Collaborative Research: Phylogenomics and evolutionary history of the anaerobic fungal group, Neocallimastigomycota

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The anaerobic gut fungi (AGF) differ from all other groups of fungi by having a restricted habitat (the rumen and alimentary tract of herbivores), and by growing in the absence of atmospheric oxygen. They have evolved hundreds of millions of years ago and represent one of the oldest fungal groups. However, the evolutionary history of anaerobic fungi is currently unclear. Specifically, the exact relationship between anaerobic fungi and other fungal groups, as well as the timing and sequence of events that lead to their sequestration into the herbivorous gut remain unclear. Further, it is not exactly known how the retention of anaerobic fungi in the herbivorous gut has affected their genomes and evolution. This project will tackle these questions by sequencing the genomes of a large, diverse collection of anaerobic fungi, and analyzing the data produced using a wide range of computational procedures. The project will engage multiple high school and undergraduate students in research, with special effort to engage minority (especially Native American) students to advance the participation of underrepresented groups in STEM disciplines. 
Overall research progress on anaerobic fungi has been slow, and sequencing of AGF genomes has been hampered by their extremely high AT content and the proliferation of intergenic repeats in their genomes. This project will utilize a new approach that combines multiple sequencing technologies to sequence the genomes and transcriptomes of a large and diverse collection of anaerobic fungal isolates. This research will utilize the data generated to conduct an extensive phylogenomic analysis, aiming to resolve their evolutionary history within the fungal tree of life, correlate the timing of AGF diversification events to the evolution of their herbivorous hosts, resolve the diversification pattern of anaerobic fungal genera, and investigate the impact of the unique habitat and evolutionary trajectory on their genomic architecture. The proposed efforts will lead to significant advances in the understanding of the history of this peculiar group of fungi and factors driving their evolution. Further, the genomic and transcriptomic data obtained would be of extreme interest to a broader group of scientists working in the areas of biofuel research, animal nutrition, and molecular biology of fungi.