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。在……里面 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直序蛋白质组(COG)的集群系统。这个数据库正在被 不断更新，以纳入新出现的基因组。COG允许对每个被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%的真核蛋白质符合 归入这些团体。除了功能预测之外，这种方法还提供了一组古老的、保守的蛋白质家族的系统描述，这些家族在 特定的基因组。对直系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，水平基因在进化模式中起着重要作用 原核生物进化中的基因转移和谱系特异性基因丢失。更具体地说，我们发现了在古菌之间、古菌和古菌之间存在大量水平基因的证据 嗜热菌和细菌寄生虫与它们的真核宿主之间的相互作用。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. In order to take advantage of this information, we developed a system of Clusters of Orthologous Groups of proteins (COGs) from 30 completely sequenced genomes. This database is being continuously updated to incorporate newly appearing genomes. The COG allows nearly automatic functional annotation of 60-80% of the proteins encoded in each of the tested bacterial and archaeal genomes, although only about 30% of the eukaryotic proteins fit into these groups. In addition to functional prediction, this approach provides for the systematic delineation of the set of ancient, 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.