Comparative genomics and phylogenomic investigation of the class Geoglossomycetes provide insights into ecological specialization and the systematics of Pezizomycotina

Melie T., Pirro S., Miller A.N., Smith S.D., Schutz K.S. & Quandt C.A.
115(4): 499‒512
Despite their global presence and ubiquity, members of the class Geoglossomycetes (Pezizomycotina, Ascomycota) are understudied systematically and ecologically. These fungi have long been presumed saprobic due to their occurrence in or near leaf litter and soils. Additionally, they lack an apparent association with other organisms, reinforcing this perception. However, observations of sporocarps near ericaceous shrubs have given rise to an alternative hypothesis that members of Geoglossomycetes may form ericoid mycorrhizae or ectomycorrhizae. This claim, however, has yet to be confirmed via microscopy or amplicon-based studies examining root communities. As a result, our current understanding of their ecology is based on cursory observations. This study presents a comparative analysis of genomic signatures related to ecological niche to investigate the hypothesis of an ericoid mycorrhizal or ectomycorrhizal ecology in the class. We compared the carbohydrate-active enzyme (CAZyme) and secondary metabolite contents of six newly sequenced Geoglossomycetes genomes with those of fungi representing specific ecologies across Pezizomycotina. Our analysis reveals CAZyme and secondary metabolite content patterns consistent with ectomycorrhizal (EcM) members of Pezizomycotina. Specifically, we found a reduction in CAZyme-encoding genes and secondary metabolite clusters that suggests a mutualistic ecology. Our work includes the broadest taxon sampling for a phylogenomic study of Pezizomycotina to date. It represents the first functional genomic and genome-scale phylogenetic study of the class Geoglossomycetes and improves the foundational knowledge of the ecology and evolution of these understudied fungi. Keywords: Ascomycota; concordance; gene tree conflict; Geoglossaceae; metagenome; mutualism; mycorrhizae. p. 503: "All relationships within the classes were resolved with high support. Lichinomycetes plus Coniocybomycetes were recovered as the sister group of Geoglossomycetes, with Xylonomycetes closely related to these three (FIG. 1)."; "Hierarchical clustering resulted in Geoglossomycetes grouping with both EcM and lichenized fungi due to shared contractions in many CAZyme families (FIG. 3)."
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