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Open Access Methodology article

Optical mapping as a routine tool for bacterial genome sequence finishing

Phil Latreille1, Stacie Norton1, Barry S Goldman1, John Henkhaus2, Nancy Miller1, Brad Barbazuk3, Helge B Bode4, Creg Darby5, Zijin Du1, Steve Forst6, Sophie Gaudriault7, Brad Goodner8, Heidi Goodrich-Blair9 and Steven Slater10*

Author Affiliations

1 Monsanto Company, 800 North Lindbergh Boulevard St. Louis, MO 63167, USA

2 OpGen Technologies, Inc., 510 Charmany Drive, Suite 151, Madison, WI 53719, USA

3 Donald Danforth Plant Sciences Center, 975 North Warson Road St. Louis, MO 63132, USA

4 Institut für Pharmazeutische Biotechnologie, Universität des Saarlandes, 66123 Saarbrücken, Germany

5 University of California, San Francisco, Department of Cell and Tissue Biology, San Francisco, CA 94143, USA

6 University of Wisconsin, Milwaukee, Department of Biological Sciences, Milwaukee, WI 53211, USA

7 Institut National de la Recherche Agronomique-Université de Montpellier II, 34095 Montpellier, France

8 Hiram College, Department of Biology, Hiram, OH 44234, USA

9 University of Wisconsin, Department of Bacteriology, Madison, WI 53076, USA

10 Arizona State University, The Biodesign Institute and Department of Applied Biological Sciences, 7001 E. Williams Field Road, Mesa, AZ 85212, USA

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BMC Genomics 2007, 8:321  doi:10.1186/1471-2164-8-321

Published: 14 September 2007

Abstract

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.