Genomics of Anaerobic Cellulose-Degrading Fungal Symbionts of the Herbivore Gut

As highly proficient degraders of cellulose, the Neocallimastigomycota fungi are key members of the microbiota of large mammalian and reptilian herbivores. Their remarkable cellulolytic capabilities have great potential for use in biofuel processing. They differ from other fungi 1) in possessing an extracellular cellulose-degrading complex called a fungal cellulosome, 2) in being obligate anaerobes, with hydrogenosomes instead of mitochondria, and 3) in developing flagella in certain life stages, placing them near the base of fungal phylogenies. All these distinctive characteristics touch on areas of intense interest to the US Dept. of Energy (DOE) Joint Genome Institute (JGI), including bioenergy, biotechnology, carbon cycling, fungal evolution, and symbiosis. The genomes of these interesting and important fungi are very AT-rich and highly repetitive, posing challenges to their genomic investigation. We have deployed PacBio long-read technology to overcome these challenges and to sequence, assemble, and annotate 3 Neocallimastigomycota genomes. We found modest numbers of genes (11-13k per genome) and gene families (< 1k clade-specific clusters), and confirmed low GC-content (< 25%), high repeat content (> 50%), absence of many aerobiosis-related genes (> 30 Core Eukaryotic Genes), and near-basal location in the fungal tree (branching with flagellated but aerobic Chytridiomycota). We are now using the genome to complement recent progress in elucidating the cellulosome using non-genome-based biochemical, proteomic, and transcriptomic methods.