Genome-level analyses resolve an ancient lineage of symbiotic ascomycetes.

Ascomycota account for about two-thirds of named fungal species.1 Over 98% of known Ascomycota belong to the Pezizomycotina, including many economically important species as well as diverse pathogens, decomposers, and mutualistic symbionts.2 Our understanding of Pezizomycotina evolution has until now been based on sampling traditionally well-defined taxonomic classes.3,4,5 However, considerable diversity exists in undersampled and uncultured, putatively early-diverging lineages, and the effect of these on evolutionary models has seldom been tested. We obtained genomes from 30 putative early-diverging lineages not included in recent phylogenomic analyses and analyzed these together with 451 genomes covering all available ascomycete genera. We show that 22 of these lineages, collectively representing over 600 species, trace back to a single origin that diverged from the common ancestor of Eurotiomycetes and Lecanoromycetes over 300 million years BP. The new clade, which we recognize as a more broadly defined Lichinomycetes, includes lichen and insect symbionts, endophytes, and putative mycorrhizae and encompasses a range of morphologies so disparate that they have recently been placed in six different taxonomic classes. To test for shared hidden features within this group, we analyzed genome content and compared gene repertoires to related groups in Ascomycota. Regardless of their lifestyle, Lichinomycetes have smaller genomes than most filamentous Ascomycota, with reduced arsenals of carbohydrate-degrading enzymes and secondary metabolite gene clusters. Our expanded genome sample resolves the relationships of numerous "orphan" ascomycetes and establishes the independent evolutionary origins of multiple mutualistic lifestyles within a single, morphologically hyperdiverse clade of fungi.

Taxonomy of displaced species of Tubaria.

A taxonomic treatment of vinaceous and reddish species of Tubaria (Agaricales) is presented based on morphology and nucleotide sequences. Accessions from western North America, Europe, Central America, the Caribbean and Australia are compared. Phylogenetic analysis of the 25S rRNA gene and internal transcribed spacer (ITS) regions demonstrates that Tubaria is not monophyletic. However the autonomy of six brown-spored, saprotrophic species-Naucoria vinicolor, Pholiota serrulata, Phaeomarasmius confragosus, Pholiota punicea, Tubaria rufofulva and T. bispora sp. nov.-is affirmed. All six species form a strongly supported monophyletic group that we label section Confragosae in the genus Tubaria. This section is related to T. dispersa, T. albostipitata and numerous representatives of the T. furfuracea complex. Tubaria minima is related to other lineages of dark-spored Agaricales. Taxonomic descriptions, illustrations and a key to confirmed species of section Confragosae are provided. Four new combinations are proposed, and one new species, T. bispora, is described as new from Costa Rica and Martinique. A lectotype is designated for Pholiota serrulata.