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

厌氧肠道真菌（AGF）与所有其他真菌群的不同之处在于具有有限的栖息地（瘤胃和食草动物的消化道），并且在缺乏大气氧气的情况下生长。它们在数亿年前进化而来，是最古老的真菌类群之一。然而，厌氧真菌的进化历史目前尚不清楚。具体来说，厌氧真菌和其他真菌群之间的确切关系，以及导致它们被隔离到食草性肠道中的事件的时间和顺序仍然不清楚。此外，尚不清楚厌氧真菌在食草性肠道中的保留如何影响它们的基因组和进化。该项目将通过对大量不同的厌氧真菌的基因组进行测序，并使用广泛的计算程序分析产生的数据来解决这些问题。该项目将吸引多名高中和本科生参与研究，并特别努力吸引少数民族（特别是美洲原住民）学生参与，以促进代表性不足的群体参与STEM学科。
厌氧真菌的总体研究进展缓慢，AGF基因组测序受到其极高AT含量和基因组中基因间重复序列增殖的阻碍。该项目将利用一种新的方法，结合多种测序技术，对大量不同的厌氧真菌分离株的基因组和转录组进行测序。这项研究将利用所产生的数据进行广泛的真菌基因组分析，旨在解决它们在真菌生命树中的进化历史，将AGF多样化事件的时间与其草食性宿主的进化相关联，解决厌氧真菌属的多样化模式，并调查独特的栖息地和进化轨迹对其基因组结构的影响。这些努力将导致对这一特殊真菌群的历史和推动其进化的因素的理解取得重大进展。此外，所获得的基因组和转录组数据将对在生物燃料研究、动物营养和真菌分子生物学领域工作的更广泛的科学家群体产生极大的兴趣。

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.