The source of laterally transferred genes in bacterial genomes.
The source of laterally transferred genes in bacterial genomes.
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DOI：
10.1186/gb-2003-4-9-r57
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发表时间：
2003
期刊：
影响因子：
12.3
通讯作者：
Perrière G
中科院分区：
文献类型：
--
作者：
Daubin V;Lerat E;Perrière G
与之前的假设相反，即识别横向转移基因的方法无法检测到与供体生物体具有相似碱基组成的基因，这表明横向转移基因的数量并未被低估，并且横向转移基因符合被称为“白痴”的羔羊噬菌体基因的描述。横向转移基因通常根据其与基因组中祖先基因的组成特征来识别。这些基因通常富含 A+T，认为要么存在从 G+C 含量低的供体生物体获取基因的偏见，要么从具有相似基因组基础组成的生物体获取的基因在这些分析中未被检测到。通过检查密切相关、完全测序的细菌的基因组内容，我们发现了仅限于单个基因组的基因，并检查了这些获得的基因的序列特征。分析表明，成分分析很少会忽略转移事件。大多数观察到的横向基因转移并不对应于细菌基因组之间常规基因的自由交换，而更可能代表噬菌体或其他自私元素的成分。尽管细菌往往会获得大量 DNA，但这些基因的起源仍然不清楚。我们已经证明，与通常的假设相反，它们的组成不能用以前的基因组背景来解释。相比之下，这些基因符合最近描述的羔羊噬菌体基因的描述，称为“白痴”。因此，基因组内容和检测横向转移的组成方法的结果不应被引用作为远缘相关细菌之间遗传交换的证据。
Contrary to previous hypotheses that methods for identifying laterally transferred genes cannot detect genes with similar base composition to that of the donor organism, it is suggested that the number of laterally transferred genes has not been underestimated and that laterally transferred genes fit the description of lambdoid phage genes called 'morons'. Laterally transferred genes have often been identified on the basis of compositional features that distinguish them from ancestral genes in the genome. These genes are usually A+T-rich, arguing either that there is a bias towards acquiring genes from donor organisms having low G+C contents or that genes acquired from organisms of similar genomic base compositions go undetected in these analyses. By examining the genome contents of closely related, fully sequenced bacteria, we uncovered genes confined to a single genome and examined the sequence features of these acquired genes. The analysis shows that few transfer events are overlooked by compositional analyses. Most observed lateral gene transfers do not correspond to free exchange of regular genes among bacterial genomes, but more probably represent the constituents of phages or other selfish elements. Although bacteria tend to acquire large amounts of DNA, the origin of these genes remains obscure. We have shown that contrary to what is often supposed, their composition cannot be explained by a previous genomic context. In contrast, these genes fit the description of recently described genes in lambdoid phages, named 'morons'. Therefore, results from genome content and compositional approaches to detect lateral transfers should not be cited as evidence for genetic exchange between distantly related bacteria.
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影响因子：
14.9
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