1. Shotgun Optical Maps of the Whole Escherichia coli O157:H7 Genome
- Author
-
David C. Schwartz, Arvind Ramanathan, Alex Lim, John Skiadas, Rong Qi, Frederick R. Blattner, Bhubaneswar Mishra, Jennifer Apodoca, Galex Yen, Jeremiah D. Hackett, Konstantinos Potamousis, Jieyi Lin, Chunhong Tao, Valerie Burland, Bob Mau, Guy Plunkett, Nicole T. Perna, Thomas Anantharaman, and Eileen T. Dimalanta
- Subjects
Genetics ,XhoI ,biology ,Contig ,Shotgun sequencing ,Restriction Mapping ,Sequence Analysis, DNA ,Bacterial genome size ,Computational biology ,Escherichia coli O157 ,Genome ,Contig Mapping ,Optical mapping ,Methods ,biology.protein ,Genomic library ,Genome, Bacterial ,Software ,Genetics (clinical) - Abstract
We have constructed NheI and XhoI optical maps ofEscherichia 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.
- Published
- 2001
- Full Text
- View/download PDF