福菜乳杆菌重庆亚种与福菜乳杆菌福菜亚种的基因组比较分析

Comparative Analysis of the Genomes of Lactobacillus futsaii subsp.chongqingii CQ16Z1 and Lactobacillus futsaii subsp.futsaii YM0097

目的研究福菜乳杆菌重庆亚种CQ16Z1(简称CQ16Z1)与福菜乳杆菌福菜亚种YM0097(简称Y97)的基因组差异。方法采用二、三代测序技术对CQ16Z1菌株进行全基因组测序,计算CQ16Z1与Y97菌株的核苷酸一致性和数字DNA-DNA杂交同源性,通过比较基因组学对两株菌的基因组差异进行比较分析。结果CQ16Z1菌株的基因组大小为2654961 bp,染色体大小为2625188 bp,GC含量为35.75%;有5个质粒环,大小2000~14000 bp。全基因组基因预测结果显示,CQ16Z1菌株共有2744个基因。CQ16Z1与Y97菌株的核苷酸一致性和数字DNA-DNA杂交同源性计算结果分别为99.20%、91.00%。基因组比较分析结果显示,CQ16Z1与Y97菌株的基因组具有良好的共线性。两株菌的基因组共有基因数量为2177个,而CQ16Z1菌株具有217个特有基因,Y97菌株为267个。特有基因功能注释结果显示,两株菌在碳水化合物代谢、辅助因子和维生素代谢、膜转运、磷酸转移酶系统、噬菌体和耐药性相关的基因数量及种类差异较大。结论CQ16Z1、Y97两株菌同属福菜乳杆菌,近缘菌株遗传特征存在一定差异,其差异可能会影响该菌株表型,为福菜乳杆菌的应用研究奠定遗传学基础。

Objective To study the genomic differences between Lactobacillus futsaii subsp.chongqingii CQ16Z1(hereinafter referred to as CQ16Z1)and Lactobacillus futsaii subsp.futsaii YM0097(hereinafter referred to as Y97).Methods The whole genome of CQ16Z1 strain was sequenced based on the second and third generation sequencing technology.And the average nucleotide identity and digital DNA-DNA hybridization value of CQ16Z1 and Y97 strain were calculated.The genomes of the two strains were compared and analyzed through comparative genomics to analyze the difference of coding genes between the two strains.Results The genome of CQ16Z1 was 2654961 bp,the chromosome was 2625188 bp,and the GC content was 35.75%,including 5 circular plasmids with a size between 2000-14000 bp.The whole genome gene prediction results statistics showed that CQ16Z1 encoded a total of 2744 genes.The calculated results of the average nucleotide identity and digital DNA-DNA hybridization value of CQ16Z1 and Y97 were 99.20%and 91.00%,respectively.Genome comparison analysis showed that the genomes of CQ16Z1 and Y97 had a good collinear relationship.The number of shared genes in the genomes of the two strains was 2177,while CQ16Z1 had 217 unique genes and Y97 had 267.The results of unique gene annotation showed that there were differences in the number and types of genes related to carbohydrate metabolism,cofactors and vitamins metabolism,membrane transport,phosphotransferase system,phage and drug resistance between the two strains.Conclusion Both strains CQ16Z1 and Y97 belong to Lactobacillus futsaii,and the genetic characteristics of the closely related strains are different,which may affect the phenotype of the strains.This study lays a genetic foundation for the application and research of Lactobacillus futsaii.