Sequenced E. coli Genomes: Difference between revisions

Revision as of 22:00, 27 July 2010

EcoliWiki plans to create gene lists for all available laboratory E. coli K-12, B, and C strains. Although pathogenic strains of E. coli are not the focus of EcoliWiki, numerous strains of E. coli, non-pathogenic or pathogenic, have been sequenced or projects are in progress to do so. Use this table to track which genomes are available and from where. Please add or edit any strains you know are being sequenced or are finished.

Strain	Sequencing status	Accessions (if applicable)	In EcoliWiki	Comments	Taxon ID
MG1655	complete	NC_000913	yes	PMID:9278503^[1]	511145
W3110	complete	AC_000091	yes	PMID:16738553^[2]	316407
DH10B	complete	NC_010473	yes	PMID:18245285^[3] This genome has now been incorporated into EcoliWiki.	316385
REL606	complete	NC_012967	yes	Information about the genes of this E. coli B strain is now available from EcoliWiki International E. coli B Consortium Entrez Genome Project	413997
E. coli BL21 (DE3)	complete	CP001509.3 & NC_012947.1 & CP001665.1	not yet	We are working on adding this strain to EcoliWiki. DOE Joint Genome Institute Entrez Genome Project	469008
E. coli 101-1	in progress	Whole Genome Shotgun Sequence 101-1	no	JCVI Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project Enteroaggregative.	358709
E. coli 53638	in progress	Whole Genome Shotgun Sequence 53638	no	JCVI Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project Enteroinvasive.
E. coli B171	in progress	Whole Genome Shotgun Sequence B171	no	JCVI Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project Enteropathogenic.
E. coli B7A	in progress	Whole Genome Shotgun Sequence B7A	no	JCVI Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project Enterotoxigenic.
E. coli E110019	in progress	Whole Genome Shotgun Sequence E110019	no	JCVI Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project Atypical enteropathogenic.
E. coli E22	in progress	Whole Genome Shotgun Sequence E22	no	JCVI Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project Enteropathogenic.	340185
E. coli E24377A	complete	NC_009801	no	JCVI Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project Enterotoxigenic.	331111
E. coli F11	in progress	Whole Genome Shotgun Sequence F11	no	JCVI Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project Extra-intestinal pathogenic.	340197
E. coli HS	complete	NC_009800	no	JCVI Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project Human commensal isolate.	331112
E. coli SMS-3-5	complete	NC_010498	no	PMID:18708504^[4] SECEC SMS-3-5 at JCVI Entrez Genome Project Highly antibiotic resistant, including ciprofloxacin & moxifloxacin.	439855
E. coli O157:H7 EC4024	in progress	Whole Genome Shotgun Sequence EC4024	no	JCVI Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project Enterohemorrhagic.	444454
E. coli O157:H7 EC4042	in progress	Whole Genome Shotgun Sequence EC4042	no	JCVI Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project Enterohemorrhagic.	444449
E. coli O157:H7 EC4045	in progress	Whole Genome Shotgun Sequence EC4045	no	JCVI Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project Enterohemorrhagic.	444448
E. coli O157:H7 EC4076	in progress	Whole Genome Shotgun Sequence EC4076	no	JCVI Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project Enterohemorrhagic.	444453
E. coli O157:H7 EC4113	in progress	Whole Genome Shotgun Sequence EC4113	no	JCVI Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project Enterohemorrhagic.	444452
E. coli O157:H7 EC4115	complete	NC_011353	no	JCVI Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project Enterohemorrhagic.	444450
E. coli O157:H7 EC4196	in progress	Whole Genome Shotgun Sequence EC4196	no	JCVI Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project Enterohemorrhagic.	444451
E. coli O157:H7 EC4206	in progress	Whole Genome Shotgun Sequence EC4206	no	JCVI Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project Enterohemorrhagic.	444447
E. coli O157:H7 EC4401	in progress	Whole Genome Shotgun Sequence EC4401	no	JCVI Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project Enterohemorrhagic.	478004
