Skip to content
naulon
Get started

No retraction, correction or concern found when last checked on Oct 20, 2026.

Complete Genome Sequence of Escherichia coli BW25113

Frédéric Grenier, Dominick Matteau, Vincent Baby and 1 more

Genome Announcements · 2014 · CC BY

doi:10.1128/genomea.01038-14

Abstract

Escherichia coli BW25113 is the parent strain of the Keio collection comprising nearly 4,000 single-gene deletion mutants. We report the complete 4,631,469-bp genome sequence of this strain and the key variations from the type strain E. coli MG1655.

Full text

From PubMed Central, U.S. National Library of Medicine, as current on Oct 20, 2026. Paragraph numbers are ours, so an answer can point at one.

GENOME ANNOUNCEMENT

Escherichia coli BW25113 is a common laboratory strain that was created in the laboratory of Barry L. Wanner and was utilized in a method taking advantage of the bacteriophage lambda red recombination system to perform gene disruptions with double-stranded PCR products. E. coli BW25113 later became the parent strain for the Keio collection, a major resource consisting of approximately 4,000 single-gene deletion mutants. The strain and its derivatives are being used in countless laboratories for a variety of studies, including systematic phenotypic surveys and synthetic biology efforts. Despite this, the complete genome sequence of this strain surprisingly remained unavailable for the scientific community.

E. coli BW25113 was obtained from the Coli Genetic Stock Center (CGSC) (strain 7636). An Illumina library was prepared from size-selected DNA fragments of approximately 450 to 550 bp and sequenced with paired-end reads of 300 bp on a MiSeq instrument to assemble longer composite reads covering the entire insert. All sequences were de novo and reference assembled using the Roche gsAssembler version 2.6. The assemblies were merged and manually inspected before manual finishing with Sanger sequencing reads obtained from PCR products. The resulting circular chromosome (of 4,631,469 bp) was annotated by comparison with E. coli MG1655 (RefSeq accession no. NC_000913.3) using RATT and manual curation. The key differences between the two organisms were accounted for in the genotype of E. coli BW25113 [Δ(araD-araB)567 Δ(rhaD-rhaB)568 ΔlacZ4787 (::rrnB-3) hsdR514 rph-1], with the deletion of araBAD and rhaDAB and the replacement of a section of lacZ with four tandem rrnB terminators as well as a frameshift mutation in hsdR resulting in a premature translation stop codon. As noted by others, we observed that the strain contains the lacI+ allele and not lacIq as initially reported. The genome sequence also confirmed the presence of the rph-1 allele and revealed 20 substitutions as well as 11 indels (see http://bioinfo.ccs.usherbrooke.ca/BW25113.html for a complete list).

Nucleotide sequence accession number.

The complete genome sequence of Escherichia coli BW25113 was deposited in GenBank under accession number CP009273.

References 10

  1. 1.

    Datsenko KA Wanner BL. 2000. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. U. S. A. 97:6640–6645.

    Not in our library10.1073/pnas.120163297

  2. 2.

    Baba T Ara T Hasegawa M Takai Y Okumura Y Baba M Datsenko KA Tomita M Wanner BL Mori H. 2006. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2:2006.0008.

    Not in our library10.1038/msb4100050

  3. 3.

    Yamamoto N Nakahigashi K Nakamichi T Yoshino M Takai Y Touda Y Furubayashi A Kinjyo S Dose H Hasegawa M Datsenko KA Nakayashiki T Tomita M Wanner BL Mori H. 2009. Update on the Keio collection of Escherichia coli single-gene deletion mutants. Mol. Syst. Biol. 5:335.

    Not in our library10.1038/msb.2009.92

  4. 4.

    Nichols RJ Sen S Choo YJ Beltrao P Zietek M Chaba R Lee S Kazmierczak KM Lee KJ Wong A Shales M Lovett S Winkler ME Krogan NJ Typas A Gross CA. 2011. Phenotypic landscape of a bacterial cell. Cell 144:143–156.

    Not in our library10.1016/j.cell.2010.11.052

  5. 5.

    Mutalik VK Guimaraes JC Cambray G Mai QA Christoffersen MJ Martin L Yu A Lam C Rodriguez C Bennett G Keasling JD Endy D Arkin AP. 2013. Quantitative estimation of activity and quality for collections of functional genetic elements. Nat. Methods 10:347–353.

    Not in our library10.1038/nmeth.2403

  6. 6.

    Mutalik VK Guimaraes JC Cambray G Lam C Christoffersen MJ Mai QA Tran AB Paull M Keasling JD Arkin AP Endy D. 2013. Precise and reliable gene expression via standard transcription and translation initiation elements. Nat. Methods 10:354–360.

    Not in our library10.1038/nmeth.2404

  7. 7.

    Cambray G Guimaraes JC Mutalik VK Lam C Mai Q-A Thimmaiah T Carothers JM Arkin AP Endy D. 2013. Measurement and modeling of intrinsic transcription terminators. Nucleic Acids Res. 41:5139–5148.

    Not in our library10.1093/nar/gkt163

  8. 8.
    Unlocking Short Read Sequencing for Metagenomics · 2010
    No notice
  9. 9.

    Otto TD Dillon GP Degrave WS Berriman M. 2011. RATT: rapid annotation transfer tool. Nucleic Acids Res. 39:e57.

    Not in our library10.1093/nar/gkq1268

  10. 10.

    Lessard IA Pratt SD McCafferty DG Bussiere DE Hutchins C Wanner BL Katz L Walsh CT. 1998. Homologs of the vancomycin resistance D-Ala-D-Ala dipeptidase VanX in Streptomyces toyocaensis, Escherichia coli and Synechocystis: attributes of catalytic efficiency, stereoselectivity and regulation with implications for function. Chem. Biol. 5:489–504.

    Not in our library10.1016/s1074-5521(98)90005-9

Cited by papers we hold 6

Reads

Read by people on this page

None yet.

Checked or read by AI through naulon

None yet.

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.

Are you an author?

Is this your paper?

Claim it to add your note and be paid when agents cite it. Free.