Elucidation of quantitative structural diversity of remarkable rearrangement regions, shufflons, in IncI2 plasmids.
Elucidation of quantitative structural diversity of remarkable rearrangement regions, shufflons, in IncI2 plasmids.
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DOI：
10.1038/s41598-017-01082-y
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发表时间：
2017-04-19
影响因子：
4.6
通讯作者：
Kuroda M
中科院分区：
文献类型：
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作者：
Sekizuka T;Kawanishi M;Ohnishi M;Shima A;Kato K;Yamashita A;Matsui M;Suzuki S;Kuroda M
多重DNA倒置系统，改组，存在于不亲和性(INC)I1和I2质粒中。改组蛋白产生PilV蛋白的变体，PilV蛋白是细毛的一个次要成分。即使在分离的细菌克隆中，由于其结构的多样性，改组也是从头组装基因组最困难的区域之一。我们使用单分子、实时(SMRT)测序和Illumina测序确定了三株大肠杆菌的完整基因组序列，包括携带mcr-1的IncI2质粒的全基因组序列。仅使用SMRT测序组装的序列在洗牌子中包含错误组装的区域。SMRT和Illumina测序的杂交分析解决了错误组装的区域，并显示除改组区域外的三个IncI2质粒高度保守。此外，通过对SMRT数据的定量结构变异分析，可以确定整体改组结构的丰度比，这表明IncI2质粒中存在显著的整体改组结构变异的异质性。这些发现表明，即使在细菌克隆群体中，显著的重排区域也应该用长读和短读测序数据来验证，洗牌子中PilV的结构变异可能与水平基因转移所涉及的质粒介导的转接的表型异质性密切相关。
A multiple DNA inversion system, the shufflon, exists in incompatibility (Inc) I1 and I2 plasmids. The shufflon generates variants of the PilV protein, a minor component of the thin pilus. The shufflon is one of the most difficult regions for de novo genome assembly because of its structural diversity even in an isolated bacterial clone. We determined complete genome sequences, including those of IncI2 plasmids carrying mcr-1, of three Escherichia coli strains using single-molecule, real-time (SMRT) sequencing and Illumina sequencing. The sequences assembled using only SMRT sequencing contained misassembled regions in the shufflon. A hybrid analysis using SMRT and Illumina sequencing resolved the misassembled region and revealed that the three IncI2 plasmids, excluding the shufflon region, were highly conserved. Moreover, the abundance ratio of whole-shufflon structures could be determined by quantitative structural variation analysis of the SMRT data, suggesting that a remarkable heterogeneity of whole-shufflon structural variations exists in IncI2 plasmids. These findings indicate that remarkable rearrangement regions should be validated using both long-read and short-read sequencing data and that the structural variation of PilV in the shufflon might be closely related to phenotypic heterogeneity of plasmid-mediated transconjugation involved in horizontal gene transfer even in bacterial clonal populations.