Whole genome sequencing of Lactobacillus paracasei PC-01 and comparative genomics analysis about Lactobacillus paracasei strains

Abstract:

[Background] Lactobacillus paracasei, as one of the important strains in lactic acid bacteria, is often considered as a potential resource for the development of probiotics. [Objective] L. paracasei PC-01 and L. paracasei Zhang were taken as examples to analyze the genomic differences and genetic backgrounds of different L. paracasei strains, in order to laying a foundation for the identification and development of strains. [Methods] the whole genome sequencing of L. paracasei PC-01 was sequenced by PacBio SMRT third-generation sequencing technology, combining with 2 L. paracasei model strains and the whole genome data of 36 strains which had published. through the comparative genomics methods to revealed the differences of 39 L. paracasei strains. [Results] The genome of L. paracasei PC-01 has one chromosome, with a size of 2 829 251 bp and it's GC content was 46.64%; L. paracasei Zhang contained a plasmid and the genome size was 2 898 456 bp and it's GC content was 46.51%. There were some differences of L. paracasei strains about genome size, the number of plasmid and GC content. L. paracasei is an open genome with a high genome diversity. Phylogenetic tree constructed by core genes has the best effect on species differentiation of L. paracasei. What's more, L. paracasei PC-01 and L. paracasei Zhang were in different evolutionary branches. L. paracasei PC-01 and Zhang had a fragment matching rate is 91% of their genomes, and L. paracasei PC-01 has 10 specific genes related to transcriptional regulation and rhamnoglycan metabolism, such as aguA and clpB. L. paracasei Zhang contains mshA, ltrA specific genes were related to glycosyl transfer and other functions. [Conclusion] Through the comparative genomics revealed the genetic information of L. paracasei PC-01 and Zhang and found the differences of L. paracasei strains, which laid the genetic foundation for the identification and application of L. paracasei in the future.

Key words:Lactobacillus paracasei;whole genome sequencing;genome atlas;comparative genomics analysis