Fig. 5: Fraction of identical genes a genome shares with all other genomes within or between genomovar, phylogroup, and species.

Each genome was compared to all other genomes within each group (A–F) and the cumulative fraction of shared identical genes was recorded and plotted using the custom script Allv_RBM_Violinplot.py. The groups were as follows: A genomes within the same genomovar, B genomes in each separate genomovar within the same phylogroup, excluding genomes from the same genomovar, C genomes in each separate genomovar within different phylogroups, D genomes of the other species (S. pepae for Sal. ruber and E. fergusonii for E. coli), E genomes within the same phylogroup excluding genomes from the same genomovar, F genomes within the same species excluding genomes from the same phylogroup. Data are presented in hybrid violin plots where the top and bottom whiskers show the minimum and maximum values, the middle whisker shows the median value, the black boxes show the interquartile range, and the shaded light blue regions show the density of values along the y-axis. The top graph shows results for Sal. ruber genomes; the bottom graph shows E. coli genomes. For Sal. ruber the number of genomes used in each group were, n = 67 for (A), 422 for (B), 897 for (C), 67 for (D), 176 for (E), and 192 for (F). For E. coli, n = 199 for (A), 2213 for (B), 2910 for (C), 425 for (D), 422 for (E), and 433 for (F). The right panel shows a graphical representation for comparisons performed for both graphs on the left. See also Fig. S6 for graphical examples of the underlying data. Note that while one or a few genomes create extreme outliers, overall, the fraction of identical genes gradually decreases among more divergent genomes compared. Also, note that our modeling analysis (red circles on the graph; see “Methods” section for more details) suggests—for example—that only about 6–7% of the total genes in the genome should be expected to be identical among genomes showing around 98.5% ANI if there is no recent recombination (i.e., the b and e groups); both species show many more such genes in one-to-one genomovar (group B) or one-to-many genomovars (group E) at this level, revealing extensive recent gene exchange.