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

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.