Bacterial sequencing

The Sanger Institute bacterial sequencing effort is concentrated on pathogens and model organisms. Below is a list of projects funded, underway or completed; all data from these projects are immediately and freely available. Please read our data release policy and guidelines and conditions on use of data.

Organism	Size (Mb)	G+C	Status	Funding

Alivibrio salmonicida	3.33 + 1.21	39.0%	Hjerde et al., BMC Genomics 9, 616 (2008)	Wellcome Trust
Bacteriovorax marinus	3.44	36.7%	Finished	Wellcome Trust
Bacteroides fragilis NCTC9343	5.20	43.1%	Cerdeño-Tárraga et al., Science 307, 1463-1465 (2005)	Beowulf Genomics
Bacteroides fragilis 638R	5.373	43.4%	Finished	Beowulf Genomics
Bordetella avium	3.73	61.6%	Sebaihia et al., J. Bacteriol. 188, 6002-6005 (2006)	USDA
Bordetella bronchiseptica RB50	5.34	68.1%	Parkhill et al. Nature Genetics 35 32-40 (2003)	Beowulf Genomics
Bordetella bronchiseptica strain 253	~5	~68%	Shotgun in progress	Wellcome Trust
Bordetella bronchiseptica MO149	~5	~68%	Shotgun in progress	Wellcome Trust
Bordetella parapertussis 12822	4.77	68.1%	Parkhill et al. Nature Genetics 35 32-40 (2003)	Beowulf Genomics
Bordetella parapertussis Bpp5	~5	~68%	Shotgun in progress	Wellcome Trust
Bordetella pertussis Tohama I	4.09	67.7%	Parkhill et al. Nature Genetics 35 32-40 (2003)	Beowulf Genomics
Bordetella pertussis strain 18323	~5	~68%	shotgun in progress	Wellcome Trust
Burkholderia cenocepacia (formerly Burkholderia cepacia genomovar III)	3.87 + 3.22 + 0.88	66.9%	Holden et al., J. Bacteriol. 191, 261-277 (2009)	Beowulf Genomics
Burkholderia pseudomallei	4.07 + 3.17	68%	Holden et al., Proc. Natl. Acad. Sci. USA 101, 14240-14245 (2004)	Beowulf Genomics
Campylobacter jejuni	1.64	30.6%	Parkhill et al., Nature 403, 665-668 (2000)	Beowulf Genomics
Chlamydia trachomatis serovar A	1.052	41.3%	Finished	Wellcome Trust
Chlamydia trachomatis serovar B	1.052	41.3%	Seth-Smith et al., BMC Genomics 10, 239 (2009)	Wellcome Trust
Chlamydia trachomatis Jali	1.051	41.3%	Seth-Smith et al., BMC Genomics 10, 239 (2009)	Wellcome Trust
Chlamydia trachomatis L2	1.039	41.3 %	Thomson et al., Genome Research 18, 161-171	Wellcome Trust
Chlamydophila abortus	1.14	39.9%	Thomson et al., Genome Research 15, 629-640	The Scottish Office
Citrobacter freundii ballerup 7851	4.905	52%	357 contigs; Petty et al., J. Bacteriol., 192, 525-538 (2010)	Wellcome Trust
Citrobacter rodentium	5.347	54.7%	Petty et al., J. Bacteriol. 192, 525-538 (2010)	Wellcome Trust
Clavibacter michiganensis	3.404	72.38%	Bentley et al., J. Bacteriol. epublication (2008)	USDA
Clostridium botulinum Hall strain A	3.89	28.2%	Sebaihia et al., Genome Research epublication (2007)	Beowulf Genomics
Clostridium botulinum 17B	~3.9	~30%	Finishing/gap closure	Wellcome Trust
Clostridium difficile 630	4.29	29.06%	Sebaihia et al., Nature Genetics 38, 779-786 (2006)	Beowulf Genomics
Clostridium difficile 196	~4.3	~30%	Finishing/gap closure	Wellcome Trust
Clostridium difficile BI1	~4.3	~30%	Finishing/gap closure	Wellcome Trust
Clostridium difficile M120	~4.3	~30%	Finishing/gap closure	Wellcome Trust
Clostridium difficile M68	~4.3	~30%	Finishing/gap closure	Wellcome Trust
Clostridium difficile SM	~4.3	~30%	Finishing/gap closure	Wellcome Trust
Clostridium difficile CF5	~4.3	~30%	Finishing/gap closure	Wellcome Trust
Clostridium difficile 855	~4.3	~30%	Finishing/gap closure	Wellcome Trust
Corynebacterium diphtheriae	2.49	52%	Cerdeño-Tárraga et al., Nucleic Acids Research 31(22), 6516-6523 (2003)	Beowulf Genomics
Ehrlichia (Cowdria) ruminantium	1.516	27.5%	Collins et al., Proc. Natl. Acad. Sci. USA 102, 838-843 (2005)	NWO
Erwinia amylovora	3.81	53.5%	Finished	USDA
Erwinia carotovora	5.06	50.97%	Bell et al., Proc. Natl. Acad. Sci. USA 101, 11105-11110 (2004)	The Scottish Executive
Escherichia coli 042	5.355	50.5%	Finished	Beowulf Genomics
Escherichia coli E2348/69	4.966	50.6%	Iguchi et al., J Bacteriol 191 347-354 (2009)	Beowulf Genomics
Escherichia coli H10407	5.15	50.7%	Finished	BBSRC
Escherichia coli non-K1 clinical isolate	~5.0	~50%	Funded	Beowulf Genomics
Haemophilus influenzae 10810	1.98	38.1%	Finished	Wellcome Trust
Haemophilus influenzae F3031	1.99	38.2%	Finished	Wellcome Trust
Haemophilus influenzae F3047	~2.1	~40%	Finishing/ gap closure	Wellcome Trust
