Reconstructing 700 Million Years of the Evolution of Genome Organization: Tools and Community Resources

重建基因组组织 7 亿年的进化：工具和社区资源

• 批准号: 0850294
• 负责人: Nicholas Putnam
• 金额: $ 93.35万
• 依托单位: William Marsh Rice University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-01 至 2013-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0850294&HistoricalAwards=false
• 关键词: Reconstructing; 700; Million; Years; Evolution

This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5). Researchers at Rice University have been awarded a grant for an interdisciplinary project in software development, evolutionary biology and comparative genomics that will create new computational methods and web-based resources for comparing and interpreting how genes are organized in the chromosomes of humans, other animals, plants and other complex organisms. Biologists studying the large-scale organization of genomes -- the arrangement of genes on chromosomes -- recently discovered that species that had diverged more than 500 million years ago still have genomes that are organized in similar ways. It is not known whether the conservation is due to a very slow decay of a neutral feature of genome organization, or due to the action of selection through an unknown functional link between genome organization and phenotype. The project will take two new approaches to the problem. The first approach uses a heuristic search procedure to identify the most parsimonious historical scenario explaining the data. The second approach uses Bayesian Markov-chain Monte Carlo to estimate the probabilities of historical scenarios given a model of genome evolution. The tools and databases created by this project will allow scientists to more easily compare and contrast the structure of genomes. In particular, the tools will allow scientists to do side-by-side studies of both modern and reconstructed ancient genomes. By comparing and contrasting the organizational structure of genomes, scientists hope to better understand evolution, biodiversity and the mechanisms species use to fight stress and disease. This project will provide interdisciplinary training in software development, evolutionary biology and comparative genomics to the researchers and students who participate. The web-based interface to the results will be used as a source of projects and exercises in an undergraduate course in evolution and bioinformatics taught by the project leader. To learn more about this project, including the most recent progress, visit the project web site at http://putnamlab.org/genome-evolution.

该奖项是根据2009年美国复苏和再投资法案（公法111-5）资助的。莱斯大学的研究人员获得了一笔赠款，用于软件开发，进化生物学和比较基因组学的跨学科项目，该项目将创建新的计算方法和基于网络的资源，用于比较和解释基因如何在人类，其他动物，植物和其他复杂生物体的染色体中组织。 研究基因组大规模组织（染色体上基因的排列）的生物学家最近发现，5亿多年前分化的物种仍然有以类似方式组织的基因组。目前尚不清楚这种保守性是由于基因组结构的中性特征非常缓慢的衰减，还是由于通过基因组结构和表型之间未知的功能联系进行的选择作用。该项目将采取两种新的方法来解决这个问题。第一种方法使用启发式搜索过程来确定最简约的历史情景解释的数据。第二种方法使用贝叶斯马尔可夫链蒙特卡罗估计的概率，给定的基因组进化模型的历史情景。该项目创建的工具和数据库将使科学家能够更容易地比较和对比基因组的结构。特别是，这些工具将允许科学家对现代和重建的古代基因组进行并行研究。 通过比较和对比基因组的组织结构，科学家们希望更好地了解进化、生物多样性以及物种用来对抗压力和疾病的机制。 该项目将为参与的研究人员和学生提供软件开发、进化生物学和比较基因组学方面的跨学科培训。基于网络的结果界面将被用作项目和练习的来源，在进化和生物信息学的本科课程由项目负责人教。要了解有关此项目的更多信息，包括最新进展，请访问项目网站http://putnamlab.org/genome-evolution。