The pan-genome of V. anguillarum. The flower plots represent the number of shared (core) and specific (accessory/dispensable) genes based on cluster orthologs for each chromosome. Petals display numbers of strain-specific genes found in each genome of V. anguillarum strains with core gene numbers in the center. The gray colors indicate the virulence category as found in three fish larva model systems (31).
Phylogenetic tree of 163 concatenated virulence factors shared by all V. anguillarum strains. The phylogenetic tree was constructed based on the maximum likelihood algorithm, using a concatenated alignment of 163 amino acid sequences inferred from putative virulence factors identified in V. anguillarum strain 775 (20) (Table S2). Bootstrap values <80% were removed from the tree. The horizontal bar at the base of the figure represents 0.01 substitutions per amino acid site. The virulence ranking of the strains is based on three fish larva models (31). HV, high virulence; LV, low virulence; MV, medium virulence.
Core genome phylogeny of V. anguillarum strains. The maximum likelihood tree was obtained from a concatenated nucleotide sequence alignment of the orthologous core genes (1,723 genes for both chromosomes) for the 28 V. anguillarum strains. The virulence properties of the strains and geographical places of isolation were added to improve comparison. Bootstrap values of <80% were removed from the tree. The horizontal bar at the base of the figure represents 0.6 substitution per nucleotide site. The virulence ranking of the strains is based on three fish larva models (31). HV, high virulence; LV, low virulence; MV, medium virulence.
Schematic representation of accessory elements carrying virulence or fitness factors in the V. anguillarum strains. (A) Genomic islands in strain 90-11-286. (B) Genomic islands in strains PF4 and PF7. (C) Genomic islands in strains S2 2/9 and HI610. (D) Genomic island in strain DSM21597. (E) Prophage-related elements in V. anguillarum strains T265 and Ba35 that contain a gene related to zonula occludens toxin (Zot). The positions of GIs and prophage-like elements are shown in Tables S4 and S7. The colors were assigned according to the possible role of each ORF as shown in the figure.
Schematic representation of accessory gene clusters in V. anguillarum strains PF4, PF430-3, PF7, 4299, HI610, DSM21597, S2 2/9, and 90-11-286. The position of the core genome was assigned according to V. anguillarum strain 775.
V. anguillarum pan-genome and core and accessory genome evolution according to the number of sequenced genomes. (A) Total numbers of genes (pan-genome), shared genes (core genome), and unique genes (accessory genome) for a given number of genomes sequentially added. (B) COG subcategories of predicted genes within the core genomes of V. anguillarum for chromosomes I and II. Each category or subcategory is graphed as a percentage of the total number of genes in the core genome. Download FIG S1, DOCX file, 0.5 MB.
Distribution of genomic islands (GIs) previously identified in V. anguillarum strain 775. Shown is a graphic representation of the distribution of 10 GIs (GIs 1 to 10) in the V. anguillarum collection. Black and white squares represent the presence and absence of GI, respectively. Download FIG S2, DOCX file, 0.3 MB.
Hypothetical evolution pathway in V. anguillarum. The model of V. anguillarum evolution suggests insertions and deletion of genomic islands (Table S4) and infection by bacteriophages (Tables S6 and S7). The graphic representation of the genetic diversity is based on the core genome phylogeny. Putative ancestral strains are indicated as open circles. The virulence ranking of the strains is based on three fish larval models (1). Download FIG S3, DOCX file, 0.4 MB.