E. coli O157:H7 EC4486	in progress	Whole Genome Shotgun Sequence EC4486	no	JCVI Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project Enterohemorrhagic.	478005
E. coli O157:H7 EC4501	in progress	Whole Genome Shotgun Sequence EC4501	no	JCVI Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project Enterohemorrhagic.	478006
E. coli O157:H7 EC508	in progress	Whole Genome Shotgun Sequence EC508	no	JCVI Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project Enterohemorrhagic.	478007
E. coli O157:H7 TW14359	complete	NC_013008	no	Entrez Genome Project Enterohemorrhagic.	544404
E. coli O157:H7 EC869	in progress	Whole Genome Shotgun Sequence EC869	no	JCVI Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project Enterohemorrhagic.	478008
E. coli O157:H7 FRIK966	in progress		no	MBRI Entrez Genome Project Bovine isolate; does not express Shiga toxin.	570506
E. coli O157:H7 TW14588	in progress	Whole Genome Shotgun Sequence TW14588	no	JCVI Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project Enterohemorrhagic.	502346
E. coli O157:H7 GZ-021210/cattle	in progress		no	Entrez Genome Project Enterohemorrhagic bovine isolate.	410290
E. coli O157:H7	complete	NC_002695	no	PMID:11258796^[5] This strain is also referred to as E. coli O157:H7 Sakai Entrez Genome Project	83334
E. coli APEC O1	complete	NC_008563	no	PMID:17293413^[6] Nolan Lab Bacterial Pathogenesis Laboratory Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project	405955
E. coli UTI89	complete	NC_007946	no	PMID:16585510^[7] Entrez Genome Project	364106
E. coli 042	complete	FN554766	no	Sanger Institute Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project Enteroaggregative.	216592
E. coli 536	complete	NC_008253	no	PMID:16879640^[8] University of Gottingen Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project Uropathogenic.	362663
E. coli RS218	in progress		no	PMID:16988236^[9] University of Wisconsin Genome Center Entrez Genome Project E. coli K1; Neonatal meningitis E. coli (NMEC).	439184
E. coli CFT073	complete	NC_004431	no	PMID:12471157^[10] University of Wisconsin Genome Center Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project Uropathogenic.	199310
E. coli ATCC 8739	complete	NC_010468	not yet	E. coli Crooks strain (sometimes misnamed as E. coli B strain (see page for ATCC 8739) Joint Genome Institute Enteropathogen Resource Integration Center (ERIC) Entrez Genome Project	481805
E. coli F18+	in progress		no	Entrez Genome Project	488477
E. coli 789 A/C 1	in progress		no	Gottingen Genomics Laboratory
E. coli K-12 LW1655F+	in progress		no	Entrez Genome Project	527799
E. coli NC-7	in progress		not yet	Entrez Genome Project Cell wall-less L-form derivative of E. coli K-12.	531853
E. coli O157:H7 EDL933	complete	NC_002655.2	no	Enteropathogen Resource Integration Center (ERIC) Enterohemorrhagic.	155864
E. coli SE11	complete	NC_011415	no	Entrez Genome Project Human commensal isolate.	409438
E. coli W	in progress		no	Entrez Genome Project	566546
E. coli c7122	in progress		no	Entrez Genome Project
E. coli S88	complete	NC_011742	no	GenoScope Serotype O45:K1 strain, isolated from a case of meningitis.	585035
E. coli ED1a	complete	NC_011745	no	GenoScope Avirulent serogroup O81.	585397
E. coli IAI1	complete	NC_011741	no	GenoScope Serogroup O8.	585034
E. coli IAI39	complete	NC_011750	no	Genoscope Serotype O7:K1.	585057
E. coli 55989	complete	NC_011748	no	PMID:19165319^[11] Pathogenic strain.	585055
E. coli BW2952 MC4100(MuLac)	complete	NC_012759	yes	PMID:19376874^[12]	595496
E.coli UMN026	complete	NC_011751	no	PMID:19165319^[11] Pathogenic strain serotype O17:K52:H18	585056
E.coli O103:H2 str. 12009	complete	NC_013353	no	PMID:19815525^[13] Pathogenic.
E.coli O111:H- str. 11128	complete	NC_013364	no	PMID:19815525^[13] Pathogenic.
E. coli O127:H6 str. E2348/69	complete	NC_011601	no	PMID:18952797^[14] Pathogenic.	574521
E. coli K-12 DH1	complete	CP001637	not yet	Escherichia coli K12 DH1, ATCC 33849
E. coli O55:H7 CB9615	complete	NC_013941	no
E. coli O26:H11 str. 11368	complete	NC_013361	no	enteropathogenic strain, serovar = O26:H11
E. coli IHE3034	complete	CP001969	no	Extraintestinal Pathogenic
E. coli SE15	complete	AP009378]	no	Commensal strain.
edit table

