Examining bacterial species under the specter of gene transfer and exchange
Examining bacterial species under the specter of gene transfer and exchange
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DOI：
10.1073/pnas.0502035102
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发表时间：
2005-05-03
影响因子：
11.1
通讯作者：
Daubin, V
中科院分区：
文献类型：
--
作者：
Ochman, H;Lerat, E;Daubin, V
即使在代替一个可靠的无性生物物种的概念，分类细菌到离散的分类单位被认为是阻碍了潜在的横向基因转移（LGT）之间的谱系在几乎所有的系统发育水平。在大多数细菌基因组中，大部分基因是由LGT引入的，如它们的组成特征和/或系统发育分布所示，并且在非常远的相关生物体之间也有明显的LGT证据。通过采用全基因组方法，检查了许多细菌基因组中每个基因的历史，我们表明，LGT并不妨碍系统发育重建在许多较浅的分类水平。尽管基因获取水平很高，但检测到可观数量同源重组的唯一分类组是细菌种内。总的来说，来自完整基因库分析的结果支持目前识别和定义细菌物种的几种方法。
Even in lieu of a dependable species concept for asexual organisms, the classification of bacteria into discrete taxonomic units is considered to be obstructed by the potential for lateral gene transfer (LGT) among lineages at virtually all phylogenetic levels. In most bacterial genomes, large proportions of genes are introduced by LGT, as indicated by their compositional features and/or phylogenetic distributions, and there is also clear evidence of LGT between very distantly related organisms. By adopting a whole-genome approach, which examined the history of every gene in numerous bacterial genomes, we show that LGT does not hamper phylogenetic reconstruction at many of the shallower taxonomic levels. Despite the high levels of gene acquisition, the only taxonomic group for which appreciable amounts of homologous recombination were detected was within bacterial species. Taken as a whole, the results derived from the analysis of complete gene inventories support several of the current means to recognize and define bacterial species.