas of research. Throughout this period, P. anserina has been embroiled in a number of taxonomic controversies regarding the proper name under which it should be called. The most recent taxonomic treatment proposed to change the name of this important species to Triangularia anserina. The results of past name changes of this species indicate that the broader research community is unlikely to accept this change, which will lead to nomenclatural instability and confusion in literature. Here, we review the phylogeny of the species closely related to P. anserina and provide evidence that currently available marker information is insufficient to resolve the relationships amongst many of the lineages. We argue that it is not only premature to propose a new name for P. anserina based on current data, but also that every effort should be made to retain P. anserina as the current name to ensure stability and to minimise confusion in scientific literature. Therefore, we synonymise Triangularia with Podospora and suggest that either the type species of Podospora be moved to P. anserina from P. fimiseda or that all species within the Podosporaceae be placed in the genus Podospora.

Molecular phylogeny of Sydowiellaceae--resolving the position of Cainiella.

Cainiella is an ascomycete genus associated with arctic alpine plants. The systematic position of Cainiella has long been unclear, with current classifications placing the genus in either Sordariales or Xylariales. Our molecular results, based on mtSSU, ITS and nLSU rDNA data, clearly show that the genus belongs in the Sydowiellaceae (Diaporthales). The study also includes new sequences of Sydowiellaceae and contributes to a better knowledge of the phylogenetic relationships of that family.

Phylogenetic relationships of coprophilous Pleosporales (Dothideomycetes, Ascomycota), and the classification of some bitunicate taxa of unknown position.

The purpose of this study was to investigate the natural relationships within the large bitunicate order Pleosporales, with special focus on the coprophilous families Delitschiaceae, Phaeotrichaceae and Sporormiaceae. Parsimony and Bayesian analyses were performed using nSSU, nLSU and mtSSU rDNA sequence data. We also investigated the placement of a number of taxa with uncertain position. Our results showed that Pleosporales, including Delitschiaceae, Sporormiaceae, Zopfiaceae and Testudinaceae, form a monophyletic group with strong support. Although Delitschiaceae has been considered a synonym of Sporormiaceae, the two families do not form one monophyletic group. Similarly, Zopfiaceae and Testudinaceae should be retained as separate families as they did not group together or with Phaeotrichaceae or Sporormiaceae. Zopfiaceae and Delitchiaceae did group together, but without significant support. Eremodothis angulata (currently in Testudinaceae) is closely related to Westerdykella in Sporormiaceae. Phaeotrichaceae and Venturiaceae formed a group with strong BS support on a branch outside Pleosporales, but an alternative topology including Phaeotrichaceae and Venturiaceae within Pleosporales could not be rejected. All taxa in the present study that were placed with uncertain position in Dothideomycetes/Chaetothyriomycetes in the current classification by Eriksson, grouped within the monophyletic Dothideomycetes.