Ten years of bacterial genome sequencing: comparative-genomics-based discoveries
Ten years of bacterial genome sequencing: comparative-genomics-based discoveries
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DOI：
10.1007/s10142-006-0027-2
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发表时间：
2006-07-01
影响因子：
2.9
通讯作者：
Ussery, David W.
中科院分区：
文献类型：
--
作者：
Binnewies, Tim T.;Motro, Yair;Ussery, David W.
自第一个细菌基因组序列公布以来，已经过去了10多年。现在已有数百个细菌基因组序列可供比较基因组学研究，而在一千多个基因组中搜索给定的蛋白质将很快成为可能。这篇综述的主题将解决一个相对简单的问题：“我们从这大量的新基因组数据中学到了什么？“也许最重要的教训之一是，遗传多样性，即使是同一物种的基因组之间的大规模变异水平，也远远超过了人们的想象。经典的教科书进化观依赖于分散在整个基因组中的单个碱基水平上相对缓慢的突变事件积累，这种观点已经改变。通过检查数百个细菌基因组的序列，最明显的结论之一是存在巨大的多样性--即使是在同一细菌物种的不同基因组中也是如此。这种多样性是由多种机制产生的，包括移动的遗传元件和噬菌体。迄今为止，对20个大肠杆菌基因组测序的检查戏剧性地说明了这一点，基因组大小从4.6到5.5 Mbp不等;大部分变异似乎是噬菌体起源的。本文还讨论了移动的遗传因子，包括致病岛和转座因子的结构。至少有20种不同的方法可用于比较细菌基因组。宏基因组学提供了研究生态系统中发现的基因组序列的机会，包括难以培养的物种的基因组。已经清楚的是，基因组序列不仅仅代表生物体的基因序列的集合，并且关于生物体的环境和生长条件的信息对于基因组数据的解释是重要的。新提出的关于基因组序列标准的最小信息已经被开发以获得该信息。
It has been more than 10 years since the first bacterial genome sequence was published. Hundreds of bacterial genome sequences are now available for comparative genomics, and searching a given protein against more than a thousand genomes will soon be possible. The subject of this review will address a relatively straightforward question: "What have we learned from this vast amount of new genomic data?" Perhaps one of the most important lessons has been that genetic diversity, at the level of large-scale variation amongst even genomes of the same species, is far greater than was thought. The classical textbook view of evolution relying on the relatively slow accumulation of mutational events at the level of individual bases scattered throughout the genome has changed. One of the most obvious conclusions from examining the sequences from several hundred bacterial genomes is the enormous amount of diversity-even in different genomes from the same bacterial species. This diversity is generated by a variety of mechanisms, including mobile genetic elements and bacteriophages. An examination of the 20 Escherichia coli genomes sequenced so far dramatically illustrates this, with the genome size ranging from 4.6 to 5.5 Mbp; much of the variation appears to be of phage origin. This review also addresses mobile genetic elements, including pathogenicity islands and the structure of transposable elements. There are at least 20 different methods available to compare bacterial genomes. Metagenomics offers the chance to study genomic sequences found in ecosystems, including genomes of species that are difficult to culture. It has become clear that a genome sequence represents more than just a collection of gene sequences for an organism and that information concerning the environment and growth conditions for the organism are important for interpretation of the genomic data. The newly proposed Minimal Information about a Genome Sequence standard has been developed to obtain this information.