title: A North American Yersinia pestis draft genome sequence: SNPs and phylogenetic analysis.
abstract: BACKGROUND
  Yersinia pestis, the causative agent of plague, is responsible for some of the greatest epidemic scourges of mankind. It is widespread in the western United States, although it has only been present there for just over 100 years. As a result, there has been very little time for diversity to accumulate in this region. Much of the diversity that has been detected among North American isolates is at loci that mutate too quickly to accurately reconstruct large-scale phylogenetic patterns. Slowly-evolving but stable markers such as SNPs could be useful for this purpose, but are difficult to identify due to the monomorphic nature of North American isolates.
  
  
  RESULTS
  To identify SNPs that are polymorphic among North American populations of Y. pestis, a gapped genome sequence of Y. pestis strain FV-1 was generated. Sequence comparison of FV-1 with another North American strain, CO92, identified 19 new SNP loci that differ among North American isolates.
  
  
  CONCLUSIONS
  The 19 SNP loci identified in this study should facilitate additional studies of the genetic population structure of Y. pestis across North America.
authors.affiliation: The Translational Genomics Research Institute, Phoenix, Ariziona, United States of America. jtouchman@tgen.org
authors.forename: Jeffrey W
authors.initials: JW
authors.lastname: Touchman
authors.forename: David M
authors.initials: DM
authors.lastname: Wagner
authors.forename: Jicheng
authors.initials: J
authors.lastname: Hao
authors.forename: Stephen D
authors.initials: SD
authors.lastname: Mastrian
authors.forename: Maulik K
authors.initials: MK
authors.lastname: Shah
authors.forename: Amy J
authors.initials: AJ
authors.lastname: Vogler
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Allender
authors.forename: Erin A
authors.initials: EA
authors.lastname: Clark
authors.forename: Debbie S
authors.initials: DS
authors.lastname: Benitez
authors.forename: David J
authors.initials: DJ
authors.lastname: Youngkin
authors.forename: Jessica M
authors.initials: JM
authors.lastname: Girard
authors.forename: Raymond K
authors.initials: RK
authors.lastname: Auerbach
authors.forename: Stephen M
authors.initials: SM
authors.lastname: Beckstrom-Sternberg
authors.forename: Paul
authors.initials: P
authors.lastname: Keim
mesh_terms: D000818:Animals; D001130:Arizona / Q000453:epidemiology; D001483:Base Sequence; D004269:DNA, Bacterial / Q000235:genetics; D004196:Disease Outbreaks / Q000662:veterinary; D004197:Disease Reservoirs; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D006801:Humans; D008969:Molecular Sequence Data; D009656:North America; D010802:Phylogeny; D010930:Plague / Q000453:epidemiology / Q000382:microbiology; D020641:Polymorphism, Single Nucleotide; D012376:Rodent Diseases / Q000453:epidemiology / Q000382:microbiology; D012377:Rodentia; D012589:Sciuridae; D015010:Yersinia pestis / Q000235:genetics* / Q000302:isolation & purification; D015011:Yersinia pseudotuberculosis / Q000235:genetics
chemical_list: D004269:DNA, Bacterial