Fig. 3. Genome-wide evidence of layered expansions in centromeric αSat arrays.

(A) (Top) HOR structural variant positions across the active αSat arrays on chr7 and chr10 (gray, canonical HORs; other colors, structural variants). (Bottom) Percentages of HOR structural variant types on HiFi sequencing reads from 16 HPRC cell lines. Variant nomenclature is described in (42); canonical HOR percentages are listed on the plot. (B) Repeat periodicities identified with NTRprism for the HSat3B1 array on chr17. (C) Comparison of the age and divergence of LINE TEs embedded in different αSat SF layers. (D) (i) Four centromeres in which an active HOR array of distinct origin appears to have expanded within a now-inactive HOR array. (ii) and (iii) Monomeric SFs (rainbow colors) surrounding active HOR arrays on eight chromosomes, with major HOR-haps shown (k = 2 to 3). Red, younger, emphasized below with red rectangles; gray, older, emphasized below with asterisks. (E) Zoomed-in view of chr3 αSat HOR arrays, divided into finer symmetrical HOR-haps (k = 7). (F) (Left) Minimum evolution tree showing the phylogenetic relationships between all HORs, colored by fine (k = 7) HOR-hap assignments. Red and gray ellipses group major HOR-hap divisions into younger and older variants, respectively (42). (Right) Phylogenetic tree built from HOR-hap consensus sequences derived from branches in the left tree, rooted with a reconstructed ancestral cen3 active HOR sequence (ANC) (42). Branch lengths indicate base substitutions per position.