title: A whole-genome shotgun optical map of Yersinia pestis strain KIM.
abstract: 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.
authors.affiliation: Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, 53706, USA.
authors.forename: Shiguo
authors.initials: S
authors.lastname: Zhou
authors.forename: Wen
authors.initials: W
authors.lastname: Deng
authors.forename: Thomas S
authors.initials: TS
authors.lastname: Anantharaman
authors.forename: Alex
authors.initials: A
authors.lastname: Lim
authors.forename: Eileen T
authors.initials: ET
authors.lastname: Dimalanta
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Tian
authors.initials: T
authors.lastname: Wu
authors.forename: Tao
authors.initials: T
authors.lastname: Chunhong
authors.forename: Robert
authors.initials: R
authors.lastname: Creighton
authors.forename: Andrew
authors.initials: A
authors.lastname: Kile
authors.forename: Erika
authors.initials: E
authors.lastname: Kvikstad
authors.forename: Michael
authors.initials: M
authors.lastname: Bechner
authors.forename: Galex
authors.initials: G
authors.lastname: Yen
authors.forename: Ana
authors.initials: A
authors.lastname: Garic-Stankovic
authors.forename: Jessica
authors.initials: J
authors.lastname: Severin
authors.forename: Dan
authors.initials: D
authors.lastname: Forrest
authors.forename: Rod
authors.initials: R
authors.lastname: Runnheim
authors.forename: Chris
authors.initials: C
authors.lastname: Churas
authors.forename: Casey
authors.initials: C
authors.lastname: Lamers
authors.forename: Nicole T
authors.initials: NT
authors.lastname: Perna
authors.forename: Valerie
authors.initials: V
authors.lastname: Burland
authors.forename: Frederick R
authors.initials: FR
authors.lastname: Blattner
authors.forename: Bhubaneswar
authors.initials: B
authors.lastname: Mishra
authors.forename: David C
authors.initials: DC
authors.lastname: Schwartz
mesh_terms: D016680:Genome, Bacterial; D015183:Restriction Mapping; D015010:Yersinia pestis / Q000235:genetics*