COMPARATIVE ANALYSIS OF COMPLETELY SEQUENCED GENOMES

细菌、古细菌和真核生物基因组完全测序数据库的迅速增长（到2000年底，大约有35个基因组可用，还有更多正在进行中）为基因组研究创造了新的机遇和新的挑战。为了利用这些信息，我们从30个完全测序的基因组中开发了同源蛋白群（COGs）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。ecog几乎可以自动地对每一种被测试的细菌和古细菌基因组中编码的60-80%的蛋白质进行功能注释，尽管只有大约30%的真核生物蛋白质适合这些组。除了功能预测之外，这种方法还提供了对任何特定基因组中缺失的一组古老的、保守的蛋白质家族的系统描述。对直系生物家族的进化模式（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，我们在古细菌之间、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发现了大量水平基因的证据。此外，我们详细研究了原核生物的谱系特异性基因扩增及其可能的适应意义，并对来自完整基因组的同源物的进化速率分布进行了理论分析。

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.