Haemophilus parainfluenzae	~2.1	39.6%	Finished	Wellcome Trust
Helicobacter mustelae	1.58	42.5	Finished	Wellcome Trust
Mycobacterium africanum	4.39	65.6%	Finished	Wellcome Trust
Mycobacterium bovis AF2122/97	4.4	64%	Garnier et al., Proc. Natl. Acad. Sci. USA 100, 7877-7882 (2003)	DEFRA/ Beowulf Genomics
Mycobacterium bovis BCG	4.4	65.6%	Brosch et al., Proc. Natl. Acad. Sci. USA 104, 4496-5601 (2007)	DEFRA/ Beowulf Genomics
Mycobacterium canetti	~4.4	~64%	Finishing	Wellcome Trust
Mycobacterium leprae	3.27	57.8%	Cole et al., Nature 409, 1007-1011 (2001)	Heiser/ Follereau
Mycobacterium marinum	6.637	65.7%	Stinear et al., Genome Research online publication (2008)	Beowulf Genomics
Mycobacterium microti	~4.4	~64%	Shotgun in progress	DEFRA/ Beowulf Genomics
Mycobacterium tuberculosis	4.41	65.6%	Cole et al., Nature 393, 537-544 (1998)	Wellcome Trust
Mycoplasma amphoriforme	~1.0	ND	Funded	Wellcome Trust
Neisseria lactamica	2.2	52.3%	Finished	Wellcome Trust
Neisseria meningitidis Serogroup A strain Z2491	2.18	51.8%	Parkhill et al., Nature 404, 502-506 (2000)	Wellcome Trust
Neisseria meningitidis Serogroup C strain FAM18	2.19	51.6%	Bentley et al., PLoS Genet. 3, e23 (2007)	Beowulf Genomics
Photorhabdus asymbiotica	5.07	42.2%	Finished	BBSRC
Proteus mirabilis	4.06	38.88%	Pearson et al., J. Bacteriol. 190, 4027-37 (2008)	Wellcome Trust
Pseudomonas aeruginosa	6.602	66.3%	Winstanley et al., Genome Res 19, 12-23 (2009)	Wellcome Trust
Pseudomonas fluorescens	6.722	60.5%	Silby et al., Genome Biology 10, r51 (2009)	BBSRC
Rhizobium leguminosarum	7.751	60.86%	Young et al., Genome Biology 7, r34 (2006)	BBSRC
Rhodococcus equi	~4.5	~68%	Finished	HBLB
Ruminococcus flavefaciens 007c	3.65	~45%	High Quality Draft Sequence	Wellcome Trust
Salmonella bongori	4.46	51.3%	Finished	Beowulf Genomics
Salmonella enteritidis PT4	4.686	52.17%	Thomson et al., Genome Research epublication, (2008)	Beowulf Genomics
Salmonella gallinarum 287/91	4.747	52.2%	Thomson et al., Genome Research epublication, (2008)	Beowulf Genomics
Salmonella enterica Hadar	4.786	52.3%	Finished	Wellcome Trust
Salmonella enterica Infantis	4.711	~52.3%	Finished	Wellcome Trust
Salmonella paratyphi A	4.582	52.2%	Holt et al., BMC Genomics epublication, 10(1):36 (2009)	Wellcome Trust
Salmonella typhimurium DT104	5.02	52.1%	Finished	Beowulf Genomics
Salmonella typhimurium D23580	~5.0	~52%	Finishing/ gap closure	Wellcome Trust
Salmonella typhimurium DT2	~5	~52%	Shotgun in Progress	Wellcome Trust
Salmonella typhimurium SL1344	5.067	52.2%	Finished	Beowulf Genomics
Salmonella typhi	4.81	52.1%	Parkhill et al., Nature 413, 848-852 (2001)	Beowulf Genomics
Serratia marcescens	5.11	59.5%	Finished	Wellcome Trust / CNRS
Shigella dysenteriae	~4.7	~50%	Finishing/ gap closure	Beowulf Genomics
Shigella sonnei	4.989	50.7%	Finished	Beowulf Genomics
Staphylococcus aureus
Stenotrophomonas maltophilia	4.851	66.3%	Crossman et al. Genome Biology 9, R74 (2008)	Wellcome Trust
Streptococcus equi	2.25	41.3%	Holden et al., PLoS Path. 5, e1000346 (2009)	Home of Rest for Horses
Streptococcus pneumoniae
Streptococcus pyogenes	1.84	38.6%	Holden et al., J. Bacteriol. 188, 1473-1477 (2006)	Beowulf Genomics
Streptococcus suis P1/7	2.01	41.3%	Holden et al., PLoS One 4, e6072 (2009)	Beowulf Genomics
Streptococcus suis BM407	2.15	41.1%	Holden et al., PLoS One 4, e6072 (2009)	Wellcome Trust
Streptococcus suis SC84	2.10	41.1%	Holden et al., PLoS One 4, e6072 (2009)	Wellcome Trust
Streptococcus uberis	1.85	36.6%	Ward et al., BMC Genomics 10, 54 (2009)	Beowulf Genomics
Streptococcus zooepidemicus	2.15	41.5%	Holden et al., PLoS Path. 5, e1000346 (2009)	HBLB
Streptomyces coelicolor	8.67	72.1%	Bentley et al., Nature 417, 141-147 (2002)	BBSRC / Beowulf Genomics
Streptomyces scabies	10.148	71.45%	Finished	USDA
Tropheryma whipplei	0.93	46.3%	Bentley et al., Lancet 361, 637-644 (2003)	Beowulf Genomics
Wolbachia pipientis endosymbiont of Culex quinquefasciatus	~1.6	~34%	Finishing/ gap closure	Beowulf Genomics
Wolbachia endosymbiont of Onchocerca volvulus	~1.1	ND	Sequencing in progress	Beowulf Genomics
Yersinia enterocolitica strain 8081 Biotypes	4.62	42.3%	Thomson et al. (2006)	Wellcome Trust Wellcome Trust
Yersinia pestis	4.65	47.6%	Parkhill et al., Nature 413, 523-527 (2001)	Beowulf Genomics

