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，古细菌和真核生物的完全测序基因组的快速增长数据库（到2000年底，可用的35个基因组以及正在进行的更多基因组）为基因组研究带来了新的机会和新的挑战。为了利用这些信息，我们从30完全测序的基因组中开发了直系同源蛋白（COG）的簇簇的ASYSTER。该数据库正在不断更新以结合新出现的基因组。 THECOG允许在每个测试的细菌和古细菌基因组中编码60-80％的蛋白质的60-80％自动功能注释，尽管这些基团的真核蛋白中只有30％。除了功能性预测外，这种方法还提供了在任何特定基因组中缺少的合并，保守蛋白质家族的系统描述。对直系同源物家族中进化模式的检查（即不同物种IND系统发育谱系的表示）表明，水平基因转移和谱系特异性基因丧失在原核生物的进化中具有重要作用。更具体地说，我们发现了古细菌，古细菌和嗜热细菌以及细菌寄生虫及其真核宿主之间的大量水平基因的证据。此外，我们详细研究了原核生物中的谱系特异性基因膨胀及其可能的适应性意义，并对完全基因组中直系同源物之间进化速率的分布进行了理论。