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

该奖项是根据2009年《美国复苏和再投资法案》(公法111-5)提供资金的。莱斯大学的研究人员获得了软件开发、进化生物学和比较基因组学跨学科项目的资助，该项目将创造新的计算方法和基于网络的资源，用于比较和解释基因在人类、其他动物、植物和其他复杂生物的染色体中的组织方式。研究大规模基因组组织--基因在染色体上的排列--的生物学家最近发现，5亿多年前分化的物种仍然有以相似方式组织的基因组。目前尚不清楚这种保守是由于基因组组织的中性特征非常缓慢的衰退，还是由于通过基因组组织和表型之间未知的功能联系进行选择的作用。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程序来确定解释数据的最简约的历史情景。第二种方法使用贝叶斯马尔可夫链蒙特卡罗来估计给定基因组进化模型的历史情景的概率。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排研究。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。结果的网络界面将作为项目负责人讲授的进化论和生物信息学本科课程中的项目和练习来源。要了解有关该项目的更多信息，包括最新进展，请访问该项目的网站http://putnamlab.org/genome-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.