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首页> 外文期刊>Research in Microbiology >Repetitive extragenic palindromic sequences in the Pseudomonas syringae pv. tomato DC3000 genome: extragenic signals for genome reannotation.
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Repetitive extragenic palindromic sequences in the Pseudomonas syringae pv. tomato DC3000 genome: extragenic signals for genome reannotation.

机译：丁香假单胞菌PV中的重复基因外回文序列。番茄DC3000基因组：用于基因组重新注释的外源信号。

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Repetitive extragenic palindromic (REPs) sequences were first described in enterobacteriacea and later in Pseudomonas putida. We have detected a new variant (51 base pairs) of REP sequences that appears to be disseminated in more than 300 copies in the Pseudomonas syringae DC3000 genome. The finding of REP sequences in P. syringae confirms the broad presence of this type of repetitive sequence in bacteria. We analyzed the distribution of REP sequences and the structure of the clusters, and we show that palindromy is conserved. REP sequences appear to be allocated to the extragenic space, with a special preference for the intergenic spaces limited by convergent genes, while their presence is scarce between divergent genes. Using REP sequences as markers of extragenicity we re-annotated a set of genes of the P. syringae DC3000 genome demonstrating that REP sequences can be used for refinement of annotation of a genome. The similarity detected between virulence genes from evolutionarily distant pathogenicbacteria suggests the acquisition of clusters of virulence genes by horizontal gene transfer. We did not detect the presence of P. syringae REP elements in the principal pathogenicity gene clusters. This absence suggests that genome fragments lacking REP sequences could point to regions recently acquired from other organisms, and REP sequences might be new tracers for gaining insight into key aspects of bacterial genome evolution, especially when studying pathogenicity acquisition. In addition, as the P. syringae REP sequence is species-specific with respect to the sequenced genomes, it is an exceptional candidate for use as a fingerprint in precise genotyping and epidemiological studies.
机译：重复的基因外回文（REPs）序列首先在肠杆菌科中描述，随后在恶臭假单胞菌中描述。我们已经检测到一个新的REP序列变异体（51个碱基对），该变异体似乎在丁香假单胞菌DC3000基因组中以300多个拷贝的形式传播。在丁香假单胞菌中发现REP序列证实了这种重复序列在细菌中的广泛存在。我们分析了REP序列的分布和簇的结构，并表明回文是保守的。 REP序列似乎分配给了外源空间，特别偏爱受会聚基因限制的基因间空间，而在分歧基因之间却很少出现。使用REP序列作为外源性的标记，我们重新注释了丁香假单胞菌DC3000基因组的一组基因，证明REP序列可用于完善基因组注释。在来自进化距离遥远的致病细菌的毒力基因之间检测到的相似性表明，通过水平基因转移获得了毒力基因簇。我们未在主要致病性基因簇中检测到丁香假单胞菌REP元素的存在。这种缺乏表明缺乏REP序列的基因组片段可能指向最近从其他生物获得的区域，而REP序列可能是新的示踪剂，用于深入了解细菌基因组进化的关键方面，尤其是在研究致病性获取时。另外，由于丁香假单胞菌REP序列相对于测序的基因组是物种特异性的，因此它是在精确的基因分型和流行病学研究中用作指纹的特殊候选者。

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