title: Complete genome sequence and comparative genome analysis of a new special Yersinia enterocolitica.
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.
authors.affiliation: Zhejiang Provincial Centre for Disease Control and Prevention, Hangzhou, People's Republic of China.
authors.forename: Guoxiang
authors.initials: G
authors.lastname: Shi
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China.|University of Chinese Academy of Sciences, Beijing, People's Republic of China.
authors.forename: Mingming
authors.initials: M
authors.lastname: Su
authors.affiliation: National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, 155 Changbai Road Changping District, Beiing, 102206, People's Republic of China.|Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, People's Republic of China.
authors.forename: Junrong
authors.initials: J
authors.lastname: Liang
authors.affiliation: National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, 155 Changbai Road Changping District, Beiing, 102206, People's Republic of China.|Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, People's Republic of China.
authors.forename: Ran
authors.initials: R
authors.lastname: Duan
authors.affiliation: Yunnan Provincial Centre for Disease Control and Prevention, Kunming, People's Republic of China.
authors.forename: Wenpeng
authors.initials: W
authors.lastname: Gu
authors.affiliation: National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, 155 Changbai Road Changping District, Beiing, 102206, People's Republic of China.|Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, People's Republic of China.
authors.forename: Yuchun
authors.initials: Y
authors.lastname: Xiao
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China.
authors.forename: Zhewen
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, 155 Changbai Road Changping District, Beiing, 102206, People's Republic of China.|Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, People's Republic of China.
authors.forename: Haiyan
authors.initials: H
authors.lastname: Qiu
authors.affiliation: Zhejiang Provincial Centre for Disease Control and Prevention, Hangzhou, People's Republic of China.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Wenzhou Municipal Centre for Disease Control and Prevention, Wenzhou, People's Republic of China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Li
authors.affiliation: Wenzhou Municipal Centre for Disease Control and Prevention, Wenzhou, People's Republic of China.
authors.forename: Xiaohe
authors.initials: X
authors.lastname: Zhang
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China.|University of Chinese Academy of Sciences, Beijing, People's Republic of China.
authors.forename: Yunchao
authors.initials: Y
authors.lastname: Ling
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China.|University of Chinese Academy of Sciences, Beijing, People's Republic of China.
authors.forename: Lai
authors.initials: L
authors.lastname: Song
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China.|University of Chinese Academy of Sciences, Beijing, People's Republic of China.
authors.forename: Meili
authors.initials: M
authors.lastname: Chen
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China.|University of Chinese Academy of Sciences, Beijing, People's Republic of China.
authors.forename: Yongbing
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China.
authors.forename: Jiayan
authors.initials: J
authors.lastname: Wu
authors.affiliation: National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, 155 Changbai Road Changping District, Beiing, 102206, People's Republic of China.|Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, People's Republic of China.
authors.forename: Huaiqi
authors.initials: H
authors.lastname: Jing
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China.
authors.forename: Jingfa
authors.initials: J
authors.lastname: Xiao
authors.affiliation: National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, 155 Changbai Road Changping District, Beiing, 102206, People's Republic of China. wangxin@icdc.cn.|Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, People's Republic of China. wangxin@icdc.cn.
authors.forename: Xin
authors.initials: X
authors.lastname: Wang
mesh_terms: D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping; D055028:Comparative Genomic Hybridization; D004926:Escherichia coli / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D010802:Phylogeny; D010957:Plasmids; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012338:RNA, Ribosomal, 23S / Q000235:genetics; D051381:Rats; D014508:Urea / Q000378:metabolism; D015008:Yersinia enterocolitica / Q000145:classification* / Q000235:genetics*
chemical_list: D012336:RNA, Ribosomal, 16S; D012338:RNA, Ribosomal, 23S; D014508:Urea
keywords: Comparative genome analysis; Complete genome sequence; Phylogenetic analysis; Yersinia