Genome Sequence Project Bibliography E. coli K-12

Genome Sequence Project Bibliography
E. coli K-12

These papers are reports of Escherichia coli K-12 genome DNA sequence from the University of Wisconsin and Japanese consortium sequencing projects. The Genbank/EMBL/DDBJ records corresponding to these publications are listed. The Genbank/EMBL/DDBJ records containing unpublished E. coli DNA sequences from the systematic genome sequencing projects in the laboratories of George Church and Ron Davis are also listed.


All of the genes of E. coli K-12 MG1655 were reported in the final sequencing paper from the Blattner laboratory:

Blattner F.R., Plunkett G., Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. (1997) The complete genome sequence of Escherichia coli K-12. Science 277:1453-1462.
Genbank/EMBL/DDBJ record: U00096.2

U00096.1 was previously broken up into 400 separate Genbank/EMBL/DDBJ records: AE000111-AE000510. The current Genbank record U00096.2 has the DNA sequence updated, in part as a result of a Japanese K-12 W3310 genome sequence project completion and reconciliation reported in Hayashi et al., 2006.

For additional information, please go to the E. coli Genome Project at the University of Wisconsin.

Leading up to this final publication there were six publications of large regions of the E. coli genome sequenced by the Blattner laboratory:

Daniels D.L., Plunkett G., Burland V., Blattner F.R. (1992) Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes. Science 257:771-778.
Genbank/EMBL/DDBJ record: M87049.

Burland V., Plunkett G., Daniels D.L., Blattner F.R. (1993) DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication. Genomics 16:551-561.
Genbank/EMBL/DDBJ record: L10328.

Plunkett G., Burland V., Daniels D.L., Blattner F.R. (1993) Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87.2 to 89.2 minutes. Nucleic Acids Res 21:3391-3398.
Genbank/EMBL/DDBJ record: L19201.

Blattner F.R., Burland V., Plunkett G., Sofia H.J., Daniels D.L. (1993) Analysis of the Escherichia coli genome. IV . DNA sequence of the region from 89.2 to 92.8 minutes. Nucleic Acids Res 21:5408-5417.
Genbank/EMBL/DDBJ record: U00006.

Sofia H.J., Burland V., Daniels D.L., Plunkett G., Blattner F.R. (1994) Analysis of the Escherichia coli genome. V. DNA sequence of the region from 76.0 to 81.5 minutes. Nucleic Acids Res 22:2576-2586.
Genbank/EMBL/DDBJ record: U00039.

Burland V., Plunkett G., Sofia H.J., Daniels D.L., Blattner F.R. (1995) Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes. Nucleic Acids Res 23:2105-2119.
Genbank/EMBL/DDBJ record:U14003.


There were six publications from a consortium of Japanese laboratories that sequenced a set of bacteriophage lambda clones derived from E. coli K-12 strain W3110. Four of them are accompanied by a Supplement with a separate citation that can be retrieved via a hyperlink following the main citation. The sequencing results from these four publications are available in the range of Genbank/EMBL/DDBJ records listed, but not linked. Additional information from the E. coli genome sequencing project of this Japanese consortium is available at the Escherichia coli WWW HOME PAGE

Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K., Mizobuchi K., Nakata A. (1992) Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 min region. Nucleic Acids Res 20:3305-3308.
Genbank/EMBL/DDBJ record: D10483.

Fujita N., Mori H., Yura T., Ishihama A. (1994) Systematic sequencing of the Escherichia coli genome: analysis of the 2.4-4.1 min (110,917-193,643 bp) region. Nucleic Acids Res 22:1637-1639.
Genbank/EMBL/DDBJ record:D26562.

Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Horiuchi T., et al (1996) A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map. DNA Res 3:137-155.
Genbank/EMBL/DDBJ records: D90699 to D90760. Supplement

Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S., Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Horiuchi T., et al (1996) A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map. DNA Res 3:363-377.
Genbank/EMBL/DDBJ records: D90763 to D90821; D90852; D90853.Supplement

Itoh T., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Kasai H., Kimura S., Kitakawa M., Kitagawa M., Makino K. , Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S., Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y., Horiuchi T., et al (1996) A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 40.1-50.0 min region on the linkage map. DNA Res 3:379-392.
Genbank/EMBL/DDBJ records: D90822 to D90851.Supplement

Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Horiuchi T., et al (1997) Construction of a contiguous 874-kb sequence of the Escherichia coli - K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features. DNA Res 4:91-113.
Genbank/EMBL/DDBJ records: D90854 to D90897.Supplement


The Davis and Church laboratories also engaged in the systematic sequencing of the E. coli K-12 genome. These results have not been published, but they are present in Genbank/EMBL/DDBJ submissions:
The laboratory of Ron Davis sequenced a large portion of the E. coli MG1655 genome.

Chung,E., Allen,E., Araujo,R., Aparicio,A., Davis,K., Duncan,M., Federspiel,N., Hyman,R., Kalman,S., Komp,C., Kurdi,O., Lew,H., Lin,D., Namath,A., Oefner,P., Roberts,D., Schramm,S. and Davis,R.W. (1996) Sequence of minutes 4-25 of Escherichia coli. Unpublished.
Genbank/EMBL/DDBJ records:U70214, 4 to 6 minutes, U73857, 6 to 9 minutes, U82664, 9 to 12 minutes, U82598, 12 to 15 minutes


The laboratory of George Church sequenced two long regions of E. coliK-12 EMG2 .

Richterich,P., Lakey,N., Gryan,G., Jaehn,L., Mintz,L., Robison,K. and Church,G.M. (1993) Automated multiplex sequencing of the E. coli genome. Unpublished.

Genbank/EMBL/DDBJ records:U00007 and U00008.

Additional information on the Church laboratory functional and bioinformatic studies of E. coli can be found at their website: Lipper Center for Computational Genetics