单核细胞增生李斯特菌LMXJ15全基因组测序及分析

Whole Genome Sequencing and Analysis of Listeria monocytogenes Strain LMXJ15

为了解新疆地区单核细胞增生李斯特菌LMXJ15菌株的的基因组特征和进化关系。采用PacBio和Illumina HiSeq测序对LMXJ15菌株进行全基因组测序,使用相关软件对测序数据进行预测、注释,并进行多位点序列分型(mutilocus sequence typing,MLST)及共线性分析菌株间的同源性。结果显示单核细胞增生李斯特菌LMXJ15菌株基因组总长度为3017732 bp,平均GC含量为37.81%,预测到3154个编码基因,编码基因总长度为2734315 bp;包含6个rRNA操纵子和57个tRNA。编码基因通过CRT预测,发现一个CRISPR序列;通过GO数据库的对比分析,得到三类功能方面的2241个基因。预测到可能的毒力基因88个。MLST分析显示LMXJ15菌株为ST8型(sequence type,ST),属于CC8(clonal complex,CC)复合克隆系;进化分析显示其与意大利分离株IZSAM_Lm_15_17439_A144、瑞士分离株LmN1546和一株从熏鲑鱼分离菌株R479a在同一个进化分支上,具有相同的ST型和血清型(1/2a),并通过比较基因组分析显示4株LM的基因组之间的共线性较好。该研究初步分析了LMXJ15菌株基因组特征,毒力基因携带情况,为新疆地区单核细胞增生李斯特菌毒力和进化关系研究提供基础数据。

In order to understand the genomic characteristic and evolutionary relationship of Listeria monocytogenes LMXJ15 from Xinjiang,PacBio and Illumina HiSeq platforms were used to have the whole genome sequencing of LMXJ15,then the relevant software were applied to predict and annotate the sequenced data.Multilocus sequence typing(MLST)and collinearity analysis were conducted to analyze the homologies among the LM strains.The results showed that the length of LMXJ15 genome was 3017732 bp with a GC value of 37.81%.It was predicted to contain 3154 protein-coding genes with a total length of 2734315bp.The genome of LMXJ15 contained 6 rRNA operons and 57 tRNA,88 virulence genes being predicted from the genome.Through the CRT prediction,a CRISPR sequence was found in the LMXJ15 genome sequence.A total 2241 genes of 3 GO contents were obtained by comparing GO database.Total 88 possible virulence genes were predicted.MLST analysis showed that LMXJ15 was sequence type(ST)8 and belonged to CC8(clonal complex 8).Evolutionary analysis showed that the LMXJ15 had a close evolutionary relationship with two clinical IZSAM_Lm_15_17439_A144 isolates from Italy,LmN1546 isolates from Switzerland,R479a isolates from smoked salmon,and had the same ST type and serotype(1/2a),and comparative genomics among 4 LM strains showed scant collinearity.In summary,we preliminarily analyzed the genomic characteristics and virulence genes situation of LMXJ15 isolate,which may provide basic data for analysis of the evolution relationship and the virulence of L.monocytogenes in Xinjiang province.