Comparative genomics and divergence time estimation of the anaerobic fungi in herbivorous mammals

Abstract

The anaerobic gut fungi (AGF) or Neocallimastigomycota inhabit the rumen and alimentary tract of herbivorous mammals, where they play an important role in the degradation of plant fiber. Comparative genomic and phylogenomic analysis of the AGF has long been hampered by their fastidious growth pattern as well as their large and AT-biased genomes. We sequenced 21 AGF transcriptomes and combined them with 5 available genome sequences of AGF taxa to explore their evolutionary relationships, time their divergence, and characterize patterns of gene gain/loss associated with their evolution. We estimate that the most recent common ancestor of the AGF diverged 66 ({+/-}10) million years ago, a timeframe that coincides with the evolution of grasses (Poaceae), as well as the mammalian transition from insectivory to herbivory. The concordance of these independently estimated ages of AGF evolution, grasses evolution, and mammalian transition to herbivory suggest that AGF have been important in shaping the success of mammalian herbivory transition by improving the efficiency of energy acquisition from recalcitrant plant materials. Comparative genomics identified multiple lineage-specific genes and protein domains in the AGF, two of which were acquired from an animal host (galectin) and rumen gut bacteria (carbohydrate-binding domain) via horizontal gene transfer (HGT). Four of the bacterial derived "Cthe_2159" genes in AGF genomes also encode eukaryotic Pfam domains ("Atrophin-1", "eIF-3_zeta", "Nop14", and "TPH") indicating possible gene fusion events after the acquisition of "Cthe_2159" domain. A third AGF domain, plant-like polysaccharide lyase N-terminal domain ("Rhamnogal_lyase"), represents the first report from fungi that potentially aids AGF to degrade pectin. Analysis of genomic and transcriptomic sequences confirmed the presence and expression of these lineage-specific genes in nearly all AGF clades supporting the hypothesis that these laterally acquired and novel genes in fungi are likely functional. These genetic elements may contribute to the exceptional abilities of AGF to degrade plant biomass and enable metabolism of the rumen microbes and animal hosts.