Figure 1.
Circular maps of the sequence contigs of V. vulnificus JY1305, JY1701, and E64MW.
From the outside in, the first circle (red) represents V. vulnificus JY1305 genomic contigs, the second circle (green) represents V. vulnificus JY1701 genomic contigs, and third circle (blue) represents V. vulnificus E64MW genomic contigs. The circles represent BLAST alignment of contigs against the V. vulnificus CMCP6 reference genome. Circle 4 shows GC content. Figure generated using CGView [21].
Table 1.
Summary of assembly and annotation characteristics for the V. vulnificus JY1305, E64MW, and JY1701 genomes.
Figure 2.
Genomic alignment of Vibrio vulnificus Biotype 1 strains CMCP6, YJ016, MO6-24/O, JY1305, E64MW, and JY1701.
Locally conserved block based alignment between the reference genome CMCP6 and the newly sequenced genomes of JY1305, E64MW, and JY1701 as locally collinear blocks (LCB). Figure generated using Mauve [23].
Figure 3.
Vibrio vulnificus genomic content differential Venn diagram.
A 6-way Venn diagram representing the differential and shared gene counts between the V. vulnificus YJ016, CMCP6, MO6-24/O, JY1305, E64MW, and JY1701. The main Venn diagram represents the overlap between C- and E- genotype groups, while the nested Venn diagrams represent the content relationships among the individual C-genotype or E-genotype strains. Gene counts are based on presence or absence of orthologs, where orthology is defined by OrthoMCL [74], using as a clustering criterion shared sequence similarity of 70% or greater.
Figure 4.
Phylogenetic relationships among sequenced Vibrio genomes.
Phylogenetic relationships computed using maximum likelihood estimation, from a random sampling of 175 single copy gene ortholog sequences common among the newly sequenced E-genotype genomes and other sequenced Vibrio species. Three randomly sampled replicates produce trees with highly similar topologies. Purple box indicates strains classified as C-genotypes and green box indicates strains classified as E-genotypes for V. vulnificus.
Table 2.
Key differential genes between found in V. vulnificus C-genotypes that are NOT present in the E-genotypes.
Table 3.
Key differential genes found in V. vulnificus E-genotypes but not in C-genotypes.
Figure 5.
Gene Ontology (GO) functional differences between C- and E- genotypes.
Figure shows GO functional categories which are enriched in C-genotypes of V. vulnificus relative to E-genotypes (blue) or E-genotypes relative to C-genotypes (red). Percentages represent percent of genes under each category that are differential between the genotypes. Percentages of less than 20% are not depicted.