Study Of Population And Functional Genomics Of 1,008 Lactococcus Lactis Isolates

Lactococcus lactis(L.lactis)is an important food microorganism,with a high economic value and high research value.L.lactis is mainly distributed in habitats,such as plants,dairy products,and animal intestines.However,current population and functional genomics studies of L.lactis are limited by a small number of strains,few isolation sources and location.It is important to systematically analyze the genetic background and evolutionary history of L.lactis on a global scale for its further development and utilization.This study completed the genome resequencing of 551 L.lactis isolates.Together with252 previously sequenced genomes by our research team and the public accessible genome data of 205 isolates retrieved from the NCBI database,this study constructed a genome dataset of 1,008 isolates from six habitats in five continents worldwide.This study analyzed the genetic background and functional characteristics of L.lactis globally and achieved the following conclusions:1)The pan-core gene set and pan-core intergenic region set of L.lactis were constructed,including 49,146 pan genes and 35 core genes,29,301 pan intergenic regions,and 33 core intergenic regions.Both the pan-gene set and the pan-intergenic region set were open,suggesting that L.lactis is genetically highly diverse The core genes phylogenetic tree and core intergenic regions phylogenetic tree shared a similar structure,with a more obvious aggregation trend of isolation sources among dairy and plant isolates than the isolated area,even though their worldwide geographical distribution.Such result suggested that dairy and plant-originated L.lactis had undergone habitat adaptation evolution.2)Through population and functional genomics analysis,107,660 core single nucleotide polymorphism(SNP)loci were found,and phylogenetic analysis revealed two genetic branches(A and B).Genetic branch B accounted for 96.83% of the population strains and was the main genetic branch in the population.It can be further divided into 9 genetic lineages,including one main plant source lineage and three main dairy source lineages.The population genetic and functional genomic characteristics of different dairy lineages also varied obviously,indicating that they have undergone different evolutionary processes,and supporting the "multiple domestication" hypothesis.3)Compared with other common lactic acid bacteria species,this population has a higher recombination rate.It was found that the plant source lineage were located in the ancestor position of dairy source lineages,with no gene flow migration events,few mobile genetic elements,and a medium number of horizontal gene transfer events.The dairy source lineages had at least two gene flow migration events,accompanied by a large number of horizontal gene transfer events and more mobile genetic elements.Therefore,these results suggested that the ancestors of dairy source lineages experienced multiple gene flow events for adapting to dairy habitats.This study investigated the population and functional genomics of L.lactis worldwide based on population and functional genomics approaches,established the first pan-core intergenic regions set of L.lactis,revealed the genetic features,population structure,and functional genomics characteristics of this species,and reconstructed its evolutionary history through analyzing the intrapopulation horizontal gene transfer events.This study has provided a solid genetic foundation for the development and utilization of lactic acid bacteria resources.