副干酪乳杆菌PC-01全基因组测序及不同副干酪乳杆菌菌株比较基因组学分析

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

摘要:

[背景] 副干酪乳杆菌（Lactobacillusparacasei）作为乳酸菌中重要菌种之一，常被认为是优良益生菌开发的潜在资源。[目的] 以L. paracasei PC-01和L. paracasei Zhang为例，分析不同L. paracasei的基因组差异和遗传背景，为菌株的鉴定和开发奠定基础。[方法] 采用PacBio SMRT三代测序技术对L. paracasei PC-01进行全基因组测序，结合2株L. paracasei模式菌株和公开的36株全基因组数据，通过比较基因组学方法揭示39株L. paracasei菌株之间的差异。[结果] L. paracasei PC-01基因组不包含质粒，染色体大小为2 829 251 bp，GC含量为46.64%；L. paracasei Zhang包含一个质粒基因组大小为2 898 456 bp，GC含量为46.51%；不同L. paracasei菌株基因组大小、质粒数及GC含量均存在一定差异。L. paracasei群体为开放式基因组，基因组具有高度多样性。基于核心基因构建系统发育树对于L. paracasei种内区分效果最好，L. paracasei PC-01和L. paracasei Zhang处于不同的进化分支。约占L. paracasei PC-01基因组长度91%的片段与L. paracasei Zhang基因组匹配率大于90%，L. paracasei PC-01注释到10个与转录调节鼠李糖代谢功能相关的特有基因，如aguA、clpB等；L. paracasei Zhang包含mshA、ltrA等特有基因，与糖基转移等功能相关。[结论] 通过比较基因组学揭示L. paracasei PC-01和L. paracasei Zhang的遗传信息，解析了不同L. paracasei菌株之间的差异，为L. paracasei的鉴定和应用奠定了遗传学基础。

关键词:副干酪乳杆菌;全基因组测序;基因组图谱;比较基因组学分析

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