Duplications showed significant higher recombination rates than inversions, deletions, and insertions
It is long known that SVs are derived from the mutational process during meiosis by nonallelic homologous recombination (NAHR) [66]. However, it is still unclear whether recombination rates would be different among SVs and which type of SVs has the highest recombination rates. Here, we addressed this question by inferring the historical and long-term recombination rates (ρ/bp) using pyrho, which utilized population genomic data and took population demography into account [33]. This fine-scale and genome-wide mapping strategy revealed a similar landscape among chromosomes. Specifically, recombination rates were higher toward the distal regions of chromosomes and lower around the centromeres (Supplementary figure 3), which is consistent with the long-held knowledge of a “U shape” distribution at the chromosome level in animals and plants [67-70].
The comparison between four types of SVs called from three methods universally revealed that duplications showed significantly the highest fine-scale recombination rates (Wilcoxon rank sum test, p < 0.05 for all comparisons) (Figure 4A). This pattern was also consistent when comparing upstream and downstream regions (1000bp) of all SVs, suggesting no abrupt changes of fine-scale recombination rates within and around SVs. Interestingly, these comparisons were found to be more consistent for SVs identified from NanoSV and SyRI (Figure 4A). We further compared the distribution of recombination rates for four SVs types (Figure 4B). We found that the recombination rates of duplications showed two peaks, with one peak of recombination rates around 10-8, which is close to peaks of other three SVs types, and the other peak with higher recombination rate of 1.26x10-7.