基于比较基因组学揭示不同植物乳杆菌的遗传特征及菌株差异——以Lactobacillus plantarum P9和Lp-6研究为例

Comparative genomics revealed genetic characteristics of different Lactobacillus plantarum strains: using P9 and Lp-6 strains as examples

摘要:

[目的] 植物乳杆菌（Lactobacillus plantarum，L.plantarum）在食品、医药和动物养殖等多个领域均有应用。本文以L.plantarum P9和Lp-6为例，解析L.plantarum遗传背景和基因组特征，为其鉴定和开发奠定基础。[方法] 本研究采用PacBio SMRT测序技术完成了L.plantarum P9和Lp-6全基因组测序，结合已公开的110株L.plantarum全基因组数据和1株模式菌株ATCC 14917^T数据，通过比较基因组学方法探究L.plantarum基因组的差异。[结果] L.plantarum P9和Lp-6基因组大小分别为3314.1和3482.5 kb，GC含量（%）分别为44.38%和44.32%，二者分别含有8个和9个质粒。113株L.plantarum系统发育树结果显示，L.plantarum P9与L.plantarum ATCC 14917^T遗传距离更近，L.plantarum Lp-6更接近祖先群体分支。与L.plantarum WCSF1相比，含有xerS等基因的22.0 kb基因组片段在L.plantarum Lp-6上发生了倒位，在L.plantarum P9基因组中缺失；L.plantarum Lp-6染色体插入含tagF等基因的13.0 kb片段；包含gpmA等基因的14.4 kb基因片段插入到L.plantarumP9染色体中。[结论] 通过比较基因组学方法解析L.plantarum P9和Lp-6遗传信息，发现不同L.plantarum菌株的遗传特征存在差异。

Abstract:

[Objective] This study aimed to analyze the genetic characteristics of Lactobacillus (L.) plantarum P9 and Lp-6, to provide information for future identification of L. plantarum. [Methods] Whole genome sequencing of L. plantarum strains P9 an Lp-6 was performed with PacBio SMRT sequencing and comparatively analyzed together with 110 genome sequences to identify characteristics usable in differentiating between L. plantarum strains. [Results] The genome length of P9 and Lp-6 strains was 3314.2 kb and 3482.5 kb, respectively. The GC content (%) of Lp-6 and P9 strains was 44.38% and 44.32%, and they contained 8 and 9 plasmids, respectively. Phylogenetic analysis showed a close genetic distance between L. plantarum P9 and ATCC 14917, and Lp-6 was closer to the ancestral branch. Comparing with L. plantarum WCSF1, the 22 kb-genome fragment of xerS was inverted in Lp-6 and was missing in P9 strain. A 13 kb-genomic fragment with the tagF gene was inserted in the Lp-6 genome; a 14.4 kb-gene fragment (containing the gpmA gene) was inserted in the P9 genome. [Conclusion] Through comparative genomic analysis of P9 and Lp-6 together with other L. plantarum, some specific genomic features were identified, which could be used for differentiation between strains.