title: Single-molecule approach to bacterial genomic comparisons via optical mapping.
abstract: Modern comparative genomics has been established, in part, by the sequencing and annotation of a broad range of microbial species. To gain further insights, new sequencing efforts are now dealing with the variety of strains or isolates that gives a species definition and range; however, this number vastly outstrips our ability to sequence them. Given the availability of a large number of microbial species, new whole genome approaches must be developed to fully leverage this information at the level of strain diversity that maximize discovery. Here, we describe how optical mapping, a single-molecule system, was used to identify and annotate chromosomal alterations between bacterial strains represented by several species. Since whole-genome optical maps are ordered restriction maps, sequenced strains of Shigella flexneri serotype 2a (2457T and 301), Yersinia pestis (CO 92 and KIM), and Escherichia coli were aligned as maps to identify regions of homology and to further characterize them as possible insertions, deletions, inversions, or translocations. Importantly, an unsequenced Shigella flexneri strain (serotype Y strain AMC[328Y]) was optically mapped and aligned with two sequenced ones to reveal one novel locus implicated in serotype conversion and several other loci containing insertion sequence elements or phage-related gene insertions. Our results suggest that genomic rearrangements and chromosomal breakpoints are readily identified and annotated against a prototypic sequenced strain by using the tools of optical mapping.
authors.affiliation: Laboratory for Molecular and Computation Genomics, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Shiguo
authors.initials: S
authors.lastname: Zhou
authors.forename: Andrew
authors.initials: A
authors.lastname: Kile
authors.forename: Michael
authors.initials: M
authors.lastname: Bechner
authors.forename: Michael
authors.initials: M
authors.lastname: Place
authors.forename: Erika
authors.initials: E
authors.lastname: Kvikstad
authors.forename: Wen
authors.initials: W
authors.lastname: Deng
authors.forename: Jun
authors.initials: J
authors.lastname: Wei
authors.forename: Jessica
authors.initials: J
authors.lastname: Severin
authors.forename: Rodney
authors.initials: R
authors.lastname: Runnheim
authors.forename: Christopher
authors.initials: C
authors.lastname: Churas
authors.forename: Daniel
authors.initials: D
authors.lastname: Forrest
authors.forename: Eileen T
authors.initials: ET
authors.lastname: Dimalanta
authors.forename: Casey
authors.initials: C
authors.lastname: Lamers
authors.forename: Valerie
authors.initials: V
authors.lastname: Burland
authors.forename: Frederick R
authors.initials: FR
authors.lastname: Blattner
authors.forename: David C
authors.initials: DC
authors.lastname: Schwartz
mesh_terms: D048168:Escherichia coli K12 / Q000235:genetics*; D016680:Genome, Bacterial; D023281:Genomics; D007091:Image Processing, Computer-Assisted; D015183:Restriction Mapping / Q000379:methods*; D012763:Shigella flexneri / Q000235:genetics*; D015010:Yersinia pestis / Q000235:genetics*