Deciphering the evolution pattern of structural variations overlapped with repetitive sequence during cattle evolution

Repetitive sequences (REPs) are crucial for understanding the evolutionary trajectory of eukaryotic genomes, yet their evolutionary dynamics in domesticated animals have not been as extensively studied as in plants. Here, we integrated eighty-three long-read individuals from globally distributed cattle to provide a detailed landscape of structural variations (SVs) overlapping with REPs (hereafter referred to as rep-SVs) in ecological contexts. Overall, rep-SVs are unevenly distributed between the X chromosome and autosomes. Large rep-SVs accumulated on the X chromosome, whereas certain types of rep-SVs were depleted therein. These distribution patterns coincided with the subspeciation process between taurine and indicine cattle. A specific expansion involving several types of rep-SVs occurred in indicine during this subspeciation process. Notably, this expansion highlighted the role of PDGFD (mediated by bovine-specific Bov-A2 REP), a growth factor that exhibits higher expression in the larger hump, a typical trait distinguishing indicine from taurine. Guided by compositional analysis, a rep-SV in the ROR2 gene (mediated by a satellite copy loss) was found to influence zebrafish growth, thereby potentially contributing to the large body size of the beef cattle breeds. Collectively, these findings clarify the patterns shaping REP dynamics in cattle and provide candidate markers for molecular breeding and evolutionary genetics research.