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Published online before print August 16, 2001, 10.1101/gr.172101
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Vol. 11, Issue 9, 1584-1593, September 2001

METHODS
Shotgun Optical Maps of the Whole Escherichia coli O157:H7 Genome

Alex Lim,1,2 Eileen T. Dimalanta,1,2 Konstantinos D. Potamousis,1 Galex Yen,1 Jennifer Apodoca,1 Chunhong Tao,1,2 Jieyi Lin,3,8 Rong Qi,3,9 John Skiadas,3,10 Arvind Ramanathan,1,3 Nicole T. Perna,4,11 Guy Plunkett III,4 Valerie Burland,4 Bob Mau,4 Jeremiah Hackett,4,12 Frederick R. Blattner,4 Thomas S. Anantharaman,1,5 Bhubaneswar Mishra,6 and David C. Schwartz1,2,7,13

1 Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; 2 Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; 3 W.M. Keck Laboratory for Biomolecular Imaging, New York University, New York, New York 10003, USA; 4 Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; 5 Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; 6 Courant Institute of Mathematical Sciences, New York University, Department of Computer Science, New York, New York 10012, USA; 7 Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA

We have constructed NheI and XhoI optical maps of Escherichia coli O157:H7 solely from genomic DNA molecules to provide a uniquely valuable scaffold for contig closure and sequence validation. E. coli O157:H7 is a common pathogen found in contaminated food and water. Our approach obviated the need for the analysis of clones, PCR products, and hybridizations, because maps were constructed from ensembles of single DNA molecules. Shotgun sequencing of bacterial genomes remains labor-intensive, despite advances in sequencing technology. This is partly due to manual intervention required during the last stages of finishing. The applicability of optical mapping to this problem was enhanced by advances in machine vision techniques that improved mapping throughput and created a path to full automation of mapping. Comparisons were made between maps and sequence data that characterized sequence gaps and guided nascent assemblies.

Present addresses: 8Cereon Genomics, Cambridge, MA 02139 USA; 9Celera Genomics, Rockville, MD, 20850 USA; 10Department of Viticulture and Enology, University of California-Davis, Davis, CA 95616 USA; 11Animal Health and Biomedical Sciences, University of Wisconsin-Madison, Madison, WI 53706 USA; 12Interdisciplinary Programs, University of Iowa, Iowa City, IA 52242 USA.

13 Corresponding author.

11:1584-1593 ©2001 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/01 $5.00
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