Detection and analysis of complete genome sequence of Yersinia pestis human-avirulent strain 91001 / 解放军医学杂志

ABSTRACT

Objective To better understand the pathogenicity and evolution of Yersinia pestis, we carried out the whole genome sequencing of human-avirulent Yersinia pestis strain 91001, which was isolated from a species of rodent-Microtus brandti. Methods We utilized “whole genome shotgun” approach to get the genome sequence of 91001. Based on the finished and annotated genome sequence of 91001, as well as the previously published genome sequences of CO92 and KIM, we performed detailed comparative genomics analysis on their chromosomes and plasmids. Results The genome of 91001 consisted of one chromosome and four plasmids (pPCP1, pCD1, pMT1 and pCRY). The pPCP1 plasmid of 9 609bp was almost identical with its counterparts from reference strains, which possessed 10 CDS. Plasmid pCD1 was found to be a plasmid of the type III secretory apparatus, and its length was 70 159bp. Although its CDS are quite similar to those of the reference plasmids, there were obvious rearrangements which produced certain differences in structure among them. Another plasmid was pMT1, a 106 642bp plasmid, which showed slightly different architecture compared with the reference ones. There was no mutation in virulent-related genes of pMT1 and pMT1 of 91001, which seemed to have retained more fragments of an ancestor plasmid. pCRY was a novel plasmid discovered in this work. It was 21 742bp long and harbored a group of gene encoding type IV secretory system. pCRY seemed to be able to replicate. The length of chromosome of 91001 was 4 595 065bp, and among its 4 037 predicted CDS (coding sequences), 141 were possibly pseudogenes. There were many IS in the chromosome. Due to the rearrangments mediated by IS, the structure of 91001 chromosome showed significant differences compared with CO92 and KIM. According to the results of comparative genomics analysis, we deduced the genetic mechanisms of nitrate reduction, glycerol fermentation, arabinose and milibiose utilization in 91001. Conclusion According to the analysis of plasmids structure, pseudogenes distribution, nitrate reduction negative mechanism, gene comparison and chromosome architecture, we conclude that 91001 and other strains isolated from Microtus brandti and Microtus fuscus evolved from ancestor Y. pestis and then developed into a different lineage. The deletion of large genome fragments from 91001 chromosome and pseuogenes might contribute to its unqiue pathogenicity and host-specificity.