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

合作研究：厌氧真菌类群 Neocallimastigomycota 的系统发育学和进化史

• 批准号: 1557110
• 负责人: Jason Stajich
• 金额: $ 31.76万
• 依托单位: University of California-Riverside
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-04-01 至 2020-03-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1557110&HistoricalAwards=false
• 关键词: Collaborative; Research; Phylogenomics; evolutionary; history

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.

厌氧肠道真菌（AGF）与所有其他真菌群体不同，它具有受限制的栖息地（食草动物的瘤胃和消化道），并且在没有大气氧气的情况下生长。他们已经发展了数亿年前，代表了最古老的真菌群体之一。但是，目前尚不清楚厌氧菌真菌的进化史。具体而言，厌氧菌真菌与其他真菌群之间的确切关系，以及导致它们隔离为草食性肠道的时机和序列尚不清楚。此外，尚不清楚厌氧真菌在草食性肠道中的保留如何影响其基因组和进化。该项目将通过对大量，多样化的厌氧菌真菌的基因组进行测序，并分析使用广泛的计算程序产生的数据来解决这些问题。该项目将与多个高中和本科生一起参与研究，并特别努力吸引少数群体（尤其是美国原住民）学生，以推动代表性不足的群体参与STEM学科。厌氧菌真菌的总体研究进展很慢，并且对AGF基因组的测序受到其在含量极高的含量和基因组中基因间重复序列的增殖的阻碍。该项目将利用一种结合多个测序技术的新方法来对大量厌氧真菌分离株集合的基因组和转录组进行测序。这项研究将利用生成的数据进行广泛的系统基因组分析，旨在解决其在生命真菌树中的进化历史，将AGF多样化事件的时机与草药宿主的演变相关联，解决厌氧真菌属的多元化模式，并研究其独特的栖息地和进化型的影响。拟议的努力将在理解这种奇特的真菌群体和推动其进化的因素方面取得重大进展。此外，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对获得的基因组和转录组数据将引起极大的兴趣。

项目成果

Fungal Genomes and Insights into the Evolution of the Kingdom.

• DOI: 10.1128/microbiolspec.funk-0055-2016
• 发表时间: 2017-07
• 期刊: Microbiology spectrum
• 影响因子: 3.7
• 作者: Stajich JE