Fig. 4

Distribution of single nucleotide polymorphisms (SNP), recombination fragments, and codons under selection in the genome of Xanthomonas oryzae pv. oryzae (Xoo) populations in the Philippines. a Percentage of SNPs acquired through mutation, recombination, and mobile genetic elements (MGE) in each of the six major Xoo populations. Recombinant and nonrecombinant SNPs are further subdivided into synonymous, nonsynonymous, and intergenic. b Distribution showing the length of the recombination event tracts (bp) in the six Xoo populations. The black line is a fitted exponential decay curve with a rate of decay of 2.92 × 10⁻⁴ bp⁻¹. c Distribution showing the strength of natural selection in each of the six Xoo populations using 10,182 codon sites. Selection affecting each codon is classified as either purifying (dN–dS < 0) or positive (dN–dS > 0) selection using FUBAR analysis [35]. To compare the distribution of the dN–dS values affecting every codon in each of the six populations, Wilcoxon rank sum tests were performed. All combinations of the comparison have p < 0.0001. Populations PX-A1, PX-A2, PX-A3, PX-B1, PX-B2, and PX-C1 are color-coded