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Journal of Bacteriology, November 2004, p. 7773-7782, Vol. 186, No. 22
0021-9193/04/$08.00+0     DOI: 10.1128/JB.186.22.7773-7782.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Single-Molecule Approach to Bacterial Genomic Comparisons via Optical Mapping{dagger}

Shiguo Zhou,1,2,3 Andrew Kile,1,2,3 Michael Bechner,1,2,3 Michael Place,1,2,3 Erika Kvikstad,1,2,3 Wen Deng,3 Jun Wei,3 Jessica Severin,1,2,3 Rodney Runnheim,1,2,3 Christopher Churas,1,2,3 Daniel Forrest,1,2,3 Eileen T. Dimalanta,1,2,3 Casey Lamers,1,2,3 Valerie Burland,3 Frederick R. Blattner,3 and David C. Schwartz1,2,3*

Laboratory for Molecular and Computational Genomics,1 Department of Chemistry,2 Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin3

Received 3 December 2003/ Accepted 19 May 2004

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.

* Corresponding author. Mailing address: Laboratory for Molecular and Computation Genomics, 425 Henry Mall, University of Wisconsin-Madison, Madison, WI 53706. Phone: (608) 265-0546. Fax: (608) 265-6743. E-mail: dcschwartz{at}facstaff.wisc.edu.

{dagger} Presented in part at the 11th International Conference on Microbial Genomes, Durham, N.C., 28 September to 2 October 2003.

Journal of Bacteriology, November 2004, p. 7773-7782, Vol. 186, No. 22
0021-9193/04/$08.00+0     DOI: 10.1128/JB.186.22.7773-7782.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



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