Other projects	Size	G+C	Status	Funding

Ectromelia (mousepox) virus	208 kb	34.0%	Finished	Wellcome Trust
Emiliania huxleyi virus 86	410 kb	39.9%	Wilson et al., Science 309, 1090-1092 (2005)	Marine Biological Association
Streptococcus pneumoniae capsular loci	90 x ~20kb	~35%	Bentley et al., PLoS Genetics 2(3), e31 (2006)	W.H.O.

Data Release Statement

This sequencing centre plans on publishing the completed and annotated sequences in a peer-reviewed journal as soon as possible. Permission of the principal investigator should be obtained before publishing analyses of the sequence/open reading frames/genes on a chromosome or genome scale.

Data is accessible in a number of ways; for each organism there is a BLAST server, allowing you to search the sequences with your own query and retrieve the matching contigs. Sequences can also be downloaded directly by FTP.

Our primary sequence viewer and annotation tool, Artemis is available for download. This is a portable Java program which is used extensively within the Microbial Genomes group for the analysis and annotation of sequence data from cosmids to whole genomes. The Artemis Comparison Tool (ACT) is also useful for interactive viewing of the comparisons between large and small sequences.

Enquiries about sequencing or analysis should be directed to Director of Sequencing and faculty member in Pathogen Genomics, Julian Parkhill.

webmaster@sanger.ac.uk

Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK Tel:+44 (0)1223 834244

Last Modified Tue Feb 2 13:49:43 2010

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