Optical mapping as a routine tool for bacterial genome sequence finishing

  • Background: In sequencing the genomes of two Xenorhabdus species, we encountered a large number of sequence repeats and assembly anomalies that stalled finishing efforts. This included a stretch of about 12 Kb that is over 99.9% identical between the plasmid and chromosome of X. nematophila. Results: Whole genome restriction maps of the sequenced strains were produced through optical mapping technology. These maps allowed rapid resolution of sequence assembly problems, permitted closing of the genome, and allowed correction of a large inversion in a genome assembly that we had considered finished. Conclusion: Our experience suggests that routine use of optical mapping in bacterial genome sequence finishing is warranted. When combined with data produced through 454 sequencing, an optical map can rapidly and inexpensively generate an ordered and oriented set of contigs to produce a nearly complete genome sequence assembly.

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Author:Phil Latreille, Stacie Norton, Barry S. Goldman, John Henkhaus, Nancy Miller, Brad Barbazuk, Helge Björn BodeORCiDGND, Creg Darby, Zijin Du, Steve Forst, Sophie Gaudriault, Brad Goodner, Heidi Goodrich-Blair, Steven Slater
URN:urn:nbn:de:hebis:30:3-271412
DOI:https://doi.org/10.1186/1471-2164-8-321
ISSN:1471-2164
Pubmed Id:https://pubmed.ncbi.nlm.nih.gov/17868451
Parent Title (English):BMC genomics
Publisher:BioMed Central
Place of publication:London
Document Type:Article
Language:English
Year of Completion:2007
Date of first Publication:2007/09/14
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2012/12/19
Volume:8
Issue:321
Page Number:6
Note:
© 2007 Latreille et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
HeBIS-PPN:315856432
Institutes:Biowissenschaften / Biowissenschaften
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
Sammlungen:Universitätspublikationen
Sammlung Biologie / Biologische Hochschulschriften (Goethe-Universität)
Licence (German):License LogoCreative Commons - Namensnennung 2.0