Shotgun optical maps of the whole Escherichia coli 0157

H7 genome

Alex Lim, Eileen T. Dimalanta, Konstantinos D. Potamousis, Galex Yen, Jennifer Apodoca, Chunhong Tao, Jieyi Lin, Rong Qi, John Skiadas, Arvind Ramanathan, Nicole T. Perna, Guy Plunkett, Valerie Burland, Bob Mau, Jeremiah Hackett, Frederick R. Blattner, Thomas S. Anantharaman, Bhubaneswar Mishra, David C. Schwartz

Research output: Contribution to journalArticle

73 Citations (Scopus)

Abstract

We have constructed Nhel and Xhol 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.

Original languageEnglish (US)
Pages (from-to)1584-1593
Number of pages10
JournalGenome Research
Volume11
Issue number9
DOIs
StatePublished - 2001
Externally publishedYes

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Escherichia coli O157
Firearms
Genome
Escherichia coli
Bacterial Genomes
Automation
DNA
Clone Cells
Technology
Food
Polymerase Chain Reaction
Water

ASJC Scopus subject areas

  • Genetics

Cite this

Lim, A., Dimalanta, E. T., Potamousis, K. D., Yen, G., Apodoca, J., Tao, C., ... Schwartz, D. C. (2001). Shotgun optical maps of the whole Escherichia coli 0157: H7 genome. Genome Research, 11(9), 1584-1593. https://doi.org/10.1101/gr.172101

Shotgun optical maps of the whole Escherichia coli 0157 : H7 genome. / Lim, Alex; Dimalanta, Eileen T.; Potamousis, Konstantinos D.; Yen, Galex; Apodoca, Jennifer; Tao, Chunhong; Lin, Jieyi; Qi, Rong; Skiadas, John; Ramanathan, Arvind; Perna, Nicole T.; Plunkett, Guy; Burland, Valerie; Mau, Bob; Hackett, Jeremiah; Blattner, Frederick R.; Anantharaman, Thomas S.; Mishra, Bhubaneswar; Schwartz, David C.

In: Genome Research, Vol. 11, No. 9, 2001, p. 1584-1593.

Research output: Contribution to journalArticle

Lim, A, Dimalanta, ET, Potamousis, KD, Yen, G, Apodoca, J, Tao, C, Lin, J, Qi, R, Skiadas, J, Ramanathan, A, Perna, NT, Plunkett, G, Burland, V, Mau, B, Hackett, J, Blattner, FR, Anantharaman, TS, Mishra, B & Schwartz, DC 2001, 'Shotgun optical maps of the whole Escherichia coli 0157: H7 genome', Genome Research, vol. 11, no. 9, pp. 1584-1593. https://doi.org/10.1101/gr.172101
Lim A, Dimalanta ET, Potamousis KD, Yen G, Apodoca J, Tao C et al. Shotgun optical maps of the whole Escherichia coli 0157: H7 genome. Genome Research. 2001;11(9):1584-1593. https://doi.org/10.1101/gr.172101
Lim, Alex ; Dimalanta, Eileen T. ; Potamousis, Konstantinos D. ; Yen, Galex ; Apodoca, Jennifer ; Tao, Chunhong ; Lin, Jieyi ; Qi, Rong ; Skiadas, John ; Ramanathan, Arvind ; Perna, Nicole T. ; Plunkett, Guy ; Burland, Valerie ; Mau, Bob ; Hackett, Jeremiah ; Blattner, Frederick R. ; Anantharaman, Thomas S. ; Mishra, Bhubaneswar ; Schwartz, David C. / Shotgun optical maps of the whole Escherichia coli 0157 : H7 genome. In: Genome Research. 2001 ; Vol. 11, No. 9. pp. 1584-1593.
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