A whole-genome shotgun optical map of Yersinia pestis strain KIM

Shiguo Zhou, Wen Deng, Thomas S. Anantharaman, Alex Lim, Eileen T. Dimalanta, Jun Wang, Tian Wu, Tao Chunhong, Robert Creighton, Andrew Kile, Erika Kvikstad, Michael Bechner, Galex Yen, Ana Garic-Stankovic, Jessica Severin, Dan Forrest, Rod Runnheim, Chris Churas, Casey Lamers, Nicole T. PernaValerie Burland, Frederick R. Blattner, Bhubaneswar Mishra, David C. Schwartz

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Pages (from-to)6321-6331
Number of pages11
JournalApplied and Environmental Microbiology
Issue number12
StatePublished - Dec 1 2002

ASJC Scopus subject areas

  • Applied Microbiology and Biotechnology
  • Food Science
  • Biotechnology
  • Ecology


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