A quantitative account of genomic island acquisitions in prokaryotes.
A quantitative account of genomic island acquisitions in prokaryotes.
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DOI：
10.1186/1471-2164-12-427
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发表时间：
2011-08-24
期刊：
影响因子：
4.4
通讯作者：
van Passel MW
中科院分区：
文献类型：
--
作者：
Roos TE;van Passel MW
微生物基因组的进化不仅仅是通过缓慢的突变积累，而且在一个被称为水平基因转移的过程中吸收新的DNA，这一过程往往更为戏剧性。这些获得新性状的创新飞跃可以通过单个基因的渗入来实现，也可以通过获得大的基因簇来实现，这些基因簇被称为基因组岛。由于所有DNA多样性中只有一小部分被测序，因此很难通过数据库中的序列比对找到获得基因的合适供体。相比之下，相对寡核苷酸频率在原核生物中代表了一个非常稳定的基因组特征，这有助于作为系统发育相关性的无比对选择的组成比较。在这个项目中，我们测试了在单个细菌基因组中鉴定的基因组岛是否具有相似的基因组特征，就相对二核苷酸频率而言，因此可以预期它们来自一个共同的供体物种。当单个基因组中存在多个基因组岛时，我们发现高达28%的基因组岛在组成上彼此非常相似，这表明从同一供体到同一受体的频繁重复获取。这是对原核生物进化史上常见的定向转移事件的第一次定量评估。我们认为，每个原核生物基因组的许多常驻基因组岛起源于同一来源，这可能与它们的调节相互作用有关，并有助于阐明这些获得性基因簇的共同起源。
Microbial genomes do not merely evolve through the slow accumulation of mutations, but also, and often more dramatically, by taking up new DNA in a process called horizontal gene transfer. These innovation leaps in the acquisition of new traits can take place via the introgression of single genes, but also through the acquisition of large gene clusters, which are termed Genomic Islands. Since only a small proportion of all the DNA diversity has been sequenced, it can be hard to find the appropriate donors for acquired genes via sequence alignments from databases. In contrast, relative oligonucleotide frequencies represent a remarkably stable genomic signature in prokaryotes, which facilitates compositional comparisons as an alignment-free alternative for phylogenetic relatedness. In this project, we test whether Genomic Islands identified in individual bacterial genomes have a similar genomic signature, in terms of relative dinucleotide frequencies, and can therefore be expected to originate from a common donor species. When multiple Genomic Islands are present within a single genome, we find that up to 28% of these are compositionally very similar to each other, indicative of frequent recurring acquisitions from the same donor to the same acceptor. This represents the first quantitative assessment of common directional transfer events in prokaryotic evolutionary history. We suggest that many of the resident Genomic Islands per prokaryotic genome originated from the same source, which may have implications with respect to their regulatory interactions, and for the elucidation of the common origins of these acquired gene clusters.
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影响因子：
3
作者：
Langille MG;Hsiao WW;Brinkman FS
通讯作者：
Brinkman FS
DOI：
10.1073/pnas.0335853100
发表时间：
2003-02-04
影响因子：
11.1
作者：
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3
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影响因子：
14.9
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