Correlation of the unique core genome size and phylogeny. The number of unique core genes was calculated when starting from different end nodes and then successively adding more genomes according to the phylogenetic tree (see Figure 3). Depending on the starting point for the calculations, local maxima are typically found when all genomes of a taxon (or all taxa with the same phylogenetic distance to the starting point) are added. When starting from (A) V. cholerae or (B) V. parahaemolyticus strains of most recent origins, then the first local maxima were found after inclusion of all strains of the respective Vibrio species (i.e., 12 and 124 genes, respectively). With V. cholerae as the starting point succeeding maxima were found after inclusion of all representatives of V. mimicus and two additional representatives of the Vibrio species(31), the genus Vibrio (37) and the genus Photobacterium (15). When starting with V. parahaemolyticus the corresponding local maxima were found after inclusion of all strains of V. parahaemolyticus (124), V. alginolyticus and V. sp. EX25 (70), V. harveyi (57) and V. vulnificus (19), the complete genus Vibrios (15) and all isolates from genus Photobacterium (6).
Kahlke et al. BMC Genomics 2012 13:179 doi:10.1186/1471-2164-13-179