Study On Population Genetics And Functional Genomic Of Lactiplantibacillus Plantarum

Lactiplantibacillus plantarum,as a type species of Lactiplantibacillus,is a popular lactic acid bacteria.It has good acid and bile salt resistance,excellent extracellular polysaccharide production,bacteriocin production and immune regulation,and is often used in food industry and medical industry.It is of far-reaching significance to systematically analyze the genetic diversity and evolution law of L.plantarum for the development and utilization of L.plantarum.In this study,the genome of 109 strains of L.plantarum isolated from fermented plant products in Hubei,China was determined by Illumina Novaseq high-throughput sequencing platform,and combined with 306 representative strains of L.plantarum in NCBI Refseq database,population genetics and functional genomics were studied,and the conclusions were as follows:(1)The 415 strains of L.plantarum in this study have an open genome,and their gene frequencies show an asymmetric "U" distribution,and most of the genes exist in the form of cloud genes.At the same time,the genetic diversity of L.plantarum is extremely rich by combining the values of ANI and π.(2)The population of L.plantarum 415 can be divided into pedigree 1,pedigree 2 and pedigree 3 by phylogenetic relationship,which supports the early discovery that the isolated strains from milk,fruit fly and human body will evolve adaptively to adapt to their unique habitats.The strains isolated from fermented plant products in China,Hubei and Zhejiang also have habitat adaptability.(3)A total of 126,585 SNP loci were identified from 415 strains of L.plantarum,and the phylogenetic tree based on SNP loci was consistent with that constructed by core genes.The average SNP distance between strains of pedigree 2 is the shortest and three high-frequency regions are formed,namely,human source,milk source and plant source.The SNP distance of strains of pedigree 2 is the shortest,with an average distance of 7,979,and that of plants is the longest,with an average distance of 27,639 and that of milk source of14,893.Strains of different sources form different high-frequency regions,while strains of pedigree 3 have only one high-frequency region,with an average distance of 37,463.The results showed that the strains from milk,human and plant in pedigree 2 were environmentally adaptive,and there was little difference among the strains from different sources in pedigree 3.(4)There are differences in the function prediction results between L.plantarum pedigree 2 and pedigree 3.The functions of strains isolated from different habitats in pedigree 2 were significantly different,while the functions of strains isolated from different habitats in pedigree 3 were similar.It shows that different adaptive evolution rules have taken place among different lineages,in which habitat plays a key role in the evolution of strains in pedigree 2,while habitat in pedigree 3 has little influence on strains.Based on population genetics and functional genomics,this study explored the genetic evolution process and functional characteristics of L.plantarum from the gene level,and analyzed the different adaptive evolution laws among different lineages.It provides a theoretical basis for further research and industrial application of L.plantarum.