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

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.

Patterns and determinants of the global herbivorous mycobiome

“…Khoyollomyces and associated genera (AL3 and NY54) to members of the Equidae [6,67,68], as well as the general basal position of additional hindgutpreferring genera, e.g. Piromyces (41)(42)(43)(44)(45)(46)(47)(48)(49)(50)(51)(52)(53)(54)(55) and Paucimyces (38)(39)(40)(41)(42)(43)(44)(45)(46)(47)(48)(49)(50). This is in agreement with the fact that early mammals roaming the Earth past the K-Pg boundary (~65.5 Mya) were hindgut fermenters.…”

“…Phylogenetically, 32 of the novel lineages identified clustered within the 4 recently proposed families in the Neocallimastigomycota [41], with 13, 7, 9, and 3 genera clustering with the families Neocallimastigaceae, Caecomycetaceae, Anaeromycetaceae , and Piromycetaceae , respectively). Another 17 novel genera formed additional 4 well-supported family-level clusters with orphan cultured genera (5, 4, 5, and 3 novel genera forming family-level clusters with the orphan genera Joblinomyces, Buwchfawromyces-Tahromyces, Aklioshbomyces , and Khoyollomyces , respectively).…”

“…Here, we added 20 transcriptomes from 7 additional genera, isolated during a long term multi-year isolation effort in the authors laboratory [26,28], and included an extra 11 publicly available transcriptomic datasets [37][38][39][40]. The dataset of 52 transcriptomes was used for phylogenomic analysis as described in [41]. For RNA extraction, cultures grown in rumen fluid-cellobiose medium [74] were vacuum filtered then grounded with a pestle under liquid nitrogen.…”

Patterns and determinants of the global herbivorous mycobiome

“…Phylogenetically, 32 of the novel lineages identi ed clustered within the 4 recently proposed families in the Neocallimastigomycota [41], with 13, 7, 9, and 3 genera clustering with the families Neocallimastigaceae, Caecomycetaceae, Anaeromycetaceae, and Piromycetaceae, respectively). Another 17 novel genera formed additional 4 well-supported family-level clusters with orphan cultured genera (5, 4, 5, and 3 novel genera forming family-level clusters with the orphan genera Joblinomyces, Buwchfawromyces-Tahromyces, Aklioshbomyces, and Khoyollomyces, respectively).…”

“…Khoyollomyces and associated genera (AL3 and NY54) to members of the Equidae [6, 67, 68], as well as the general basal position of additional hindgutpreferring genera, e.g. Piromyces (41)(42)(43)(44)(45)(46)(47)(48)(49)(50)(51)(52)(53)(54)(55) and Paucimyces (38-50 Mya). This is in agreement with the fact that early mammals roaming the Earth past the K-Pg boundary (~ 65.5 Mya) were hindgut fermenters.…”