PRJNA532972
Population genetics and functional genomics of Lactococcus lactis subsp. lactis in naturally fermented milk
Lactococcus lactis subsp. lactis (L. lactis subsp. lactis) is a model species of Lactococcus genera, one of common lactic acid bacteria in naturally fermented milk, and one of the commonly used starter cultures for the production of fermented dairy products such as cheese and low-temperature fermented milk. L.lactis subsp. lactis has broad application prospect, so it has highly economic value. Systematic analysis of the genetic background, evolution and functional characteristics of L. lactis subsp. lactis is of great significance for the development and utilization of L. lactis subsp. lactis. lactis. However, studies on the genetic background and functional characteristics of L. lactis subsp. lactis at the genome level have rarely been reported.This research adopts the genome sequencing technology has completed the whole genome sequence of 227 L. lactis subsp. lactis strains isolated from naturally fermented dairy products, combined with NCBI has announced the 89 strains of whole genome sequence, using population genetics method resolved the genetic background and phylogenetic relationship of L. lactis subsp. lactis group population structure, analyses the features of different genetic lineage strains, and by using the genome-wide association analysis (GWAS) of key phenotypic the location in the genome. The main research results are as follows:(1) Completed the 227 strains of L. lactis subsp. lactis of genome mapping, genetic diversity of L. lactis subsp. lactis was analyzed from the whole gene level, and combined with ANI value and TNI value, it showed that the genetic diversity of L. lactis subsp. lactis was high, which was higher than the subspecies level in the traditional bacterial taxonomy definition.(2) Single nucleotide polymorphisms were analyzed using L. lactis subsp. lactis IL1403 as the reference sequence, and a total of 78,624 SNP sites and 4,517 InDel were identified. The driving force of population evolution was analyzed at the whole gene level. The whole population had fewer mutations, more recombination, larger effective population size, and was subjected to strong purification selection pressure.(3) Combined with the 89 strains published by NCBI, 435 core genes and 18,719 pan-gene sets were constructed. Further phylogenetic analysis and population structure analysis showed that L. lactis subsp. lactis population could be divided into four branches, including one environmental lineage and three domestication lineages. There are at least two separate domestication events between the four lineages. The environmental strain appeared first and was the provider of genetic diversity of the whole population, and then appeared after domestication lineage.(4) Functional genomics studies have found that among strains of different genetic lineages, there are significant differences in the copy number of functional genes, such as carbohydrate active enzyme, cold and hot emergency protein, and most of these differences are caused by movable genetic elements, such as insertion sequence and plasmid. Therefore, it is speculated that mobile genetic elements may help strains of different lineages adapt to the environment.5) genome-wide association analysis (GWAS) was used to associate the bacterial genome with the fermentation phenotype data and locate the gene loci affecting the key phenotypes. GWAS located a total of 76 loci and 152 genes associated with 34 phenotypes, and the associated genes were mainly concentrated in five genes, namely proteolytic enzyme pepF, pepO, oligopeptide transporter oppC, oppD and competing protein CoiA. The above genes may affect the growth of the strain, so most phenotypes are affected. Based on the above sites, a random deep-forest model was established to distinguish the fermentation speed of bacterial strains. The AUC of the model was as high as 82.06%.In this study, the genetic background and functional characteristics of L. lactis subsp. lactis were analyzed based on population genetics and functional genomics, and the key functional gene loci of phenotypic differences were located, providing scientific guidance for the discovery of strains with excellent production characteristics, which has important practical production significance.