Higher-order Architecture Shapes Concerted Evolution in a Y-linked repeat array

The maintenance of functional repeat arrays on nonrecombining sex chromosomes presents an evolutionary paradox: tandem repeats are intrinsically unstable yet must preserve sequence identity and copy number to remain functional. The Y-linked Suppressor of Stellate (Su(Ste)) locus in Drosophila melanogaster is a large tandem array that produces piRNAs to silence the X-linked meiotic driver Stellate, but how such arrays are maintained remains unclear. Here, we reconstruct and compare repeat-resolved assemblies of the Su(Ste)/PCKR tandem array across three strains and show that the array is partitioned into discrete domains of elevated sequence identity. These domains exhibit an alternating pattern of similarity, in which nonadjacent regions are more similar to each other than to neighboring regions, and this organization is conserved across strains. Copy-number variation occurs primarily within specific domains, while overall array architecture remains stable. These results indicate that concerted evolution in the Su(Ste) array operates within structurally defined domains rather than uniformly across the array. The association of domain boundaries with inverted repeat elements suggests that higher-order structure constrains gene conversion, shaping both sequence homogenization and copy-number dynamics. In contrast, Y-linked rDNA arrays show uniform sequence similarity across long genomic distances, indicating a distinct mode of homogenization. Together, our findings demonstrate that gene conversion on nonrecombining chromosomes is structured by higher-order array architecture, providing a general framework for the maintenance of functional repeat arrays.