COMPARATIVE ANALYSIS OF COMPLETELY SEQUENCED GENOMES

全测序基因组的比较分析

• 批准号: 6111075
• 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/6111075
• 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 20 genomes available by the end of 1998 and many more in progress) creates both new opportunities and new challenges. In order to take advantage of this information, we developed a system of conserved protein families that include likely orthologous proteins (direct counterparts) from 8 completely sequenced genomes. The process of incorporation of all the remaining completely sequenced genomes is in progress. This system allows nearly automatic functional annotation of more 50% of the proteins encoded in each of the tested bacterial and archaeal genomes, though only about 20% 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, comparative analysis of the first available genome of hyperthermophilic bacterium (Aquifex aeolicus) and archaeal genomes indicates massive gene exchange between archaeal and bacterial thermophiles. Comparative genomics has now become a part of any study on the evolution of a particular protein family or a functional system. Frequently examination of the phylogenetic distribution of structural domains and proteins with specific domain architectures provides for the possibility of detailed reconstructions of evolutionary scenarios. Such analyses were performed for the DNA repair systems of bacteria, archaea and eukaryotes and for the eukaryotic programmed cell death systems. Significant roles of horizontal gene transfer and multiple domain rearrangements in the evolution of both systems were demonstrated and a number of new functional predictions were made.

完全增长的数据库 细菌，古细菌和真核生物的测序基因组 （到1998年底，大约有20个基因组，许多基因组 正在进行的更多）既创造新机会又创造新的机会 挑战。为了利用这些信息，我们 开发了一种保守蛋白质家族的系统，其中包括 完全来自8的源源蛋白（直接蛋白（直接对应） 测序的基因组。纳入所有的过程 剩余的完全测序的基因组正在进行中。这 系统允许几乎自动的功能注释50％ 在每个测试的细菌和古细菌中编码的蛋白质 基因组，尽管只有大约20％的真核蛋白适合 这些群体。除了功能性预测，这种方法 规定了古老的， 保守的蛋白质家族在任何特定的特定 基因组。检查进化模式（即表示 在不同物种的系统发育谱系中） 直系同源物表明水平基因转移和 原核生物进化中的谱系特定基因丧失。更多的 具体而言，对第一个可用基因组的比较分析 超疗细菌（Aquifex aeolicus）和古细菌 基因组表明古细菌和 细菌嗜热剂。比较基因组学现已成为 关于特定蛋白质家族或A演变的任何研究的一部分 功能系统。经常检查系统发育 具有特定结构域的结构结构域和蛋白质的分布 体系结构提供了详细重建的可能性 进化场景。进行了此类分析 细菌，古细菌和真核生物的DNA修复系统以及用于 真核编程的细胞死亡系统。重要的作用 水平基因转移和多个领域重排 展示了两个系统的演变，并有许多新的 做出了功能预测。