title: Pseudogene accumulation might promote the adaptive microevolution of Yersinia pestis.
abstract: Plague is a natural focus-based disease, and for better understanding of this disease it is crucial to determine the molecular mechanisms of its pathogen, Yersinia pestis, for adapting to different foci. Gene inactivation, loss and acquisition are the main mechanisms that contribute to a pathogen's fitness. Determination of the whole-genome sequences of three Y. pestis strains, CO92, KIM and 91001, provided a good opportunity to probe into its genome in minute detail. Many genetic variations were found between the three strains. The present work focused on adaptive microevolutionary analysis of Y. pestis from different natural plague foci in China based on pseudogene profiles. Twenty-four mutations that led to inactivation in the corresponding genes were analysed, and a PCR-based screening method was employed to investigate the distribution of these mutations among Y. pestis isolates from different foci and also among seven strains of Yersinia pseudotuberculosis. It was found that Y. pestis isolates from the same focus had identical mutation profiles, and 260 isolates of Y. pestis were divided into eight genotypes, while Y. pseudotuberculosis harboured wild-type alleles for all the mutations. The isolates of three known biovars were grouped into distinct branches in the phylogenetic tree, which supports the proposition that biovars mediaevalis and orientalis directly arose from biovar antiqua individually. The constructed phylogenetic tree suggests that the isolates from focus B should be the oldest lineage of Y. pestis in China except for isolates from foci L and M, which might be a special lineage of Y. pestis and originated differently to the others.
authors.affiliation: Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, No. 20 Dongdajie, Fengtai, Beijing 100071, China 2Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China 3Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, China.
authors.forename: Zongzhong
authors.initials: Z
authors.lastname: Tong
authors.affiliation: Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, No. 20 Dongdajie, Fengtai, Beijing 100071, China 2Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China 3Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, China.
authors.forename: Dongsheng
authors.initials: D
authors.lastname: Zhou
authors.affiliation: Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, No. 20 Dongdajie, Fengtai, Beijing 100071, China 2Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China 3Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, China.
authors.forename: Yajun
authors.initials: Y
authors.lastname: Song
authors.affiliation: Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, No. 20 Dongdajie, Fengtai, Beijing 100071, China 2Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China 3Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, China.
authors.forename: Ling
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, No. 20 Dongdajie, Fengtai, Beijing 100071, China 2Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China 3Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, China.
authors.forename: Decui
authors.initials: D
authors.lastname: Pei
authors.affiliation: Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, No. 20 Dongdajie, Fengtai, Beijing 100071, China 2Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China 3Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, China.
authors.forename: Yanping
authors.initials: Y
authors.lastname: Han
authors.affiliation: Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, No. 20 Dongdajie, Fengtai, Beijing 100071, China 2Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China 3Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Pang
authors.affiliation: Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, No. 20 Dongdajie, Fengtai, Beijing 100071, China 2Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China 3Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, China.
authors.forename: Min
authors.initials: M
authors.lastname: Li
authors.affiliation: Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, No. 20 Dongdajie, Fengtai, Beijing 100071, China 2Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China 3Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, China.
authors.forename: Baizhong
authors.initials: B
authors.lastname: Cui
authors.affiliation: Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, No. 20 Dongdajie, Fengtai, Beijing 100071, China 2Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China 3Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, China.
authors.forename: Jin
authors.initials: J
authors.lastname: Wang
authors.affiliation: Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, No. 20 Dongdajie, Fengtai, Beijing 100071, China 2Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China 3Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, China.
authors.forename: Zhaobiao
authors.initials: Z
authors.lastname: Guo
authors.affiliation: Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, No. 20 Dongdajie, Fengtai, Beijing 100071, China 2Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China 3Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, China.
authors.forename: Zhizhen
authors.initials: Z
authors.lastname: Qi
authors.affiliation: Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, No. 20 Dongdajie, Fengtai, Beijing 100071, China 2Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China 3Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, China.
authors.forename: Lixia
authors.initials: L
authors.lastname: Jin
authors.affiliation: Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, No. 20 Dongdajie, Fengtai, Beijing 100071, China 2Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China 3Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, China.
authors.forename: Junhui
authors.initials: J
authors.lastname: Zhai
authors.affiliation: Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, No. 20 Dongdajie, Fengtai, Beijing 100071, China 2Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China 3Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, China.
authors.forename: Zongmin
authors.initials: Z
authors.lastname: Du
authors.affiliation: Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, No. 20 Dongdajie, Fengtai, Beijing 100071, China 2Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China 3Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, No. 20 Dongdajie, Fengtai, Beijing 100071, China 2Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China 3Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, China.
authors.forename: Xiaoyi
authors.initials: X
authors.lastname: Wang
authors.affiliation: Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, No. 20 Dongdajie, Fengtai, Beijing 100071, China 2Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China 3Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
authors.affiliation: Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, No. 20 Dongdajie, Fengtai, Beijing 100071, China 2Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China 3Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.affiliation: Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, No. 20 Dongdajie, Fengtai, Beijing 100071, China 2Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China 3Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, China.
authors.forename: Peitang
authors.initials: P
authors.lastname: Huang
authors.affiliation: Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, No. 20 Dongdajie, Fengtai, Beijing 100071, China 2Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China 3Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, China.
authors.forename: Huanming
authors.initials: H
authors.lastname: Yang
authors.affiliation: Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, No. 20 Dongdajie, Fengtai, Beijing 100071, China 2Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China 3Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, China.
authors.forename: Ruifu
authors.initials: R
authors.lastname: Yang
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D000818:Animals; D005075:Biological Evolution; D002681:China / Q000453:epidemiology; D004197:Disease Reservoirs; D020868:Gene Silencing / Q000502:physiology*; D014644:Genetic Variation; D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D009154:Mutation; D010802:Phylogeny; D010930:Plague / Q000453:epidemiology / Q000382:microbiology* / Q000635:transmission; D011544:Pseudogenes; D014774:Virulence / Q000235:genetics; D015010:Yersinia pestis / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity / Q000502:physiology