植物乳杆菌天然质粒系统进化和起源

Phylogenetic evolution and origin of natural plasmids of Lactobacillus plantarum

摘要:

[目的] 为了探索植物乳杆菌天然质粒系统进化关系和起源。[方法] 本文利用复制起始蛋白（replication initiation protein，Rep）系统进化树、基因组共线性、基因组GC含量和宿主范围分析方法，对植物乳杆菌75个天然质粒的系统进化关系和起源进行了详细和多角度的分析。[结果] 首先，Rep系统进化树和基因组共线性分析结果均表明，植物乳杆菌所有天然质粒可以划分为6个进化关系亲密的家族、2个进化形态特殊的杂合质粒和1个独立进化质粒pLP2140。杂合质粒pMRI5.2、pLP12-1分别由家族1-2和5-6质粒融合形成，因此植物乳杆菌质粒可能起源于7个祖先。其次，基因组共线性分析可以将6个家族质粒进一步划分为17个进化关系更近的亚家族类群，并清晰、有效地揭示类群内质粒之间的系统进化关系。最后，基因组GC含量和宿主范围分析为植物乳杆菌质粒的系统进化关系和起源提供了进一步的证据。[结论] 因此上述研究可以准确、有效地揭示植物乳杆菌天然质粒的系统进化关系和起源，这对植物乳杆菌天然质粒系统进化和起源的了解和研究具有重要的参考价值。通过Rep系统进化树和基因组共线性两种分析方法优缺点的比较和组合，我们提出了一种更加有效的研究思路和分析方法，同时这种方法很可能适用于所有细菌天然质粒，因此对于天然质粒进化和起源研究具有普遍的方法学意义。

Abstract:

[Objective] In order to explore the evolutionary relationship and origin of natural plasmid of Lactobacillus plantarum.[Methods] We analyzed phylogenetic relationships and origins of 75 natural plasmids of L. plantarum by replication initiation protein (Rep) phylogenetic tree, genomic collinearity, genomic GC content and host range.[Results] Rep phylogenetic tree and genomic collinearity analysis simultaneously showed that all natural plasmids of L. plantarum could be divided into 6 families with close evolutionary relationships, 2 complex plasmids with special evolution form and 1 independent evolution plasmid pLP2140. The complex plasmids pMRI5.2 and pLP12-1 were fused by 2 different plasmids of the family 1-2 and family 5-6. Therefore, the natural plasmids of L. plantarum could be originated from 7 ancestors. The genomic collinearity analysis showed that the 6 family plasmids could be further divided into 17 subfamily groups with closer evolutionary relationships, and the phylogenetic relationships among plasmids could be clearly and effectively revealed at the subfamily level. Finally, the analysis of genomic GC content and host range provided further evidence for the phylogenetic relationship and origin of the natural plasmid of L. plantarum.[Conclusion] Therefore, the above research can accurately and effectively reveal the phylogenetic relationship and origin of the natural plasmids of Lactobacillus plantarum, which is of great reference value for the acquaintance and study of the evolution and origin of the natural plasmids of Lactobacillus plantarum. We proposed a more effective research strategy and analytical method of the evolution and origin of natural plasmids by comparing and combining the characteristics of the analytical methods of Rep phylogenetic tree and genome collinearity, and this method may be applicable to all bacterial natural plasmids, so it may have universal methodological significance for the study of the evolution and origin of natural plasmids.