title: Shotgun optical maps of the whole Escherichia coli O157:H7 genome.
abstract: 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.
authors.affiliation: Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
authors.forename: A
authors.initials: A
authors.lastname: Lim
authors.forename: E T
authors.initials: ET
authors.lastname: Dimalanta
authors.forename: K D
authors.initials: KD
authors.lastname: Potamousis
authors.forename: G
authors.initials: G
authors.lastname: Yen
authors.forename: J
authors.initials: J
authors.lastname: Apodoca
authors.forename: C
authors.initials: C
authors.lastname: Tao
authors.forename: J
authors.initials: J
authors.lastname: Lin
authors.forename: R
authors.initials: R
authors.lastname: Qi
authors.forename: J
authors.initials: J
authors.lastname: Skiadas
authors.forename: A
authors.initials: A
authors.lastname: Ramanathan
authors.forename: N T
authors.initials: NT
authors.lastname: Perna
authors.forename: G
authors.initials: G
authors.lastname: Plunkett
authors.forename: V
authors.initials: V
authors.lastname: Burland
authors.forename: B
authors.initials: B
authors.lastname: Mau
authors.forename: J
authors.initials: J
authors.lastname: Hackett
authors.forename: F R
authors.initials: FR
authors.lastname: Blattner
authors.forename: T S
authors.initials: TS
authors.lastname: Anantharaman
authors.forename: B
authors.initials: B
authors.lastname: Mishra
authors.forename: D C
authors.initials: DC
authors.lastname: Schwartz
mesh_terms: D020451:Contig Mapping / Q000379:methods*; D019453:Escherichia coli O157 / Q000235:genetics*; D016680:Genome, Bacterial; D015183:Restriction Mapping / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software