Open Access Highly Accessed Research article

SOLiD sequencing of four Vibrio vulnificus genomes enables comparative genomic analysis and identification of candidate clade-specific virulence genes

Paul A Gulig1*, Valérie de Crécy-Lagard2, Anita C Wright3, Brandon Walts1, Marina Telonis-Scott14 and Lauren M McIntyre1

Author Affiliations

1 Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA

2 Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA

3 Department of Food Science and Human Nutrition, University of Florida, Gainesville, Florida, USA

4 Department of Genetics, University of Melbourne, 3010 Australia

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BMC Genomics 2010, 11:512  doi:10.1186/1471-2164-11-512

Published: 24 September 2010

Additional files

Additional file 1:

Table S1: Coverage of the V. vulnificus biotype 2 plasmids by newly sequenced reads. SOLiD sequencing reads of each of the four newly sequenced genomes were matched with the three plasmids of V. vulnificus biotype 2 using MAQ. The size of each plasmid is shown. *Numbers of nucleotides of the reference plasmid with less than 10-fold coverage by 35-nt reads from the newly sequenced genome. **Number of nucleotides that were matched by virtue of having 10-fold or greater coverage depth. ***Percent of reference plasmid matched to the newly sequenced genome.

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Additional file 2:

Table S2: Identification of ORFs in newly sequenced V. vulnificus genomes by matching with the V. cholerae NC16961 genome. SOLiD sequencing reads of each of the four newly sequenced genomes were matched with the V. cholerae NC16961 using MAQ, as described in the Methods. V. vulnificus strains: M06 - M06-24/O, B5 - 99-738 DP-B5, B8 - 99-520 DP-B8, ATCC - ATCC 33149. Genes were considered matched if there was five-fold or higher depth of coverage over five tandem 100-nt windows.

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Additional file 3:

Table S3A: Matches of CMCP6 genes from the YJ016 reference genome and the four newly sequenced genomes. The CMCP6 genes are shown by their tag, gene name (if annotated), and product (if known). Matching of each gene with the newly sequenced genomes was determined using MAQ, as described in the Methods. Matches with the YJ016 genome were obtained using GenPlot at http://www.ncbi.nlm.nih.gov webcite using default parameters. Genes from each queried genome that were not matched to the CMCP6 genome are indicated with an X. If a CMCP6 gene is missing from all of the other five genomes, it is indicated with an × in the CMCP6-Specific column. V. vulnificus strains: M06 - M06-24/O, B5 - 99-738 DP-B5, B8 - 99-520 DP-B8, ATCC - ATCC 33149.

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Additional file 4:

Table S3B: Matches of YJ016 genes from the CMCP6 reference genome and the four newly sequenced genomes. The YJ016 genes are shown by their tag, gene name (if annotated), and product (if known). Matching of each gene with the newly sequenced genomes was determined using MAQ, as described in the Methods. Matches with the CMCP6 genome were obtained using GenPlot at http://www.ncbi.nlm.nih.gov webcite using default parameters. Genes from each queried genome that were not matched to the YJ016 genome are indicated with an X. If a YJ016 gene is missing from all of the other five genomes, it is indicated with an × in the YJ016-Specific column. V. vulnificus strains: M06 - M06-24/O, B5 - 99-738 DP-B5, B8 - 99-520 DP-B8, ATCC - ATCC 33149.

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Additional file 5:

Table S4: The core V. vulnificus genome. Genes that were present in the two reference genomes and each of the four newly sequenced genomes are shown using the CMCP6 tag, product, gene name, and cog.

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Additional file 6:

Table S5A: SNP analysis of V. vulnificus M06-24/O compared with the CMCP6 reference genomes. MAQ was used to identify SNPs from the SOLiD sequencing reads from M06-24/O compared with the CMCP6 reference genome, as described in the Methods. Pos. - Position of the nucleotide in the genomic element. Ref. - Reference base in the reference genome. Con. - Consensus base in the newly sequenced genome. Con. QS - Consensus Quality Score. Read depth - Depth of coverage at the chosen nucleotide. Avg. hits - Average number of hits of reads covering the position. HMQ - Highest mapping quality of reads covering the position. MCQ - Minimum consensus quality in the third flanking region on each side of the site. 2nd - second best call for the nucleotide. LLR - Log likelihood ratio of the second and third best call. 3rd - Third best call.

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Additional file 7:

Table S5B: SNP analysis of V. vulnificus M06-24/O compared with the YJ016 reference genome. MAQ was used to identify SNPs from the SOLiD sequencing reads from M06-24/O compared with the YJ016 reference genome, as described in the Methods. Column headings are as for Additional File 6, Table S5A.

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Additional file 8:

Table S6A: SNP analysis of V. vulnificus 99-738 DP-B5 compared with the CMCP6 reference genome. MAQ was used to identify SNPs from the SOLiD sequencing reads from 99-738 DP-B5 compared with the CMCP6 reference genome, as described in the Methods. Column headings are as for Additional File 6, Table S5A.

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Additional file 9:

Table S6B: SNP analysis of V. vulnificus 99-738 DP-B5 compared with the YJ016 reference genome. MAQ was used to identify SNPs from the SOLiD sequencing reads from 99-738 DP-B5 compared with the YJ016 reference genome, as described in the Methods. Column headings are as for Additional File 6, Table S5A.

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Additional file 10:

Table S7A: SNP analysis of V. vulnificus 99-520 DP-B8 compared with the CMCP6 reference genome. MAQ was used to identify SNPs from the SOLiD sequencing reads from 99-520 DP-B8 compared with the CMCP6 reference genome, as described in the Methods. Column headings are as for Additional File 6, Table S5A.

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Additional file 11:

Table 7B: SNP analysis of V. vulnificus 99-520 DP-B8 compared with the YJ016 reference genome. MAQ was used to identify SNPs from the SOLiD sequencing reads from 99-520 DP-B8 compared with the YJ016 reference genome, as described in the Methods. Column headings are as for Additional File 6, Table S5A.

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Additional file 12:

Table 8A: SNP analysis of V. vulnificus ATCC 33149 compared with the CMCP6 reference genome. MAQ was used to identify SNPs from the SOLiD sequencing reads from ATCC 33149 compared with the CMCP6 reference genome, as described in the Methods. Column headings are as for Additional File 6, Table S5A.

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Additional file 13:

Table 8B: SNP analysis of V. vulnificus ATCC 33149 compared with the YJ016 reference genome. MAQ was used to identify SNPs from the SOLiD sequencing reads from ATCC 33149 compared with the YJ016 reference genome, as described in the Methods. Column headings are as for Additional File 6, Table S5A.

Format: XLSX Size: 4.6MB Download file

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