Additional file 1:

A: Schematic circular diagrams of A. salmonicida LFI1238 plasmids; B: Putative duplicated regions of the plasmids in comparison to chromosome I. A: Appropriate categories are shown as pairs of concentric circles representing both coding strands. Key to the chromosomal circular diagrams (outside to inside): scale (in kb), annotated CDSs, unique CDSs compared to the other Vibrionaceae species (red), orthologues shared with the other Vibrionaceae species (green), IS element transposases (purple), % G+C content, G+C deviation (>0% olive, <0% purple). Colour coding for CDSs (according to predicted function): dark blue, pathogenicity/adaptation; black, energy metabolism; red, information transfer; dark green, surface associated; cyan, degradation of large molecules; magenta, degradation of small molecules; yellow, central/intermediary metabolism; pale green, unknown; pale blue, regulators; orange, conserved hypothetical; brown, pseudogenes; pink, phage + IS elements; grey, miscellaneous. B: CDSs are represented as blocked arrows showing the direction of transcription. Identity at nucleotide level is indicated in grey boxes.

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Additional file 2:

Types and distribution of IS elements encoded in the A. salmonicida genome. The data provided shows the distribution of the different types of IS elements identified in the six replicons.

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Additional file 3:

Codon Adaptation Index (CAI) of genes plotted against Codon Bias Index (CBI). Colour coding for the genes are: grey, chromosomal genes; light blue, highly expressed genes (encoding ribosomal proteins and tRNA synthetases); red, pVSAL840; dark green, pVSAL320; yellow, pVSAL54; light green, pVSAL43; black triangles, duplicated genes.

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Additional file 4:

Linear DNA comparison between the chromosomes of A. salmonicida and A. fischeri. The grey bars represent the forward and reverse strands, and red and blue lines between the genomes indicate regions with similarity and inversions, respectively. Black boxes represent IS elements in A. salmonicida.

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Additional file 5:

Genomic organisation of the A. salmonicida inserted phage ϕ VS4 and comparison with the related phage K139. The red lines between the phages indicate regions with amino acid similarity. CDSs are represented as blocked arrows showing the direction of transcription, with colour codes according to their functional annotation. The length of the arrows approximately reflects the sizes of the CDSs. The G+C content and G+C average was analysed using Artemis with a window size of 500 nt.

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Additional file 6:

CDSs harboured on putative genomic islands and phages in A. salmonicida. The data in this table is additional to the data in Table 2, and provides a complete overview of all CDSs harboured on the putative genomic islands and phages listed in Table 2.

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Additional file 7:

A: The two duplicated regions in A. salmonicida LFI1238; B: Agarose gel electrophoresis of PCR products confirming the presence of the duplication in all tested A. salmonicida isolates. The first gene of each duplicate and the flanking genes are indicated as grey boxes (not drawn to scale). B) Agarose gel electrophoresis of duplication products VSAL_I0408-I0407 (PCR product 1) and VSAL_I0264-I0265 (PCR product 2), and the corresponding regions of different A. salmonicida isolates derived by PCR from genomic DNA. Primers are designed from LFI1238 and are indicated by arrows (p1 5'-CGACATGATCGTGTTTTGCT-3', p2 and p3 5'-GGAAAATAGCATCAATTGTA-3', p4 5'-CCATTGTAGAGGTGAGTTTA-3'). The A. salmonicida isolates were obtained from various outbreaks of cold water vibriosis from salmon and cod. The isolate numbers are indicated above each lane. S, 100 bp DNA ladder.

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Additional file 8:

Functional and putative non-functional A. salmonicida genes involved in key steps of the chitinolytic cascade, together with orthologues from other sequenced Vibrionaceae. The data provided in this table lists all identified A. salmonicida CDSs that are known to be involved in the chitinolytic cascade in other Vibrionaceae. Disrupted CDSs and pseudogenes are labelled in the table.

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Additional file 9:

Growth of different Vibrionaceae isolates on α-chitin and GlcNAc. The data provided shows that the A. salmonicida isolates investigated in this study are not able to utilise α-chitin or GlcNAc.

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Additional file 10:

Predicted CDSs of A. salmonicida with potential roles in pathogenicity. The data in this table gives a comprehensive list of all CDSs with possible functions that may be associated with mediating cold-water vibriosis in fish.

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Additional file 11:

Functional distribution of putative inactivated genes in the A. salmonicida genome. The data provided in this table includes all CDSs disrupted or truncated by IS elements and CDSs containing translational frameshifts of premature stop codons.

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