Quantitative assessment of insertion sequence impact on bacterial genome architecture.
Quantitative assessment of insertion sequence impact on bacterial genome architecture.
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DOI：
10.1099/mgen.0.000062
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发表时间：
2016-07
影响因子：
3.9
通讯作者：
Wright MS
中科院分区：
文献类型：
--
作者：
Adams MD;Bishop B;Wright MS
插入序列（IS）元件是基因组可塑性的重要介质，可导致具有进化意义的表型变化。在多重耐药鲍曼不动杆菌和肺炎克雷伯菌中，IS元件对编码抗微生物药物抗性的基因的动员有显著贡献。为了更全面地了解其演变的影响，需要对IS要素进行系统的分析。我们开发了一种计算方法（ISseeker）来注释基因组装配草图中的IS元件，并将该方法应用于所有公开可用的A. baumannii（>1000）和K. pneumoniae（>800）基因组序列，在系统发育背景下。A.鲍曼不动杆菌基因组是种特异性ISAba元件，而K.肺炎杆菌基因组含有大量的ISKpn元件和在整个肠杆菌科中发现的元件。A.鲍曼不动杆菌基因组中IS元件的密度高于K.肺炎，每个基因组平均约33对约27个拷贝。在K. pneumoniae中，ST 258进化枝中的大多数基因组共享几个插入位点，而在A.在鲍曼不动杆菌中，不同的IS元件在不同的系统发生群中丰富，甚至在密切相关的Global Clone 2菌株中也是如此。IS元件在相对于基因的插入位置的分布上不同，其中一些更可能破坏基因，而另一些主要在基因间区域。一些基因和基因间区域有多个独立的插入事件，这表明这些事件可能赋予选择优势。插入位置的全基因组和分类群的表征显示，IS元件一直是两个物种的基因组多样性的积极贡献者。
Insertion sequence (IS) elements are important mediators of genome plasticity and can lead to phenotypic changes with evolutionary significance. In multidrug-resistant Acinetobacter baumannii and Klebsiella pneumoniae, IS elements have contributed significantly to the mobilization of genes that encode resistance to antimicrobial drugs. A systematic analysis of IS elements is needed for a more comprehensive understanding of their evolutionary impact. We developed a computational approach (ISseeker) to annotate IS elements in draft genome assemblies and applied the method to analysis of IS elements in all publicly available A. baumannii(>1000) and K. pneumoniae(>800) genome sequences, in a phylogenetic context. Most IS elements in A. baumanniigenomes are species-specific ISAba elements, whereas K. pneumoniaegenomes contain significant numbers of both ISKpn elements and elements that are found throughout the Enterobacteriaceae. A. baumanniigenomes have a higher density of IS elements than K. pneumoniae, averaging ~33 vs ~27 copies per genome. In K. pneumoniae, several insertion sites are shared by most genomes in the ST258 clade, whereas in A. baumannii, different IS elements are abundant in different phylogenetic groups, even among closely related Global Clone 2 strains. IS elements differ in the distribution of insertion locations relative to genes, with some more likely to disrupt genes and others predominantly in intergenic regions. Several genes and intergenic regions had multiple independent insertion events, suggesting that those events may confer a selective advantage. Genome- and taxon-wide characterization of insertion locations revealed that IS elements have been active contributors to genome diversity in both species.