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

厌氧肠道真菌在两个方面与所有其他真菌不同：它们在缺乏氧气的环境中生长，以及它们在受限的栖息地(以植物为食的动物的瘤胃和消化道)生长。它们在数亿年前进化，代表着最古老的真菌群之一，但它们的进化史尚不清楚。具体地说，厌氧真菌与其他真菌群之间的确切关系，以及导致它们定位到肠道栖息地的事件的时间和序列仍不清楚。此外，目前还不清楚肠道栖息地是如何影响它们的基因组和进化的。这个项目将通过对大量不同的厌氧肠道真菌的基因组进行排序，并使用广泛的计算程序分析产生的数据来解决这些问题。拟议的努力将导致在理解这一特殊真菌群体的历史和推动它们进化的因素方面取得重大进展。此外，所获得的数据将对更多在生物燃料研究、动物营养和真菌分子生物学领域工作的科学家产生极大的兴趣。该项目将吸引多名高中生和本科生参与研究，特别是努力吸引少数族裔(特别是美国原住民)学生，以促进未被充分代表的群体参与科学、技术和数学学科。厌氧真菌的研究总体上进展缓慢，而厌氧肠道真菌(AGF)基因组的测序一直受到腺嘌呤-胸腺嘧啶含量极高和基因组中基因间重复序列增殖的阻碍。这个项目将利用一种新的方法，结合多种测序技术来对大量和多样化的厌氧真菌分离物的基因组和转录本进行排序。这项研究将利用所产生的数据进行广泛的系统基因组分析，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宿主的进化联系起来，解决厌氧真菌属的多样性格局，并调查独特的生境和进化轨迹对其基因组结构的影响。

The anaerobic gut fungi differ from all other groups of fungi in two ways: they grow in the absence of oxygen, and they grow in a restricted habitat (the rumen and alimentary tract of plant eating animals). They evolved hundreds of millions of years ago and represent one of the oldest fungal groups, yet their evolutionary history is 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 localization to a gut habitat, remains unclear. Further, it is not exactly known how the gut habitat has affected their genomes and evolution. This project will tackle these questions by sequencing the genomes of a large, diverse collection of anaerobic gut fungi, and analyzing the data produced using a wide range of computational procedures. 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 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. 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 science, technology, and math disciplines. Overall research progress on anaerobic fungi has been slow, and sequencing of anaerobic gut fungi (AGF) genomes has been hampered by their extremely high adenine-thymine 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.