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Comparative genome analysis of Lactobacillus plantarum GB-LP3 provides candidates of survival-related genetic factors

Jeon, Soomin, Jung, Jaehoon, Kim, Kwondo, Yoo, DongAhn, Lee, Chanho, Kang, Jungsun, Cho, Kyungjin, Kang, Dae-Kyung, Kwak, Woori, Yoon, Sook Hee, Kim, Heebal, Cho, Seoae
Infection, genetics, and evolution 2017 v.53 pp. 218-226
ABC transporters, Lactobacillus plantarum, animals, bacteriocins, chromosomes, fermented foods, gastrointestinal system, genes, genetic factors, genomic islands, genomics, niches, phenotype, phylogeny, quorum sensing, sequence analysis, vegetables, Korean Peninsula
Lactobacillus plantarum is found in various environmental niches such as in the gastrointestinal tract of an animal host or a fermented food. This species isolated from a certain environment is known to possess a variety of properties according to inhabited environment's adaptation. However, a causal relationship of a genetic factor and phenotype affected by a specific environment has not been systematically comprehended. L. plantarum GB-LP3 strain was isolated from Korean traditional fermented vegetable and the whole genome of GB-LP3 was sequenced. Comparative genome analysis of GB-LP3, with other 14 L. plantarum strains, was conducted. In addition, genomic island regions were investigated. The assembled whole GB-LP3 genome contained a single circular chromosome of 3,206,111bp with the GC content of 44.7%. In the phylogenetic tree analysis, GB-LP3 was in the closest distance from ZJ316. The genomes of GB-LP3 and ZJ316 have the high level of synteny. Functional genes that are related to prophage, bacteriocin, and quorum sensing were found through comparative genomic analysis with ZJ316 and investigation of genomic islands. dN/dS analysis identified that the gene coding for phosphonate ABC transporter ATP-binding protein is evolutionarily accelerated in GB-LP3. Our study found that potential candidate genes that are affected by environmental adaptation in Korea traditional fermented vegetable.