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、古生菌和真核生物基因组测序数据库的快速增长（到2009年年中可获得900多个基因组，还有更多的基因组正在开发中）为基因组研究带来了新的机遇和新的挑战。在过去的一年里，我们进行了几项研究，利用基因组信息建立基因组进化和功能的基本原则。特别是，我们进行了一个全面的比较分析的“森林”的6,901原核基因的系统发育树揭示了一致的系统发育信号，特别是在102个几乎通用的树，尽管高层次的拓扑不一致，可能是由于水平基因转移。横向转移似乎是随机分布的，并没有掩盖中心趋势。几乎普遍的树在拓扑上与许多其他树相似。因此，几乎普遍的树可能反映了一个重要的集中趋势，尽管它们不能完全代表森林。然而，拓扑结构的一致性主要是在浅树的深度和突然下降的水平上的古细菌和细菌门的辐射，这表明进化的早期阶段可能是非树样的（生物大爆炸）。在压缩的进化分支或生物大爆炸下的进化模拟产生了更好的拟合压缩的进化分支模型的树不一致性和系统发育深度之间观察到的依赖关系。水平基因转移在原核生物中普遍存在：很少有基因树是完全一致的，使得原始的生命树概念过时。一个最有可能代表垂直遗传的中心趋势在古菌和细菌的整个进化过程中是可以辨别的，尽管压缩的分支发生使主要古菌和细菌分支之间关系的明确解决变得复杂。此外，为了探索细菌和古细菌的微进化趋势，我们构建了一个41个可划分的紧密基因组簇（ATGC）的数据集。我们发现，作为衡量蛋白质序列上的纯化选择压力的非同义的同义取代率（dN/dS）的中位数的比率是一个稳定的ATGC特性。与以前的研究结果一致，寄生细菌，尽管有时戏剧性的基因组收缩引起的基因丢失，通常受到相对较弱的纯化选择，大概是由于相对较小的有效人口规模和频繁的瓶颈。然而，在任何ATGC中均未发现由强选择压力引起的基因组精简的证据。相反，一个显着的正相关性之间的基因组大小，以及基因大小，和选择压力的观察，虽然各种自由生活的原核生物非常接近的选择压力跨越几乎整个范围的基因组大小。此外，我们还研究了序列进化速率与其他基因组特征之间的联系。虽然在原核生物的进化过程中，基因序列的变化比蛋白质序列快得多，但在“重排距离”和氨基酸距离之间观察到了强的正相关性，这表明至少有一些导致基因组重排的事件受到与氨基酸序列进化相同类型的选择性约束。