Yersinia pestis is the causative agent of the bubonic, septicemic, and pneumonic plagues (also known as black death) and has been responsible for recurrent devastating pandemics throughout history. To further understand this virulent bacterium and to accelerate an ongoing sequencing project, two whole-genome restriction maps (XhoI and PvuII) of Y. pestis strain KIM were constructed using shotgun optical mapping. This approach constructs ordered restriction maps from randomly sheared individual DNA molecules directly extracted from cells. The two maps served different purposes; the XhoI map facilitated sequence assembly by providing a scaffold for high-resolution alignment, while the PvuII map verified genome sequence assembly. Our results show that such maps facilitated the closure of sequence gaps and, most importantly, provided a purely independent means for sequence validation. Given the recent advancements to the optical mapping system, increased resolution and throughput are enabling such maps to guide sequence assembly at a very early stage of a microbial sequencing project.There are 11 species in the genus Yersinia, 3 of which are pathogenic for humans (Yersinia pestis, Y. enteroclitica, and Y. pseudotuberculosis). Of the three pathogenic species, Y. pestis, which lives in rodents, transmits this pathogen to humans via fleas, causing bubonic, septicemic, and pneumonic plagues (also known as black death). Y. pestis has been responsible for many recurrent devastating pandemics throughout history, resulting in widespread loss of human life (1,7,22). To understand the molecular mechanisms that define the pathogenicity of this bacterial species, sequencing of two strains (KIM and CO-92 biovar Orientalis) of Y. pestis was funded by the National Institute of Allergy and Infectious Diseases and Beowulf Genomics. The two separate sequencing projects were conducted by F. Blattner's laboratory (University of WisconsinMadison) and Sanger Center (Hinxton, United Kingdom), using the strategy of whole-genome shotgun sequencing (11). Although this sequencing strategy has racked up an impressive number of completed microbial genomes, it can be further optimized in terms of the cost and effort required during the finishing stages. In this regard, physical maps serve to guide sequence assembly, characterize gaps, and validate the finished sequence. Furthermore, ordered restriction maps are particularly useful when attempting to assemble genomic regions containing repeats, since cleavage patterns can accurately discern such sequence elements.The costly appellation of "finished," assumed when dealing with high-quality sequence data, minimally mandates that no genomic region be excluded from the final results (23) and thus requires extensive finishing efforts. The chances that entire regions of a genome might be excluded from "completed" sequence increases in the face of limited budgets and the absence of physical mapping data. Because of these issues, optical maps were used (15) at an early stage of sequence assembly to iden...
