Open Access Research

Genomic acquisition of a capsular polysaccharide virulence cluster by non-pathogenic Burkholderia isolates

Bernice Meng Qi Sim1, Narisara Chantratita23, Wen Fong Ooi1, Tannistha Nandi1, Ryan Tewhey4, Vanaporn Wuthiekanun3, Janjira Thaipadungpanit3, Sarinna Tumapa3, Pramila Ariyaratne1, Wing-Kin Sung15, Xiao Hui Sem1, Hui Hoon Chua1, Kalpana Ramnarayanan6, Chi Ho Lin1, Yichun Liu7, Edward J Feil8, Mindy B Glass9, Gladys Tan7, Sharon J Peacock102 and Patrick Tan111*

Author Affiliations

1 Genome Institute of Singapore, 60 Biopolis Street, 138672 Singapore

2 Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, 420/6 Rajvithi Road, Bangkok 10400, Thailand

3 Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, 420/6 Rajvithi Road, Bangkok 10400, Thailand

4 Scripps Translational Science Institute, The Scripps Research Institute, 3344 North Torrey Pines Court, Suite 300, La Jolla, CA 92037, USA

5 Department of Computer Science, National University of Singapore, 13 Computing Drive, 117417 Singapore

6 National Cancer Centre Singapore, 11 Hospital Drive, 169610 Singapore

7 Defense Medical and Environmental Research Institute, DSO National Laboratories, 27 Medical Drive, 117510 Singapore

8 Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK

9 Centers for Disease Control and Prevention, 1600 Clifton Road MS G-34, Atlanta, GA 30333, USA

10 Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK

11 Duke-NUS Graduate Medical School, 8 College Road, 169857 Singapore

For all author emails, please log on.

Genome Biology 2010, 11:R89  doi:10.1186/gb-2010-11-8-r89

Published: 27 August 2010

Additional files

Additional file 1:

A list of the Burkholderia strains used to construct the Burkholderia pan-genome array (BPGA).

Format: DOC Size: 60KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 2:

A flowchart that depicts the analysis workflow for the Burkholderia pan-genome array (BPGA).

Format: DOC Size: 176KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 3:

A graph illustrating the robustness of the workflow.

Format: DOC Size: 170KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 4:

A document explaining the experimental validation of the BPGA.

Format: DOC Size: 24KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 5:

A figure that shows the results obtained from the experimental validation of the BPGA.

Format: DOC Size: 562KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 6:

A document validating BtE555 as a Bt species by ara gene PCR and 16 s sequencing.

Format: DOC Size: 786KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 7:

A chart that summarizes the average variability in each Bt strain compared against the BtE264 reference.

Format: DOC Size: 91KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 8:

A complete list of all the GIs and nGis and their associated features.

Format: DOC Size: 102KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 9:

Six representative dot matrix plots of the Bp-likeCPS from BtE555 when aligned against Bp CPS from BpK96243.

Format: DOC Size: 90KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 10:

Detailed information of the GC composition of Bt EPS and the Bp-likeCPS in BtE555.

Format: DOC Size: 123KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 11:

Experimental validation of 50 representative SNPs predicted in BtE555.

Format: DOC Size: 91KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 12:

Sequence statistics of the de novo assembled contigs from BtE555 deep sequencing paired-end reads.

Format: DOC Size: 31KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 13:

A table that ascribes BtE555 contigs that are mappable to the GI, nGi and EPS regions in BtE264.

Format: DOC Size: 61KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 14:

A list of the BtE555 unique genes and their associated contigs, when compared against reference strain BtE264.

Format: DOC Size: 75KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 15:

Two phylogenetic trees drawn with permuted data, to ensure that the aCGH clusters are robust.

Format: DOC Size: 310KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 16:

List of genes absent in three of the strains in cluster 1 (which contains the variant strains) when compared against BtE264.

Format: DOC Size: 120KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 17:

A list of strains used for both MLST and aCGH analysis.

Format: DOC Size: 178KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 18:

A figure showing the correlation between aCGH similarity and locus variance.

Format: DOC Size: 210KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 19:

A rooted phylogenetic tree (MLST) confirming that the variant strains are distinct from the rest of the Bt strains.

Format: DOC Size: 349KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 20:

A graph that charts the growth rate of the reference strain BtE264, BtE555 and the mutant CPS KO in rich media.

Format: DOC Size: 615KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data