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.Methodology/Principal FindingsTo 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/SignificanceThe 19 SNP loci identified in this study should facilitate additional studies of the genetic population structure of Y. pestis across North America.
Highlights
Plague is a disease of both historical and current importance to global health
We report here the gapped genomic sequencing of strain FV-1, the comparative analysis of FV-1 with CO92 that has resulted in the identification of multiple informative single nucleotide polymorphism (SNP) markers, and the phylogenetic stratification of 22 different North American Y. pestis isolates using these markers
The Y. pestis FV-1 isolate used in this study was obtained from a plague epizootic in a Gunnison’s prairie dog (Cynomys gunnisoni) colony near the city of Flagstaff, Arizona, U.S.A. in 2001 [12]
Summary
The causative agent of plague, is responsible for some of the greatest epidemic scourges of mankind. It is widespread in the western United States, it has only been present there for just over 100 years. 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. 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.
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