Open Access Highly Accessed Research article

Comparative genomics of the classical Bordetella subspecies: the evolution and exchange of virulence-associated diversity amongst closely related pathogens

Jihye Park12, Ying Zhang1, Anne M Buboltz13, Xuqing Zhang14, Stephan C Schuster37, Umesh Ahuja5, Minghsun Liu5, Jeff F Miller5, Mohammed Sebaihia68, Stephen D Bentley6, Julian Parkhill6 and Eric T Harvill1*

Author Affiliations

1 Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA

2 Graduate Program in Bioinformatics and Genomics, The Pennsylvania State University, University Park, PA, USA

3 Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 310 Wartik Laboratory, University Park, PA, USA

4 Graduate Program in Genetics, The Pennsylvania State University, University Park, PA, USA

5 Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, USA

6 Wellcome Trust Sanger Institute Hinxton, Cambridge, UK

7 Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technical University, Nanyang, Singapore

8 Department of Biology, University Hassiba Ben-Bouali de Chlef, Chlef, Algeria

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BMC Genomics 2012, 13:545  doi:10.1186/1471-2164-13-545

Published: 10 October 2012

Additional files

Additional file 1:

Comparative genome content of thirteen Bordetella strains. Circles indicate the presence (solid color) or absence (unfilled) of each gene family in each strain examined. Circles from outer to inner are started with B. petrii strain followed by B. avium strain and the pan-genome of the classical Bordetella strains. Then, individual circle of B. bronchiseptica, B. parapertussis and B. pertussis strains were shown. This figure was created using the Circos software [21].

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Additional file 2:

Lists of gene families that are present in the pan-genome of the classical Bordetella strains. This table summarized the gene family numbers, representative gene name, predicted function of encoding proteins, presence (1) or absence (0) of each gene family in individual genome, and the sum of each row for a sorting purpose.

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Additional file 3:

The number of SNPs in the genes and dN/dS ratios of genes that have high number of SNPs. This table summarized the start and end position of genes in RB50, gene name, strand, gene length, predicted function of encoding proteins, number of SNPs among the classical Bordetellae based on RB50, and number of SNPs per 100 base pair. dN, dS, and dN/dS ratio are included only for fifty genes that have high number of SNPs. The mean SNPs per 100 bp for the whole genome was 2.24. When the orthologs are pseudogenes, we did not calculate dN/dS ratios, indicating NA in the columns.

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Additional file 4:

Percent sequence similarity of B. pertussis ptx/ptl loci with flanking genes against Tohama I. Percent sequence similarity of B. pertussis ptx/ptl loci and flanking genes compared to Tohama I was plotted between 95% and 100% using zPicture [36]. Intergenic regions, coding regions, and a tRNA were highlighted with red, blue, and green, respectively.

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Additional file 5:

Pair-wise dN/dS ratios for individual gene in the classical Bordetellae ptx/ptl locus. dN/dS ratios of ten classical Bordetellae were plotted for individual gene in the ptx/ptl locus. B. pertussis strain Tohama I represents another B. pertussis strain CS as well because they share identical nucleotide sequences in the ptx/ptl loci. Each figure represents ptx/ptl genes (A), ptx genes (B), ptxA (C), ptxB (D), ptxD (E), ptxE (F), ptxC (G), ptl genes (H), ptlA (I), ptlB (J), ptlC (K), ptlD (L), ptlI (M), ptlE (N), ptlF (O), ptlG (P), and ptlH (Q).

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Additional file 6:

Genome-wide horizontal gene transfer candidates for the classical Bordetellae. The position of the candidates is plotted in each genome (Bpp5 (A), 12822 (B), Tohama I (C), CS (D), 18323 (E), RB50 (F), 1289 (G), 253 (H), MO149 (I), Bbr77 (J), and D445 (K)) and the height represents the score of Alien_hunter. Red line represents the threshold for each genome.

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Additional file 7:

Phylogenetic trees for the classical Bordetellae ptx/ptl locus. Phylogenetic trees were constructed by maximum likelihood method with 1,000 bootstrap replicates with individual gene sequences in the locus, or the entire ptx or ptl locus. Each figure represents the entire ptx locus (A), ptxA (B), ptxB (C), ptxD (D), ptxE (E), ptxC (F), ptl locus (G), ptlA (H), ptlB (I), ptlC (J), ptlD (K), ptlI (L), ptlE (M), ptlF (N), ptlG (O), and ptlH (P).

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Additional file 8:

Multiple sequence alignments of the classical Bordetellae ptxB and ptxC. Multiple amino acid sequence alignments of the classical Bordetellae ptxB and ptxC were presented in this figure.

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