COMPARATIVE ANALYSIS OF COMPLETELY SEQUENCED GENOMES

细菌、古生物和真核生物全序列基因组数据库的迅速增长(到2000年底约有35个基因组可用，还有更多基因组正在进行中)为基因组研究创造了新的机遇和新的挑战。为了利用这一信息，我们从30个完全测序的基因组中开发了一个由同源蛋白质组(COG)组成的集群系统。这个数据库正在不断更新，以纳入新出现的基因组。COG允许对每个测试的细菌和古菌基因组中编码的60%-80%的蛋白质进行几乎自动的功能注释，尽管只有大约30%的真核蛋白质适合这些组。除了功能预测外，这种方法还提供了一组在任何特定基因组中缺失的古老的、保守的蛋白质家族的系统描述。对同源基因家族中不同物种的进化模式(即不同物种和系统发育谱系的代表)的研究表明，水平基因转移和谱系特异性基因丢失在原核生物的进化中起着重要作用。更具体地说，我们发现了古细菌之间、古细菌和嗜热菌之间以及细菌寄生虫和它们的真核宿主之间存在大量水平基因的证据。此外，我们还详细研究了原核生物中谱系特异的基因扩展及其可能的适应性意义，并从理论上研究了进化速率在来自全基因组的直系物之间的分布。

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.