{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T08:40:39Z","timestamp":1791276039328,"version":"4.1.0"},"reference-count":42,"publisher":"American Society for Microbiology","issue":"22","license":[{"start":{"date-parts":[[2004,11,15]],"date-time":"2004-11-15T00:00:00Z","timestamp":1100476800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Bacteriol"],"published-print":{"date-parts":[[2004,11,15]]},"abstract":"<jats:title>ABSTRACT<\/jats:title><jats:p>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<jats:italic>Shigella flexneri<\/jats:italic>serotype 2a (2457T and 301),<jats:italic>Yersinia pestis<\/jats:italic>(CO 92 and KIM), and<jats:italic>Escherichia coli<\/jats:italic>were aligned as maps to identify regions of homology and to further characterize them as possible insertions, deletions, inversions, or translocations. Importantly, an unsequenced<jats:italic>Shigella flexneri<\/jats:italic>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.<\/jats:p>","DOI":"10.1128\/jb.186.22.7773-7782.2004","type":"journal-article","created":{"date-parts":[[2004,10,31]],"date-time":"2004-10-31T07:42:41Z","timestamp":1099208561000},"page":"7773-7782","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":62,"title":["Single-Molecule Approach to Bacterial Genomic Comparisons via Optical Mapping"],"prefix":"10.1128","volume":"186","author":[{"given":"Shiguo","family":"Zhou","sequence":"first","affiliation":[{"name":"Laboratory for Molecular and Computational Genomics"},{"name":"Department of Chemistry"},{"name":"Laboratory of Genetics, University of Wisconsin-Madison, Madison, 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Wisconsin"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erika","family":"Kvikstad","sequence":"additional","affiliation":[{"name":"Laboratory for Molecular and Computational Genomics"},{"name":"Department of Chemistry"},{"name":"Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wen","family":"Deng","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Wei","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica","family":"Severin","sequence":"additional","affiliation":[{"name":"Laboratory for Molecular and Computational Genomics"},{"name":"Department of Chemistry"},{"name":"Laboratory of 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Wisconsin"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eileen T.","family":"Dimalanta","sequence":"additional","affiliation":[{"name":"Laboratory for Molecular and Computational Genomics"},{"name":"Department of Chemistry"},{"name":"Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Casey","family":"Lamers","sequence":"additional","affiliation":[{"name":"Laboratory for Molecular and Computational Genomics"},{"name":"Department of Chemistry"},{"name":"Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valerie","family":"Burland","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frederick 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