Fig. 2: Frequencies of recombination events along the chromosome of the reference genome.

a Frequencies of imported blocks per 10Kb (Y-axis) in windows sliding along coordinates in the chromosome (X-axis). The high-recombination blocks (HRBs) were predicted as blocks with >50 importation events (by RecHMM) in any sliding windows of 100 Kb, and the middle-recombination blocks (MRBs) and the low-recombination block (LRB) were predicted as gaps between HRBs. The median values of frequencies of recombination events (HRB1 = 24, HRB2 = 11, HRB3 = 18.5, MRB1 = 3, MRB2 = 13, and LRB = 5. Whiskers, minimum and maximum of the data) in each block were visualized as in the inset, with pairwise significance of differences evaluated using the two-tailed student’s t-test (****p < 0.0001). b The scatter plot shows the levels of recombination in the 2266 core genes as measured by percentages of topological conflicts (Y-axis) in the 5824 representative genomes. The coordinates of the core genes in the reference genome were shown in the X-axis. The black and red dots show the level of recombination with or without the ESL genomes, and the lines show the average values of 10 neighboring core genes. The chromosomal coordinates of some genes encoding virulence factors, environmental adaptations, or biocide resistances were visualized as filled blocks between the two parts and color-coded according to the Key. Source data are provided as a Source Data file.