Fig. 2: Evidence for SST1-mediated interchromosomal exchange in human genomes.

a, All SST1 monomers from previous analysis of CHM13⁷ and from HG002 were collected and phylogenetic analysis was performed using the maximum-likelihood method based on the best-fit substitution model (Kimura two-parameter + G, parameter = 5.5047) inferred by Jmodeltest2 with 1,000 bootstrap replicates. Bootstrap values higher than 75 are indicated at the base of each node. The colour indicates the source chromosome and the shape indicates the source genome. Three major subfamilies were identified: sf1, primarily on the acrocentrics (Acros); sf2, primarily on the remaining autosomes; and sf3, primarily on the Y chromosome. Black arrows indicate the location on the phylogenetic trees of sf2 monomers S and L from the acrocentric chromosomes (Fig. 1b). b, Predicted PRDM9 DNA binding site frequency (mean sites per kb, each dot indicates one haplotype) in SST1 arrays in n haploid genomes are plotted by chromosome. ANOVA analysis with the two-sided Tukey–Kramer test for pairwise mean comparisons. c, Schematic representation of the three subfamilies of SST1. SST1-sf1 has a central gap and a predicted PRDM9 DNA binding site (red box). d, A segmental duplication of 27 kb or larger was identified on several autosomes in CHM13 that includes Y-like α-satellite DNA (α-sat) and SST1-sf3. Phylogenetic analysis was performed using the maximum-likelihood method and general time reversible (GTR)-plus-gamma substitution parameters. Bootstrap values are shown. e, Comparison of overlaps between segmental duplications (SDs; ≥10 kb) and random regions or SST1 monomers across 147 genomes. Distributions show the number of overlaps versus density. A permutation test with 10,000 iterations per genome was used to generate random region overlaps. The significant difference between distributions (Wilcoxon signed-rank test, paired, two-sided) indicates non-random association between segmental duplications and SST1 regions.