Gene Duplication and Genome Evolution

基因复制和基因组进化

• 批准号: 6630501
• 负责人: AUSTIN L. HUGHES
• 金额: $ 14.55万
• 依托单位: UNIVERSITY OF SOUTH CAROLINA AT COLUMBIA
• 依托单位国家: 美国
• 财政年份: 2002
• 资助国家: 美国
• 起止时间: 2002-08-01 至 2005-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6630501
• 关键词: biochemical evolution; chromosomes; gene duplication; gene expression; genome; method development; molecular biology information system; molecular genetics; nucleic acid sequence; statistics /biometry; yeasts

DESCRIPTION (provided by applicant): The study of the biology of humans and other organisms has entered a new phase with the availability of complete genome sequences, which will make possible the development of new approaches for understanding gene function in the life cycles of organisms in both health and disease. Complete or nearly complete genome sequences are now available from human; two invertebrate animals, the fruitfly Drosophila melanogaster and the nematode worm Caenorhabditis elegans, a plant, the thale cress Arabidopsis thaliana; yeast Saccharomyces cerevisiae, and approximately 40 species of prokaryotes (bacteria and archaebacteria). An important part of deciphering the information available in complete genome sequences will involve understanding the mechanisms by which genomes evolve, including gene duplication and deletion, duplication of genomic segments or entire genomes, and horizontal transfer of genes from one genome to another. The application of bioinformatic methods to genomic sequence data is expected to play an important role in addressing these questions. The research described in this application seeks to develop computational tools that will enhance our understanding of the mechanisms of genome evolution and to apply these tools, along with standard methods of molecular evolutionary genetics, to address major currently debated questions regarding genome evolution. The following specific questions are addressed: (1) The development of a computational method of testing for past duplication of genomes or genomic segments and its application to the human genome and to other eukaryotic genomes. (2) Application of phylogenetic analysis to test the hypothesis that genes in apparently duplicated blocks in genomes duplicated simultaneously, as predicted by the hypothesis that these regions represent the remnants of ancient events of duplication of the entire genome (polyploidization events). (3) Development of a method of testing for conserved gene linkage across genomes and application of this method to the genomes of prokaryotes. (4) Application of phylogenetic analyses to test the hypothesis that horizontal gene transfers have occurred from the genomes of prokaryotes to those of eukaryotes and vice versa. (5) Examining the role of transposable elements in duplication of genomic segments by testing for nonrandom association between these elements and putatively duplicated blocks in the yeast genome.

描述（由申请人提供）：对人类和其他生物的生物学的研究进入了一个新阶段，具有完整的基因组序列的可用性，这将使您可以开发新方法，以理解健康和疾病生命生命周期中基因功能的新方法。现在可以从人类那里获得完整或几乎完整的基因组序列；两种无脊椎动物动物，果蝇果蝇杂物素甘油果果果蝇和线虫蠕虫秀丽隐杆线虫，一种植物，Thale Cress拟南芥；酿酒酵母的酵母菌和大约40种原核生物（细菌和古细菌）。解密完整基因组序列可用信息的重要部分将涉及理解基因组进化的机制，包括基因复制和缺失，基因组段或整个基因组的重复以及将基因从一个基因组到另一个基因组的水平转移。预计生物信息学方法在基因组序列数据中的应用将在解决这些问题中起重要作用。本应用程序中描述的研究旨在开发计算工具，以增强我们对基因组进化机制的理解，并应用这些工具以及分子进化遗传学的标准方法，以解决有关基因组进化的主要辩论问题。解决了以下特定问题：（1）开发了一种测试过去重复或基因组段重复的计算方法，及其在人类基因组和其他真核基因组中的应用。 （2）将系统发育分析的应用用于检验以下假设：基因组中显然重复的基因同时复制的基因，如这些区域代表了整个基因组重复事件的残余物（多倍倍化事件）所预测的。 （3）开发一种测试跨基因组的保守基因链接的方法，并将这种方法应用于原核生物的基因组。 （4）将系统发育分析应用于测试水平基因转移的假设是从原核生物的基因组到真核生物的基因组发生的，反之亦然。 （5）通过测试这些元素之间的非随机关联和酵母基因组中的被重复的块，检查了可转座元素在基因组段重复中的作用。