The Sanger Institute is extending its program of comparative Salmonella sequencing to include further serovars of S. enterica, in collaboration with Gordon Dougan of the Wellcome Trust Sanger Institute, Dr. Paul Barrow of the Institute for Animal Health, Compton, and Dr. Mark Achtman of the Max Planck Institute for Infection Biology, Berlin.

We have funding to sequence a further nine serovars; details of the exact serovars and strains are being kept under review, and will be announced here when finalised. Each will be sequenced to completion to allow a full comparison of the genomes.

Projects:

Salmonella bongori 12419 ATCC 43975

• Status: Finished
• Assembly: 1 contig >1kb (1 contig >2kb); total size 4.460 Mb
• Shotgun: 75,084 reads totalling 42.054 Mb, theoretical genome coverage of 99.99%
• Preliminary annotation: chromosome sequence and gene prediction in Artemis format

S. enterica Enteritidis PT4 NCTC 13349

• Status: Published in Thomson et al, Genome Res., epublication, 2008.
• Assembly: 2 contigs >1kb (2 contigs >2kb); total size 4.686 Mb
• Shotgun: 68,660 reads totalling 48.605 Mb, theoretical genome coverage of 99.99%
• EMBL accession no.: AM933172

S. enterica Gallinarum 287/91 NCTC 13346

• Status: Published in Thomson et al, Genome Res., epublication, 2008.
• Assembly: 2 contigs >1kb (2 contigs >2kb); total size 4.747 Mb
• Shotgun: 80,266 reads totalling 58.710 Mb, theoretical genome coverage of 99.99%
• EMBL accession no.: AM933173

S. enterica Hadar

• Status: Finished
• Assembly: 3 contigs >1kb (3 contigs >2kb); total size 4.797 Mb
• Shotgun: 79,998 reads totalling 56.374 Mb, theoretical genome coverage of 99.99%

S. enterica Infantis

• Status: Finished
• Assembly: 1 contigs >1kb (1 contigs >2kb); total size 4.711 Mb
• Shotgun: 98,013 reads totalling 60.338 Mb, theoretical genome coverage of 99.99%

S. enterica Typhimurium DT104 NCTC 13348

• Status: Finished
• Assembly: 2 contigs >1kb (2 contigs >2kb); total size 5.028 Mb
• Shotgun: 76,534 reads totalling 54.807 Mb, theoretical genome coverage of 99.99%
• Preliminary annotation (chromosome): gene prediction in Artemis format and chromosome sequence in FASTA format.
• Please Note: The preliminary annotation of the chromosome is based on the reverse complement of the original finished genome sequence. The finished genome in its original orientation can still be found on our ftp site.

S. enterica Typhimurium DT2

• Status: Shotgun sequencing
• Assembly: 23 contigs >1kb (15 contigs >2kb); total size 4.983 Mb
• Shotgun: 76,073 reads totalling 50.381 Mb, theoretical genome coverage of 99.99%

S. enterica Typhimurium SL1344 NCTC 13347

• Status: Finished
• Assembly: 4 contigs >1kb (4 contigs >2kb); total size 5.067 Mb
• Shotgun: 81,802 reads totalling 38.198 Mb, theoretical genome coverage of 99.95%
• Preliminary annotation (chromosome): gene prediction in Artemis format and chromosome sequence in FASTA format.
• Preliminary annotation (plasmids): chromosome sequence and gene predictionof Plasmid 1, Plasmid 2 and Plasmid 3 in Artemis format

S. enterica Typhimurium D23580

• Status: Finishing/gap closure
• Assembly: 6 contigs >1kb (6 contigs >2kb); total size 5.087 Mb
• Shotgun: 89,080 reads totalling 56.194 Mb, theoretical genome coverage of 99.99%

The Sanger Institute has also sequenced and published Salmonella typhi CT18 and sequenced Salmonella paratyphi A strain AKU_12601. Full detail of both projects can be found at the given links.

The databases are available for searching on our BLAST server, and for download from our FTP site

You can obtain these strains from the NCTC or ATCC culture collections using the IDs listed with their names.

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.

Annotation: Preliminary annotation will change, although the systematic gene names will remain constant for CDS retained in the final annotation. For publication purposes please refer to our conditions of use policy

Assembly warning

Please note that the assembly database consists of unedited automatic assemblies; it will contain errors and misassemblies, along with E. coli and vector contamination. The contig numbers are not stable, and will vary with each data release. The sequences in the shotgun database are single reads from ABI sequencers; they will contain errors, along with both E. coli and vector contamination.

Finishing warning

Please note that although finishing has begun, the assembly database may still contain errors and misassemblies, and E. coli and vector contamination. The contig numbers are not stable, and will vary with each data release. The sequences in the shotgun database are single reads from ABI sequencers; they will contain errors, along with both E. coli and vector contamination.

The original project was funded by Beowulf Genomics to perform comparative sequencing of five Salmonella strains (S Enteritidis PT4, S. enterica Typhimurium DT104, S. enterica Typhimurium SL1344, Salmonella bongori 12419, and S. enterica Gallinarum 287/91) in collaboration with Prof. Mark Roberts of the Department of Veterinary Pathology, University of Glasgow, Prof. Duncan Maskell of the Centre for Veterinary Science, Dept. of Clinical Veterinary Medicine, The University of Cambridge, Dr. Paul Barrow of the Institute for Animal Health, Compton, and Prof T.J. Humphrey of the PHLS Food Microbiology Research Unit, Exeter.

Sequencing enquiries

Please address all sequencing enquiries to: parkhill@sanger.ac.uk