我国新发现的鼠疫自然疫源地鼠疫菌基因组序列测定及分析

目的 测定和分析我国新发现的鼠疫自然疫源地鼠疫菌株（耶尔森菌）的全基因组序列，探讨玉龙疫情菌株(D106004)与邻近两个疫源地剑川菌株(D182038)和西藏菌株(Z176003)的亲缘关系。方法 采用全基因鸟枪法及Solexa方法对3株鼠疫菌株进行全基因组测序，并进行比较基因组学分析。基因组间编码序列比较分析采用BLAST软件进行，基因组间重排分析采用MAUVE软件进行。结果 鼠疫菌株D106004、D 182038、Z176003均具有1个染色体和3个质粒，菌株间染色体、质粒特征基本相似；3株菌株间编码序列的蛋白相邻类的聚簇(COG)功能分类及插入序列数目比较差异无统计学意义(x2值分别为3.03、0.257，P均＞0.05)。菌株间编码序列、单核苷酸多态性(SNPs)和基因组重排结果显示，在3株菌株中，有2882个基因具有100％的同源性。其中D106004菌株预测的3636个基因中与D182038菌株一致的基因有2994个,90％以上相似的基因有240个；与Z176003菌株一致的基因有3113个，90％以上相似的基因有200个；D106004菌株与Z176003、D182038菌株的同义SNPs数为59、68个，非同义SNPs数为104、203个；D106004与Z176003菌株之间可分为11个重排片段，较之D106004与D182038菌株之间的16个重排片段数目明显减少。结论 3株鼠疫菌株基因之间具有高度同源性，D106004与Z176003菌株之间的亲缘关系较之与D182038菌株更为接近，玉龙疫源地菌株可能是由西藏疫源地菌株进化而来。

Comparison of Yersinia pestis genomes from a new natural foci in China

Objective Measurement and analysis of the complete genome sequences of Yersinia Pestis from a new plague natural foci and adjacent foci in China, to know the genetic relationship among the epidemic strain isolated in Yulong (D 106004) and Jianchuan strains (D 182038) and the Tibetan strain ( Z 176003 ). Methods Three complete genome sequences were sequenced using the whole-genome shotgun and Solexa method and comparative genomics analysis was done among the three sequences. Genome comparative analysis among the coding sequences was done by BLAST software, SNPs finding was done by the program, genome rearrangements were analyzed using MAUVE software. Results All of the genomes of Yersinia pestis strains D182038, D106004 and Z176003 consist of a single circular chromosome and three virulence plasmids, pMT1, pCD1 and pPCP1. They had similar characteristics in chromosome and plasmid features, and there were no significant difference in coming sequence (CDS) of the cluster of orthologous groups of proteins (COG) functional classification and the number of insertion sequence in the three strains (x2 =3.03, 0.257, all P ＞ 0.05). The comparative genomics results showed that the three bacteria had 2882 genes with 100％ homology, of 3636 genes predicted in D106004, 2994 were identical with D182038's and 3113 with Z176003's, and of which 240 had 90％ homology with D182038's and 200 with Z176003 's. Synonymous single nucleotide polymorphisms(sSNPs) were 59 and 68, and non-synonymous SNPs(nsSNPs) were 104 and 203 between strains D106004 and Z176003/D182038. There were 11 segments rearrangements between D106004 and Z176003, which was less than 16 segments rearrangements between D106004 and D182038. Conclusions The three strains are highly homologous, the Yulong strain has more similarity with Tibet strain than with Jianchuan strain, the strain from Yulong foci may be evolved from Tibet foci.