Optical mapping as a routine tool for bacterial genome sequence finishing
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
BMC Genomics 2007, 8:321 doi:10.1186/1471-2164-8-321Published: 14 September 2007
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.
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.
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.