S.typhi

Salmonella typhi CT18

		Sequence and annotation of Salmonella enterica serovar Typhi (S. typhi) strain CT18
Image source: GlaxoSmithKline Biologicals, Belgium

The annotation for the S. typhi CT18 genome is now accessible through GeneDB. GeneDB allows searching, browsing and download of the full annotation.

The sequenced strain, CT18, is a highly pathogenic, multiple drug resistant strain isolated from a typhoid patient in Cho Quan Hospital, Ho Chi Minh City, Vietnam. The chromosome sequence is 4,809,037 bp in length with a G+C content of 52.09%, and was generated from 97,000 shotgun reads. The start of the sequence was chosen to correspond with the start of the published E. coli K12 sequence. There are 4,599 protein-coding genes (including 204 pseudogenes). Both the sequence and annotation have been deposited in the public databases with the accession number AL513382. In addition, there are two plasmids: pHCM1 (218,150 bp, 249 CDS) with the accession number AL513383, and pHCM2 (106,516 bp, 131 CDS) with the accession number AL513384.

The published sequence data of strain CT18, for the chromosomal sequence and both plasmids, can be searched using our BLAST server and are also available for download from our ftp site, in fasta format, Artemis format and as translated peptide sequence.

The sequence and annotation was produced in collaboration with Gordon Dougan of the Department of Biochemistry, Imperial College, London.

Reference:

"Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18" Nature 413 848-852.: J. Parkhill, G. Dougan, K.D. James, N.R. Thomson, D. Pickard, J. Wain, C. Churcher, K. Mungall, S.D. Bentley, M.T.G. Holden, M. Sebaihia, S. Baker, D. Basham, K. Brooks, T. Chillingworth, P. Connerton, A. Cronin, P. Davis, R.M. Davies, L. Dowd, N. White, J. Farrar, T. Feltwell, N. Hamlin, A. Haque, T.T. Hien, S. Holroyd, K. Jagels, A. Krogh, T.S. Larsen, S. Leather, S. Moule, P. O'Gaora, C. Parry, M. Quail, K. Rutherford, M. Simmonds, J. Skelton, K. Stevens, S. Whitehead, and B.G. Barrell

We have also generated sequence data from several strains of S. typhi using rapid resequencing technologies, 454 and Illumina/Solexa.

Comparative analysis of these genomes is presented in the following publication:

"High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi" Nature Genetics 40 987-993. (free access): Kathryn E Holt, Julian Parkhill, Camila J Mazzoni, Philippe Roumagnac, Francois-Xavier Weill, Ian Goodhead, Richard Rance, Stephen Baker, Duncan J Maskell, John Wain, Christiane Dolecek, Mark Achtman and Gordon Dougan.

454/Roche GS20 and FLX.

454 sff files are available at the European Read Archive (ERA) under accession ERA000001

Reads were assembled into contigs using the 454 proprietary software newbler, version 1.1.

Contigs generated by mapped assemblies (with reference to the S. typhi CT18 finished sequence) and de novo assemblies are available below.

De novo assembled contigs have been deposited as whole genome shotgun (WGS) at EMBL (accessions CAAQ-CAAZ) and and are searchable here.

Solexa/Illumina 1G.

Illumina/Solexa reads fastq files are available at the European Read Archive (ERA) under accession ERA000001. Quality scores in these fastq files reflect phred-like scores rather than Solexa-style scores.

Reads were mapped to the S. Typhi CT18 finished sequence using maq version 0.6.

Mapped consensus sequences are available below. (Bases in lower case are essentially repeats or do not have sufficient coverage; bases in upper case indicate regions where SNPs can be reliably called. In the quality lines, ASCII of a character minus 33 gives the PHRED quality.)

		454				Solexa

Strain	plasmid	model	fold coverage	de novo (fasta/quality)	mapped (fasta/quality)	fold coverage	mapped genomic sequence (fastq)	mapped plasmid sequence (fastq)
E00-7866	-	GS20	10.5x	seq qual	seq qual	-	-	-
E01-6750	-	GS20	8.2x	seq qual	seq qual	-	-	-
E02-1180	-	GS20	13.1x	seq qual	seq qual	-	-	-
E98-0664	-	GS20	10.8x	seq qual	seq qual	-	-	-
E98-2068	-	GS20	10.9x	seq qual	seq qual	-	-	-
J185	-	GS20	13.5x	seq qual	seq qual	-	-	-
M223	-	FLX	11.1x	seq qual	seq qual	-	-	-
404ty	pBSSB1	GS20	8.5x	seq qual	seq qual	24.6x	fastq	pBSSB1
AG3	-	GS20	10.1x	seq qual	seq qual	13.1x	fastq	-
E98-3139	-	FLX	11.1x	seq qual	seq qual	5.4x	fastq	-
150(98)S	-	-	-	-	-	8.6x	fastq	-
CT18	pHCM1, pHCM2	-	-	-	-	9.8x	fastq	pHCM1 pHCM2
E02-2759	pHCM2	-	-	-	-	65.5x	fastq	pHCM2
E03-4983	pBSSB1	-	-	-	-	7.4x	fastq	pBSSB1
E03-9804	pAKU1	-	-	-	-	8.2x	fastq	pAKU1
ISP-03-07467	pAKU1	-	-	-	-	7.9x	fastq	pAKU1
ISP-04-06979	pAKU1	-	-	-	-	72.9x	fastq	pAKU1
Ty2	-	-	-	-	-	8.6x	fastq	-

Please note that this sequence is unchecked and unedited, and will contain errors. The 454 is known to have problems with homopolymeric tracts, and these are therefore likely to contain significant numbers of errors.

This project is funded by Beowulf Genomics

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.

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.

Sequencing enquiries

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

webmaster@sanger.ac.uk

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

Last Modified Thu Feb 12 11:02:52 2009

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