Open Access Highly Accessed Research article

Genomic taxonomy of vibrios

Cristiane C Thompson1*, Ana Carolina P Vicente1, Rangel C Souza2, Ana Tereza R Vasconcelos2, Tammi Vesth3, Nelson Alves4, David W Ussery3, Tetsuya Iida5 and Fabiano L Thompson4*

Author Affiliations

1 Laboratory of Molecular Genetics of Microrganims, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil

2 National Laboratory for Scientific Computing, Department of Applied and Computational Mathematics, Laboratory of Bioinformatics, Av. Getúlio Vargas 333, Quitandinha, 25651-070, Petropolis, RJ, Brazil

3 Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark

4 Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, UFRJ, Brazil

5 Laboratory of Genomic Research on Pathogenic Bacteria, International Research Center for Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan

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BMC Evolutionary Biology 2009, 9:258  doi:10.1186/1471-2148-9-258

Published: 27 October 2009

Additional files

Additional file 1:

Table S1. BLAST matrix. The matrix lists the identity between proteomes of different strains of vibrios. The number of proteins and gene families in each genome are shown directly beneath the strain number. The hypotenuse (red) corresponds to the paralogs. The data provided the identity between proteomes of different strains of vibrios. The number of proteins and gene families in each genome are shown directly beneath the strain number. The hypotenuse (red) corresponds to the paralogs.

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Additional file 2:

Figure S1A-C. Phylogenetic trees based on the maximum parsimony method using 16S rRNA gene, MLSA (i.e. ftsZ, gyrB, mreB, pyrH, recA, rpoA and topA; 10,141 bp), and supertree (i.e. aminopeptidase P, alaS, aspS, ftsZ, gltX, gyrB, hisS, ileS, infB, metG, mreB, pntA, pheT, pyrH, recA, rpoA, rpoB, rpsH, signal recognition particle protein, threonyl-tRNA synthetase, topA, valS and 30S ribosomal protein S11; 41,617 bp). Bootstrap percentages after 2000 replications are shown. Because some genomes used in this study are not completely sequenced, for the comparison of 16S rRNA, MLSA and supertree, we used 16 genomes of vibrios. The genes used in MLSA and supertree were found only in these 16 genomes. The data provided the phylogenetic relationship between vibrio strains

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Additional file 3:

Figure S2A-C. Phylogenetic trees based on the neighbour-joining method using 16S rRNA gene, MLSA (i.e. ftsZ, gyrB, mreB, pyrH, recA, rpoA and topA; 10,141 bp), and supertree (i.e. aminopeptidase P, alaS, aspS, ftsZ, gltX, gyrB, hisS, ileS, infB, metG, mreB, pntA, pheT, pyrH, recA, rpoA, rpoB, rpsH, signal recognition particle protein, threonyl-tRNA synthetase, topA, valS and 30S ribosomal protein S11; 41,617 bp). Bootstrap percentages after 2000 replications are shown. Because some genomes used in this study are not completely sequenced, for the comparison of 16S rRNA, MLSA and supertree, we used 16 genomes of vibrios. The genes used in MLSA and supertree were found only in these 16 genomes. The data provided the phylogenetic relationship between vibrio strains

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Additional file 4:

Table S2. Percentage of average amino acid identity (AAI) between vibrio species. Representative genomes were used for the calculations. The data provided the percentage of average amino acid identity (AAI) between vibrio species.

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Additional file 5:

Table S3. Genomic dissimilarity [δ(f,g)] values between vibrio especies. Representative genomes were used for the calculations. The data provided the genomic dissimilarity [δ(f,g)] values between vibrio species.

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