Comparative Analysis Of Completely Sequenced Genomes

完全测序的基因组的比较分析

• 批准号: 7969213
• 负责人: Eugene V Koonin
• 金额: $ 195.34万
• 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/7969213
• 关键词: Affect; Agreement; Amino Acid Sequence; Amino Acids; Archaea; Bacteria; Biological; Characteristics; DNA Sequence Rearrangement; Data Set; Databases; Dependence; Drops; Eukaryota; Event; Evolution; Gene Order; Gene Transfer; Genes; Genome; Genomics; Horizontal Gene Transfer; Individual; Life; Measures; Methods; Organism; Orthologous Gene; Peptide Sequence Determination; Phase; Phylogenetic Analysis; Phylogeny; Population Sizes; Process; Prokaryotic Cells; Radiation; Research; Resolution; Signal Transduction; Trees; comparative; forest; genome sequencing; insight; mathematical model; paralogous gene; pressure; simulation; trend

The rapidly growing database of completely sequenced genomes of bacteria, archaea and eukaryotes (over 900 genomes available by the middle of 2009 and many more in progress) creates both new opportunities and new challenges for genome research. During the last year, we performed several studies that took advantage of the genomic information to establish fundamental principles of genome evolution and function. In particular, we performed a comprehensive comparative analysis of a 'forest' of 6,901 phylogenetic trees for prokaryotic genes revealed a consistent phylogenetic signal, particularly among 102 nearly universal trees, despite high levels of topological inconsistency, probably due to horizontal gene transfer. Horizontal transfers seemed to be distributed randomly and did not obscure the central trend. The nearly universal trees were topologically similar to numerous other trees. Thus, the nearly universal trees might reflect a significant central tendency, although they cannot represent the forest completely. However, topological consistency was seen mostly at shallow tree depths and abruptly dropped at the level of the radiation of archaeal and bacterial phyla, suggesting that early phases of evolution could be non-tree-like (Biological Big Bang). Simulations of evolution under compressed cladogenesis or Biological Big Bang yielded a better fit to the observed dependence between tree inconsistency and phylogenetic depth for the compressed cladogenesis model.Horizontal gene transfer is pervasive among prokaryotes: very few gene trees are fully consistent, making the original tree of life concept obsolete. A central trend that most probably represents vertical inheritance is discernible throughout the evolution of archaea and bacteria, although compressed cladogenesis complicates unambiguous resolution of the relationships between the major archaeal and bacterial clades. Additionally, in order to explore microevolutionary trends in bacteria and archaea, we constructed a data set of 41 alignable tight genome clusters (ATGCs). We show that the ratio of the medians of nonsynonymous to synonymous substitution rates (dN/dS) that is used as a measure of the purifying selection pressure on protein sequences is a stable characteristic of the ATGCs. In agreement with previous findings, parasitic bacteria, notwithstanding the sometimes dramatic genome shrinkage caused by gene loss, are typically subjected to relatively weak purifying selection, presumably owing to relatively small effective population sizes and frequent bottlenecks. However, no evidence of genome streamlining caused by strong selective pressure was found in any of the ATGCs. On the contrary, a significant positive correlation between the genome size, as well as gene size, and selective pressure was observed, although a variety of free-living prokaryotes with very close selective pressures span nearly the entire range of genome sizes. In addition, we examined the connections between the sequence evolution rate and other genomic features. Although gene order changes much faster than protein sequences during the evolution of prokaryotes, a strong positive correlation was observed between the "rearrangement distance" and the amino acid distance, suggesting that at least some of the events leading to genome rearrangement are subjected to the same type of selective constraints as the evolution of amino acid sequences.

细菌，古细菌和真核生物的完全测序基因组的快速增长的数据库（2009年中期可用的900多个基因组以及正在进行的更多基因组）为基因组研究带来了新的机会和新的挑战。在过去的一年中，我们进行了几项研究，利用基因组信息来建立基因组进化和功能的基本原理。特别是，我们对原核基因的6,901棵系统发育树的“森林”进行了全面的比较分析，揭示了尽管水平转移的拓扑不一致，但尽管有很高的拓扑不一致，但尽管拓扑不一致，但在102个几乎通用树中，尤其是在102个几乎普遍的树中的一致性信号。水平转移似乎是随机分布的，并不掩盖核心趋势。几乎普遍的树在拓扑上与许多其他树木相似。因此，尽管它们不能完全代表森林，但几乎普遍的树木可能反映出一种重要的中心趋势。但是，拓扑一致性主要在浅树深处看到，并在古细菌和细菌门的辐射水平上突然降低，这表明进化的早期阶段可能是非树状的（生物大爆炸）。在压缩弹药或生物学大爆炸下进行进化的模拟可以使观察到的依赖性在树木不一致和系统发育深度之间的依赖性相适应压缩的cladogenesecogeny模型。原发性基因转移在原核生物中普遍存在：很少的基因树完全一致，使生命概念的原始树是过时的原始树。在古细菌和细菌的整个演变中，最有可能代表垂直遗传的核心趋势是可见的，尽管压缩的cladogenogeny使主要古细菌和细菌分支之间的关系明确地分辨出复杂化。此外，为了探索细菌和古细菌的微观进化趋势，我们构建了一个41个可校准紧密基因组簇（ATGC）的数据集。我们表明，非同步的中位数与同义替代速率（DN/DS）的比例，该比例被用作蛋白质序列的纯化选择压力的量度是ATGCS的稳定特征。与以前的发现一致，寄生细菌有时是由于基因丧失引起的戏剧性基因组收缩，通常会受到相对较弱的纯化选择，这可能是由于相对较小的有效人口大小和频繁的瓶颈。但是，在任何ATGC中，没有发现由强烈选择压力引起的基因组精简的证据。相反，观察到基因组大小以及基因大小和选择性压力之间的显着正相关，尽管各种具有非常接近选择性压力的自由生活原核生物几乎遍及整个基因组大小的范围。此外，我们研究了序列演化速率和其他基因组特征之间的联系。尽管基因顺序的变化速度比原核生物进化过程中的蛋白质序列快得多，但是在“重排距离”和氨基酸距离之间观察到很强的阳性相关性，这表明至少有一些导致基因组重排的事件受到相同类型的选择性约束，因为氨基酸序列的进化。