↑ Blattner, FR et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277 1453-62 PubMed
↑ Hayashi, K et al. (2006) Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol. Syst. Biol. 2 2006.0007 PubMed
↑ Durfee, T et al. (2008) The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J. Bacteriol. 190 2597-606 PubMed
↑ Fricke, WF et al. (2008) Insights into the environmental resistance gene pool from the genome sequence of the multidrug-resistant environmental isolate Escherichia coli SMS-3-5. J. Bacteriol. 190 6779-94 PubMed
↑ Hayashi, T et al. (2001) Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res. 8 11-22 PubMed
↑ Johnson, TJ et al. (2007) The genome sequence of avian pathogenic Escherichia coli strain O1:K1:H7 shares strong similarities with human extraintestinal pathogenic E. coli genomes. J. Bacteriol. 189 3228-36 PubMed
↑ Chen, SL et al. (2006) Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. Proc. Natl. Acad. Sci. U.S.A. 103 5977-82 PubMed
↑ Hochhut, B et al. (2006) Role of pathogenicity island-associated integrases in the genome plasticity of uropathogenic Escherichia coli strain 536. Mol. Microbiol. 61 584-95 PubMed
↑ Teng, CH et al. (2006) Effects of ompA deletion on expression of type 1 fimbriae in Escherichia coli K1 strain RS218 and on the association of E. coli with human brain microvascular endothelial cells. Infect. Immun. 74 5609-16 PubMed
↑ Welch, RA et al. (2002) Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 99 17020-4 PubMed
↑ ^11.0 ^11.1 Touchon, M et al. (2009) Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet. 5 e1000344 PubMed
↑ Ferenci, T et al. (2009) Genomic sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli K-12. J. Bacteriol. 191 4025-9 PubMed
↑ ^13.0 ^13.1 Ogura, Y et al. (2009) Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 106 17939-44 PubMed
↑ Iguchi, A et al. (2009) Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69. J. Bacteriol. 191 347-54 PubMed

[PMID:9278503-1] Blattner, FR et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277 1453-62 PubMed

[PMID:16738553-2] Hayashi, K et al. (2006) Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol. Syst. Biol. 2 2006.0007 PubMed

[PMID:18245285-3] Durfee, T et al. (2008) The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J. Bacteriol. 190 2597-606 PubMed

[PMID:18708504-4] Fricke, WF et al. (2008) Insights into the environmental resistance gene pool from the genome sequence of the multidrug-resistant environmental isolate Escherichia coli SMS-3-5. J. Bacteriol. 190 6779-94 PubMed

[PMID:11258796-5] Hayashi, T et al. (2001) Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res. 8 11-22 PubMed

[PMID:17293413-6] Johnson, TJ et al. (2007) The genome sequence of avian pathogenic Escherichia coli strain O1:K1:H7 shares strong similarities with human extraintestinal pathogenic E. coli genomes. J. Bacteriol. 189 3228-36 PubMed

[PMID:16585510-7] Chen, SL et al. (2006) Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. Proc. Natl. Acad. Sci. U.S.A. 103 5977-82 PubMed

[PMID:16879640-8] Hochhut, B et al. (2006) Role of pathogenicity island-associated integrases in the genome plasticity of uropathogenic Escherichia coli strain 536. Mol. Microbiol. 61 584-95 PubMed

[PMID:16988236-9] Teng, CH et al. (2006) Effects of ompA deletion on expression of type 1 fimbriae in Escherichia coli K1 strain RS218 and on the association of E. coli with human brain microvascular endothelial cells. Infect. Immun. 74 5609-16 PubMed

[PMID:12471157-10] Welch, RA et al. (2002) Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 99 17020-4 PubMed

[PMID:19165319-11] 11.0 ^11.1 Touchon, M et al. (2009) Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet. 5 e1000344 PubMed

[PMID:19376874-12] Ferenci, T et al. (2009) Genomic sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli K-12. J. Bacteriol. 191 4025-9 PubMed

[PMID:19815525-13] 13.0 ^13.1 Ogura, Y et al. (2009) Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 106 17939-44 PubMed

[PMID:18952797-14] Iguchi, A et al. (2009) Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69. J. Bacteriol. 191 347-54 PubMed

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Sequenced E. coli Genomes: Difference between revisions

Revision as of 22:00, 27 July 2010

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