A North American Yersinia pestis draft genome sequence: SNPs and phylogenetic analysis.
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.
Touchman
Jeffrey W
JW
The Translational Genomics Research Institute, Phoenix, Ariziona, United States of America. jtouchman@tgen.org
Wagner
David M
DM
Hao
Jicheng
J
Mastrian
Stephen D
SD
Shah
Maulik K
MK
Vogler
Amy J
AJ
Allender
Christopher J
CJ
Clark
Erin A
EA
Benitez
Debbie S
DS
Youngkin
David J
DJ
Girard
Jessica M
JM
Auerbach
Raymond K
RK
Beckstrom-Sternberg
Stephen M
SM
Keim
Paul
P
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
D004269:DNA, Bacterial