Escherichia coli K-12 MG1655 sequence and annotations
U00096.2 (aka version m56)

Sequence Updates Annotation Updates

Sequence update (June 10, 2004)

    The completion of the E. coli K-12 strain W3110 genome sequence, and its comparison to that of MG1655 (U00096.1), led to indications of possible sequence discrepancies, as described by Hayashi et al. 2006 [1]. Communication of these results prior to their publication led Monica Riley and Margrethe 'Gretta' Serres to organize a workshop on the annotation of Escherichia coli K-12, held at the Marine Biological Laboratory, Woods Hole, MA on November 14 - 18, 2003 [2,3]. Workshop participants reconciled sequence differences as well as doing extensive work on the annotations of both strains. These corrections, and additional corrections made at UW, were incorporated into a sequence update (designated version m56) which was made public via the ASAP database. That updated 4,639,675 bp sequence was the source of U00096.2, deposited on June 10, 2004.

    Eight point mutation differences, the rrnE/rrnD inversion, and 13 strain-specific IS element insertion points are the only differences now remaining between the two E. coli K-12 sequenced genomes. The largest single correction was restoration of a 374 bp deletion that occurred after bp 3192853 in U00096.1. A fifth QUAD repeat sRNA gene, rygE, was missing in U00096.1 and has now been added. An Excel spreadsheet summarizes the U00096.2 update in terms of nucleotide sequence corrections and the consequent protein sequence changes.

References

  1. K. Hayashi, N. Morooka, Y. Yamamoto, K. Fujita, K. Isono, S. Choi, E. Ohtsubo, T. Baba, B. L. Wanner, H. Mori, & T. Horiuchi (2006) Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol Syst Biol 2:2006.0007. [PMID: 16738553].
  2. M. Riley (2004) Workshop on Annotation of Escherichia coli K-12 (letter). ASM News 70(1):2. (see workshop)
  3. M. Riley, T. Abe, M. B. Arnaud, M. K. Berlyn, F. R. Blattner, R. R. Chaudhuri, J. D. Glasner, T. Horiuchi, I. M. Keseler, T. Kosuge, H. Mori, N. T. Perna, G. Plunkett III, K. E. Rudd, M. H. Serres, G. H. Thomas, N. R. Thomson, D. Wishart, & B. L. Wanner (2006) Escherichia coli K-12: a cooperatively developed annotation snapshot--2005. Nucleic Acids Res 34(1):1-9. [PMID: 16397293].

Annotation updates

    Annotations were updated in ASAP as a part of ongoing projects that utilized the E. coli K-12 MG1655 genome as a core reference for annotation work on genomes of other members of the Enterobacteriaceae. [see Enteropathogen Resource Integration Center (ERIC), subsequently superseded by PATRIC; Assembling the Tree of Life: Enterobacteriaceae (AToL)]. Updates were periodically submitted to GenBank; since there were not underlying sequence changes the accession.version number remained the same. On April 17, 2007, EcoGene was designated as the submitter of record for further updates to the GenBank entry, as a collaboration between ASAP/ERIC, EcoGene, the Coli Genetic Stock Center, EcoliHub, EcoCyc, RegulonDB and UniProtKB/Swiss-Prot. The last annotation updates to the GenBank entry were released February 6, 2013. On September 26, 2013 the U00096.2 sequence was replaced by U00096.3.

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