Open Access Highly Accessed Research article

Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica

Henk C den Bakker1*, Andrea I Moreno Switt1, Gregory Govoni23, Craig A Cummings2, Matthew L Ranieri1, Lovorka Degoricija2, Karin Hoelzer1, Lorraine D Rodriguez-Rivera1, Stephanie Brown1, Elena Bolchacova2, Manohar R Furtado2 and Martin Wiedmann1

  • * Corresponding author: Henk C den Bakker hcd5@cornell.edu

  • † Equal contributors

Author Affiliations

1 Department of Food Science, Cornell University, Ithaca NY, 14853, USA

2 Life Technologies Corporation, 850 Lincoln Centre Drive, Foster City CA, 94404, USA

3 AvidBiotics Corp., 300 Utah Ave., Suite 150, South San Francisco, CA, 94080, USA

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BMC Genomics 2011, 12:425  doi:10.1186/1471-2164-12-425

Published: 22 August 2011

Additional files

Additional file 1:

Table of Genomes and strains used in comparative genomic and phylogenomic analysis. Word document containing list of genomes and strains used in comparative genomic and phylogenomic analysis.

Format: DOC Size: 252KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 2:

SNP-based maximum likelihood tree and NeighborNet phylogenetic network inferred from 8,779 SNPs found in the S. enterica subsp. enterica core genome. PDF file containing results of phylogenetic analyses of core genome SNPs.

Format: PDF Size: 194KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

Phylogenetic trees for individual genes and/or regions, without significant signal for recombination, located in SPI-18, the CdtB-islet and the GICT18/1 (artAB) islet. PDF file containing results of phylogenetic analyses of individual genes and/or regions, without significant signal for recombination, located in SPI-18, the CdtB-islet and the GICT18/1 (artAB) islet.

Format: PDF Size: 395KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4:

Histogram of pairwise nucleotide divergence for selected combinations of Salmonella serovars. PDF file containing histograms of pairwise nucleotide divergence for selected combinations of Salmonella serovars.

Format: PDF Size: 262KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 5:

Draft genome assembly statistics for 16 S. enterica strains newly sequenced in this study. Word document containing an overview of the assembly statistics of the 16 newly sequenced Salmonella genomes.

Format: DOC Size: 62KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 6:

Overview genes enriched in either clade B or A of Salmonella enterica subsp. enterica. Excel file with overview genes enriched in either clade B or A of Salmonella enterica subsp. enterica.

Format: XLS Size: 32KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 7:

Alignments of the 93 loci used in the ClonalFrame analysis. Text file with alignments of the 93 loci used in the ClonalFrame analysis in XMFA format.

Format: XMFA Size: 3.4MB Download file

Open Data

Additional file 8:

Primers and probes used for quantitave PCR experiments. Word document containing sequences of primers and probes used for quantitave PCR based population screen

Format: DOC Size: 57KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data