Phylogenomics of zygomycete fungi: impacts on a phylogenetic classification of Kingdom Fungi

Authors: WHITE, M - Oregon State University; SPATAFORA, J - Oregon State University; STAJICH, J - University Of California; BENNY, G - University Of Florida; SMITH, M - University Of Florida; LAZARUS, K - University Of Florida; BERBEE, M - University Of British Columbia; BONITO, G - Michigan State University; CORRADI, N - University Of Ottawa; O Donnell, Kerry

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 7/29/2015
Publication Date: 7/29/2015
Citation: White, M.M., Spatafora, J.W., Stajich, J.E., Benny, G., Smith, M.E., Lazarus, K., Berbee, M., Bonito, G., Corradi, N., O'Donnell, K. 2015. Phylogenomics of zygomycete fungi: impacts on a phylogenetic classification of Kingdom Fungi[abstract].

Interpretive Summary:

Technical Abstract: The zygomycetous fungi (”zygomycetes”) mark the major transition from zoosporic life histories of the common ancestor of Fungi and the earliest diverging chytrid lineages (Chytridiomycota and Blastocladiomycota). Their ecological and economic importance range from the earliest documented symbionts of the first land plants (e.g., arbuscular mycorrhizal fungi), to symbionts and pathogens of animals (e.g., “Trichomycetes”, Entomophthorales), to modern uses in industrial biology (e.g., fermentation by Rhizopus). Despite their importance, however, an accurate understanding of evolutionary relationships of “zygomycetes” lags behind that of Dikarya. To better document the diversity and evolution of “zygomycetes” we have initiated a large collaborative research project, Zygomycete Genealogy of Life (ZyGoLife) . ZyGoLife is building a phylogenomic framework to address questions in genomic and morphological evolution that pertain to the transition to the fungal phenotypes characteristic of terrestrial fungi. We are employing broad-scale genome and transcriptome sampling of zygomycete lineages including host-associated species, incorporation of fossil based dating, bioimaging of subcellular characters, improved tools for environmental sampling, and descriptions of these fungi in the Encyclopedia of Life. “Zygomycetes” have been classified both as a single monophyletic group (Zygomycota) and a series of unresolved, paraphyletic lineages (up to six subphyla). Genome data were used to evaluate the phylogenetic position of these lineages and to compare gene content and phylogenetic relationships among thousands of groups of orthologous genes with animal and zoosporic fungal outgroups and Dikarya. Initial sampling and phylogenetic analyses of more than 35 zygomycete genomes have provided substantial support for two monophyletic clades of “zygomycetes”: one comprising Entomophthoromycota, Kickxellomycotina, and Zoopagomycotina (EKZ clade) and the other consisting of Mortierellomycotina, Mucoromycotina, and Glomeromycota (MMG clade). Importantly, these results reject the recognition of a monophyletic “zygomycetes”. The primarily animal-associated and mycoparasitic EKZ clade is resolved as the earliest diverging lineage of “zygomycetes” and the primarily plant-associated MMG clade is resolved as sharing a more recent common ancestor with Dikarya. A phylogenetic classification of the MMG and EKZ clades will be discussed.