COMPARATIVE ANALYSIS OF COMPLETELY SEQUENCED GENOMES

全测序基因组的比较分析

• 批准号: 6432755
• 负责人: Eugene V Koonin
• 金额: --
• 依托单位: NATIONAL LIBRARY OF MEDICINE
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/6432755
• 关键词: Escherichia coli; Haemophilus influenzae; Mycoplasma; bacterial genetics; biochemical evolution; computer assisted sequence analysis; genome

The rapidly growing database of completely sequenced genomes of bacteria, archaea and eukaryotes (approximately 35 genomes available by the end of 2000 and many more in progress) creates both new opportunities and new challenges for genome research. Inorder to take advantage of this information, we developed asystem of Clusters of Orthologous Groups of proteins (COGs) from30 completely sequenced genomes. This database is being continuously updated to incorporate newly appearing genomes. TheCOG allows nearly automatic functional annotation of 60-80% ofthe proteins encoded in each of the tested bacterial and archaeal genomes, although only about 30% of the eukaryotic proteins fitinto these groups. In addition to functional prediction, this approach provides for the systematic delineation of the set ofancient, conserved protein families that are missing in any particular genome. Examination of evolutionary patterns (i.e. representation of different species iand phylogenetic lineages)in the families of orthologs suggests a major role of horizontal gene transfer and lineage-specific gene loss in the evolution of prokaryotes. More specifically, we found evidence of massive horizontal gene among the archaea, between archaea and thermophilic bacteria and between bacterial parasites and their eukaryotic hosts. Additionally, we investigated in detail the lineage-specific gene expansions in prokaryotes and their possible adaptive significance and performed a theoretical of the distribution of evolutionary rates among orthologs from complete genomes.

细菌、古细菌和真核生物完整测序基因组数据库的快速增长（到 2000 年底大约有 35 个基因组可用，还有更多基因组正在开发中）为基因组研究创造了新的机遇和新的挑战。为了利用这些信息，我们从 30 个完全测序的基因组中开发了一个直系同源蛋白质簇 (COG) 系统。该数据库正在不断更新以纳入新出现的基因组。 COG 可以对每个测试的细菌和古细菌基因组中编码的 60-80% 的蛋白质进行几乎自动的功能注释，尽管只有约 30% 的真核蛋白质适合这些组。除了功能预测之外，这种方法还可以系统地描述任何特定基因组中缺失的一组古老的保守蛋白质家族。对直系同源家族中进化模式（即不同物种和系统发育谱系的代表）的检查表明，水平基因转移和谱系特异性基因丢失在原核生物进化中发挥着重要作用。更具体地说，我们发现了古细菌之间、古细菌与嗜热细菌之间以及细菌寄生虫与其真核宿主之间存在大量水平基因的证据。此外，我们详细研究了原核生物中谱系特异性基因的扩展及其可能的适应性意义，并对完整基因组的直向同源物之间的进化速率分布进行了理论分析。