Pseudogene accumulation might promote the adaptive microevolution of Yersinia pestis.
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.
Tong
Zongzhong
Z
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.
Zhou
Dongsheng
D
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.
Song
Yajun
Y
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.
Zhang
Ling
L
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.
Pei
Decui
D
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.
Han
Yanping
Y
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.
Pang
Xin
X
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.
Li
Min
M
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.
Cui
Baizhong
B
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.
Wang
Jin
J
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.
Guo
Zhaobiao
Z
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.
Qi
Zhizhen
Z
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.
Jin
Lixia
L
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.
Zhai
Junhui
J
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.
Du
Zongmin
Z
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.
Wang
Jun
J
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.
Wang
Xiaoyi
X
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.
Yu
Jun
J
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.
Wang
Jian
J
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.
Huang
Peitang
P
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.
Yang
Huanming
H
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.
Yang
Ruifu
R
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.
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