COMPARATIVE ANALYSIS OF COMPLETELY SEQUENCED GENOMES

细菌、古生菌和真核生物基因组完全测序数据库的迅速增长（到2000年底可提供约35个基因组，还有更多的基因组正在开发中）为基因组研究创造了新的机会和新的挑战。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蛋白质直链组簇（COG）系统。该数据库正在不断更新，以纳入新出现的基因组。COG允许几乎自动的功能注释60-80%的蛋白质编码的每一个测试的细菌和古细菌基因组，虽然只有约30%的真核生物蛋白质适合这些群体。除了功能预测，这种方法提供了一套古老的，保守的蛋白质家族，在任何特定的基因组中丢失的系统描绘。在直系同源物的家庭的进化模式（即代表不同的物种和系统发育谱系）的检查表明，在原核生物的进化水平基因转移和谱系特异性基因丢失的主要作用。在古细菌之间、古细菌与嗜热细菌之间、细菌寄生物与真核宿主之间存在大量的水平基因。此外，我们详细研究了原核生物中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直系同源物之间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.