ABI Innovation: New Software Tools for Genome Comparisons of Non-Model Organisms

ABI Innovation：用于非模式生物基因组比较的新软件工具

• 批准号: 1619983
• 负责人: Jian Ma
• 金额: $ 55.42万
• 依托单位: Carnegie-Mellon University
• 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: 2016-01-01 至 2018-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1619983&HistoricalAwards=false
• 关键词: ABI; Innovation; New; Software; Tools

Recent advances in high-throughput sequencing technologies have allowed study of the genomes of many more non-model organisms. The comparisons of these genomes will provide new insights into the evolution of complex traits of different species. This project will develop new methods to compare more than ten new bee genomes to help elucidate the molecular signatures of eusociality using evolutionary genomics. Eusocial species have different levels of social organization while related species are solitary, providing an ideal "ladder" of species to study the evolution of social life. The genetic basis for such phenotypes has remained largely unexplored until very recently. In this research, new tools will be developed to better annotate the gene models by incorporating both RNA-seq data and information from genome sequences of related organisms. The method will fully utilize splice variants when annotating the gene models. Methods will also be developed to build high-quality cross-species sequence alignments for both coding and non-coding regions in the bee genomes. Additionally, errors in the original genome assemblies will be corrected to improve quality. Insights from this project can be applied to other species and clades as the data becomes available.This research involves interactions between computational and experimental biologists. The project will develop computational biology curricula and train graduate students in interdisciplinary research methods. The research developed in this project will be integrated into existing outreach programs (such as the G.A.M.E.S. camp and the SING workshop at the University of Illinois) to encourage undergraduate students to pursue careers in science and engineering. The tools and data produced in the project will be made available through a project website.

高通量测序技术的最新进展使得我们能够研究更多非模式生物的基因组。这些基因组的比较将为不同物种复杂性状的进化提供新的见解。该项目将开发新方法来比较十多个新的蜜蜂基因组，以帮助利用进化基因组学阐明真社会性的分子特征。真社会性物种具有不同层次的社会组织，而相关物种是孤独的，为研究社会生活的进化提供了理想的物种“阶梯”。直到最近，这种表型的遗传基础在很大程度上仍未得到探索。在这项研究中，将开发新工具，通过整合 RNA-seq 数据和相关生物体基因组序列的信息来更好地注释基因模型。该方法在注释基因模型时将充分利用剪接变体。还将开发方法来为蜜蜂基因组中的编码区和非编码区建立高质量的跨物种序列比对。此外，原始基因组组装中的错误将被纠正以提高质量。当数据可用时，该项目的见解可以应用于其他物种和分支。这项研究涉及计算生物学家和实验生物学家之间的相互作用。该项目将开发计算生物学课程并培训研究生跨学科研究方法。该项目开发的研究将整合到现有的推广计划（例如伊利诺伊大学的 G.A.M.E.S. 营和 SING 研讨会）中，以鼓励本科生从事科学和工程领域的职业。该项目产生的工具和数据将通过项目网站提供。