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Phylogenomic analysis of the Neocallimastigomycota: Proposal of Caecomycetaceae fam. nov., Piromycetaceae fam. nov., and emended description of the families Neocallimastigaceae and Anaeromycetaceae

Radwa A. Hanafy, View ORCID ProfileYan Wang, Jason E. Stajich, Carrie J. Pratt, Noha H. Youssef, Mostafa H. Elshahed
doi: https://doi.org/10.1101/2022.07.04.498725
Radwa A. Hanafy
1Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK
2Department of Chemical & Biomolecular Engineering, University of Delaware, Newark DE, USA
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Yan Wang
3Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
4Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada
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Jason E. Stajich
5Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA.
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Carrie J. Pratt
1Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK
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Noha H. Youssef
1Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK
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Mostafa H. Elshahed
1Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK
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  • For correspondence: mostafa@okstate.edu
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Abstract

The anaerobic gut fungi (AGF) represent a coherent phylogenetic clade within the Mycota. Twenty genera have been described so far. Currently, the phylogenetic and evolutionary relationships between AGF genera remain poorly understood. Here, we utilized 53 transcriptomic datasets from 14 genera to resolve AGF inter-genus relationships using phylogenomics, and to provide a quantitative estimate (amino acid identity) for intermediate rank assignments. We identify four distinct supra-genus clades, encompassing genera producing polyflagellated zoospores, bulbous rhizoids, the broadly circumscribed genus Piromyces, and the Anaeromyces and affiliated genera. We also identify the genus Khoyollomyces as the earliest evolving AGF genus. Concordance between phylogenomic outputs and RPB1 and D/D2 LSU, but not RPB2, MCM7, or ITS1, phylogenies was observed. We combine phylogenomic analysis, and AAI outputs with informative phenotypic traits to propose accommodating 13/20 AGF genera into four families: Caecomycetaceae fam. nov. (encompassing genera Caecomyces and Cyllamyces), Piromycetaceae fam. nov. (encompassing the genus Piromyces), emend the description of fam. Neocallimastigaceae to only encompass genera Neocallimastix, Orpinomyces, Pecramyces, Feramyces, Ghazallomyces, and Aestipascuomyces, as well as the family Anaeromycetaceae to include the genera Oontomyces, Liebetanzomyces, and Capellomyces in addition to Anaeromyces. We refrain from proposing families for the deeply branching genus Khoyollomyces, and for genera with uncertain position (Buwchfawromyces, Joblinomyces, Tahromyces, Agriosomyces, Aklioshbomyces, and Paucimyces) pending availability of additional isolates and sequence data. Our results establish an evolutionary- grounded Linnaean taxonomic framework for the AGF, provide quantitative estimates for rank assignments, and demonstrate the utility of RPB1 as additional informative marker in Neocallimastigomycota taxonomy.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted July 04, 2022.
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Phylogenomic analysis of the Neocallimastigomycota: Proposal of Caecomycetaceae fam. nov., Piromycetaceae fam. nov., and emended description of the families Neocallimastigaceae and Anaeromycetaceae
Radwa A. Hanafy, Yan Wang, Jason E. Stajich, Carrie J. Pratt, Noha H. Youssef, Mostafa H. Elshahed
bioRxiv 2022.07.04.498725; doi: https://doi.org/10.1101/2022.07.04.498725
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Phylogenomic analysis of the Neocallimastigomycota: Proposal of Caecomycetaceae fam. nov., Piromycetaceae fam. nov., and emended description of the families Neocallimastigaceae and Anaeromycetaceae
Radwa A. Hanafy, Yan Wang, Jason E. Stajich, Carrie J. Pratt, Noha H. Youssef, Mostafa H. Elshahed
bioRxiv 2022.07.04.498725; doi: https://doi.org/10.1101/2022.07.04.498725

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