Single-molecule approach to bacterial genomic comparisons via optical mapping.

PDF Version Also Available for Download.

Description

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 ... continued below

Physical Description

7773-7782

Creation Information

Zhou, Shiguo; Kile, A.; Bechner, M.; Kvikstad, E.; Deng, W.; Wei, J. et al. January 1, 2004.

Context

This article is part of the collection entitled: Office of Scientific & Technical Information Technical Reports and was provided by UNT Libraries Government Documents Department to Digital Library, a digital repository hosted by the UNT Libraries. It has been viewed 16 times , with 4 in the last month . More information about this article can be viewed below.

Who

People and organizations associated with either the creation of this article or its content.

Authors

Publisher

Provided By

UNT Libraries Government Documents Department

Serving as both a federal and a state depository library, the UNT Libraries Government Documents Department maintains millions of items in a variety of formats. The department is a member of the FDLP Content Partnerships Program and an Affiliated Archive of the National Archives.

Contact Us

What

Descriptive information to help identify this article. Follow the links below to find similar items on the Digital Library.

Description

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.

Physical Description

7773-7782

Subjects

STI Subject Categories

Source

  • Journal Name: Journal of Bacteriology; Journal Volume: 186; Journal Issue: 22

Language

Item Type

Identifier

Unique identifying numbers for this article in the Digital Library or other systems.

  • Report No.: DOE/ER63175- Final Report
  • Grant Number: FC02-01ER63175
  • DOI: 10.1128/JB.186.22.7773-7782.2004 | External Link
  • Office of Scientific & Technical Information Report Number: 1087909
  • Archival Resource Key: ark:/67531/metadc843172

Collections

This article is part of the following collection of related materials.

Office of Scientific & Technical Information Technical Reports

Reports, articles and other documents harvested from the Office of Scientific and Technical Information.

Office of Scientific and Technical Information (OSTI) is the Department of Energy (DOE) office that collects, preserves, and disseminates DOE-sponsored research and development (R&D) results that are the outcomes of R&D projects or other funded activities at DOE labs and facilities nationwide and grantees at universities and other institutions.

What responsibilities do I have when using this article?

When

Dates and time periods associated with this article.

Creation Date

  • January 1, 2004

Added to The UNT Digital Library

  • May 19, 2016, 9:45 a.m.

Description Last Updated

  • Dec. 1, 2016, 10:19 p.m.

Usage Statistics

When was this article last used?

Yesterday: 0
Past 30 days: 4
Total Uses: 16

Interact With This Article

Here are some suggestions for what to do next.

Start Reading

PDF Version Also Available for Download.

Citations, Rights, Re-Use

Zhou, Shiguo; Kile, A.; Bechner, M.; Kvikstad, E.; Deng, W.; Wei, J. et al. Single-molecule approach to bacterial genomic comparisons via optical mapping., article, January 1, 2004; United States. (digital.library.unt.edu/ark:/67531/metadc843172/: accessed October 23, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.