Structural divergence of sex chromosomes and conservation of the Dmy locus. (A) Dot plots between Chr X and Chr Y for Hd-rR and HNI, with male HiFi read depth. Blue and purple dots indicate forward and reverse complement matches, respectively. Yellow lines indicate global average depth. Reduced male read depth marks Y-dif regions. Centromeres showing reduced HiFi depth are supported by much longer ONT-UL reads (Fig. 1C). (B) Structural comparison of X/Y-dif regions (dark gray bars) and Y-sp regions (orange bars) between Hd-rR and HNI. (C) Schematic representation of the structural evolution of the Y-sp region and its corresponding region on Chr 9. Blue and purple boxes indicate genes; arrows, transcriptional direction. A 43 kb segment containing Dmrt1 was duplicated and inserted into the proto-Y Chromosome, giving rise to Dmy.