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Archives of Microbiology

, Volume 198, Issue 7, pp 673–687 | Cite as

Complete genome sequence and comparative genome analysis of a new special Yersinia enterocolitica

  • Guoxiang Shi
  • Mingming Su
  • Junrong Liang
  • Ran Duan
  • Wenpeng Gu
  • Yuchun Xiao
  • Zhewen Zhang
  • Haiyan Qiu
  • Zheng Zhang
  • Yi Li
  • Xiaohe Zhang
  • Yunchao Ling
  • Lai Song
  • Meili Chen
  • Yongbing Zhao
  • Jiayan Wu
  • Huaiqi Jing
  • Jingfa Xiao
  • Xin Wang
Original Paper

Abstract

Yersinia enterocolitica is the most diverse species among the Yersinia genera and shows more polymorphism, especially for the non-pathogenic strains. Individual non-pathogenic Y. enterocolitica strains are wrongly identified because of atypical phenotypes. In this study, we isolated an unusual Y. enterocolitica strain LC20 from Rattus norvegicus. The strain did not utilize urea and could not be classified as the biotype. API 20E identified Escherichia coli; however, it grew well at 25 °C, but E. coli grew well at 37 °C. We analyzed the genome of LC20 and found the whole chromosome of LC20 was collinear with Y. enterocolitica 8081, and the urease gene did not exist on the genome which is consistent with the result of API 20E. Also, the 16 S and 23 SrRNA gene of LC20 lay on a branch of Y. enterocolitica. Furthermore, the core-based and pan-based phylogenetic trees showed that LC20 was classified into the Y. enterocolitica cluster. Two plasmids (80 and 50 k) from LC20 shared low genetic homology with pYV from the Yersinia genus, one was an ancestral Yersinia plasmid and the other was novel encoding a number of transposases. Some pathogenic and non-pathogenic Y. enterocolitica-specific genes coexisted in LC20. Thus, although it could not be classified into any Y. enterocolitica biotype due to its special biochemical metabolism, we concluded the LC20 was a Y. enterocolitica strain because its genome was similar to other Y. enterocolitica and it might be a strain with many mutations and combinations emerging in the processes of its evolution.

Keywords

Complete genome sequence Comparative genome analysis Phylogenetic analysis Yersinia 

Notes

Acknowledgments

This work was supported by the National Natural Science Foundation of China (General Project, no. 31100101) and the National Sci-Tech Key Project (2012ZX10004-201, 2013ZX10004203-002). We thank Liuying Tang and Jim Nelson for critical reading of and helpful comments on our manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

203_2016_1229_MOESM1_ESM.xlsx (12 kb)
Table S1A. Annotation of LC20 plasmid 1 (XLSX 11 kb)
203_2016_1229_MOESM2_ESM.xlsx (11 kb)
Table S1B. Annotation of LC20 plasmid 2 (XLSX 11 kb)
203_2016_1229_MOESM3_ESM.xlsx (57 kb)
Table S2. COG annotation of LC20 unique genes (XLSX 56 kb)
203_2016_1229_MOESM4_ESM.docx (34 kb)
Table S3A. LC20 plasmid 1 alignments reports (DOCX 33 kb)
203_2016_1229_MOESM5_ESM.xlsx (16 kb)
Table S3B. LC20 plasmid 2 alignments reports (XLSX 16 kb)
203_2016_1229_MOESM6_ESM.xlsx (9 kb)
Table S4A. The number of strains did 16SrRNA analysis in this study (XLSX 9 kb)
203_2016_1229_MOESM7_ESM.xlsx (14 kb)
Table S4B. The detail of strains did 16SrRNA analysis in this study (XLSX 14 kb)
203_2016_1229_MOESM8_ESM.tif (895 kb)
Figure S1. 16 S rRNA phylogenetic tree of LC20 and type strains in the Yersinia genus from RDP (TIFF 895 kb)
203_2016_1229_MOESM9_ESM.tif (423 kb)
Figure S2. 23S rRNA phylogenetic tree of LC20 (TIFF 422 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Guoxiang Shi
    • 1
  • Mingming Su
    • 2
    • 3
  • Junrong Liang
    • 4
    • 5
  • Ran Duan
    • 4
    • 5
  • Wenpeng Gu
    • 6
  • Yuchun Xiao
    • 4
    • 5
  • Zhewen Zhang
    • 2
  • Haiyan Qiu
    • 4
    • 5
  • Zheng Zhang
    • 1
  • Yi Li
    • 7
  • Xiaohe Zhang
    • 7
  • Yunchao Ling
    • 2
    • 3
  • Lai Song
    • 2
    • 3
  • Meili Chen
    • 2
    • 3
  • Yongbing Zhao
    • 2
    • 3
  • Jiayan Wu
    • 2
  • Huaiqi Jing
    • 4
    • 5
  • Jingfa Xiao
    • 2
  • Xin Wang
    • 4
    • 5
  1. 1.Zhejiang Provincial Centre for Disease Control and PreventionHangzhouPeople’s Republic of China
  2. 2.CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of GenomicsChinese Academy of SciencesBeijingPeople’s Republic of China
  3. 3.University of Chinese Academy of SciencesBeijingPeople’s Republic of China
  4. 4.National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and PreventionState Key Laboratory of Infectious Disease Prevention and ControlBeiingPeople’s Republic of China
  5. 5.Collaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesBeijingPeople’s Republic of China
  6. 6.Yunnan Provincial Centre for Disease Control and PreventionKunmingPeople’s Republic of China
  7. 7.Wenzhou Municipal Centre for Disease Control and PreventionWenzhouPeople’s Republic of China

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