ParkhillJWrenBWThomsonNRTitballRWHoldenTGPrenticeMBSebaihiaMJamesKDChurcherCMungallKLBakerSBashamDBentleySDBrooksKCerdeño-TárragaAMChillingworthTCroninADaviesRMDavisPDougankGFeltwellTHamlinNHolroydSJagelsKKarlyshevAVLeatherSMouleSOystonCFQuailMRutherfordKSimmondsMSkeltonJStevensKWhiteheadSBarrellBG, 2001. Genome sequence of Yersinia pestis, the causative agent of plague. Nature413: 523–527.)| false
ChainSG, CarnielE, LarimerW, LamerdinJ, StoutlandPO, RegalaWM, GeorgescuAM, VergezLM, LandML, MotinVL, BrubakerRR, FowlerJ, HinnebuschJ, MarceauM, MedigueC, SimonetM, Chenal-FrancisqueV, SouzaB, DacheuxD, ElliottJM, DerbiseA, HauserLJ, GarciaE, 2004. Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. Proc Natl Acad Sci USA101: 13826–13831.
ChainSGCarnielELarimerWLamerdinJStoutlandPORegalaWMGeorgescuAMVergezLMLandMLMotinVLBrubakerRRFowlerJHinnebuschJMarceauMMedigueCSimonetMChenal-FrancisqueVSouzaBDacheuxDElliottJMDerbiseAHauserLJGarciaE, 2004. Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. Proc Natl Acad Sci USA101: 13826–13831.)| false
SongYTongZWangJWangLGuoZHanYZhangJPeiDZhouDQinHPangXHanYZhaiJLiMCuiBQiZJinLDaiRChenFLiSYeCDuZLinWWangJYuJYangHWangJHuangPYangR, 2004. Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans. DNA Res11: 179–197.)| false
ChainSG, HuP, MalfattiSA, RadnedgeL, LarimerF, VergezLM, WorshamP, ChuMC, AndersenGL, 2006. Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen. J Bacteriol188: 4453–4463.
ChainSGHuPMalfattiSARadnedgeLLarimerFVergezLMWorshamPChuMCAndersenGL, 2006. Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen. J Bacteriol188: 4453–4463.)| false
EppingerM, WorshamPL, NikolichMP, RileyDR, SebastianY, MouS, AchtmanM, LindlerLE, RavelJ, 2010. Genome sequence of the deep-rooted Yersinia pestis strain Angola reveals new insights into the evolution and pangenome of the plague bacterium. J Bacteriol192: 1685–1699.
EppingerMWorshamPLNikolichMPRileyDRSebastianYMouSAchtmanMLindlerLERavelJ, 2010. Genome sequence of the deep-rooted Yersinia pestis strain Angola reveals new insights into the evolution and pangenome of the plague bacterium. J Bacteriol192: 1685–1699.)| false
State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China; Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
The Yersinia pestis chromosome contains a large variety and number of insert sequences that have resulted in frequent chromosome rearrangement events. To identify the chromosomal rearrangement features of Y. pestis strains from five typical plague foci in China and study spontaneous DNA rearrangements potentially stabilized in certain lineages of Y. pestis genomes, we examined the linking mode of locally collinear blocks (LCBs) in 30 Y. pestis strains by a polymerase chain reaction-based method. Our results suggest most strains have relatively stable chromosomal arrangement patterns, and these rearrangement characteristics also have a very close relationship with the geographical origin. In addition, some LCB linking modes are only present in specific strains. We conclude Y. pestis chromosome rearrangement patterns may reflect the genetic features of specific geographical areas and can be applied to distinguish Y. pestis isolates; furthermore, most of the rearrangement events are stable in certain lineages of Y. pestis genomes.
* Address correspondence to Rong Hai, 155 Changbai Road, Changping District, Beijing 102206, China. E-mail: firstname.lastname@example.org† These authors contributed equally to this work.
Financial support: This work was supported by a grant (award 201202021) from the Special Fund for Health Sector, People's Republic of China, and grant (2012ZX10004215) from the National Key Programs for Infectious Diseases of China.