Research
Genomic acquisition of a capsular polysaccharide virulence cluster by non-pathogenic Burkholderia isolates
-
* Corresponding author: Patrick Tan tanbop@gis.a-star.edu.sg
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
Genome Biology 2010, 11:R89 doi:10.1186/gb-2010-11-8-r89
Published: 27 August 2010Additional 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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