Comparative Genomics Reveals Evolutionary Constraints of Regulatory Elements in the Sus scrofa Genome

REs play critical roles in modulating gene expression and shaping phenotypic diversity; however, their evolutionary dynamics in pigs remain incompletely understood. Based on genome alignments across 13 species, we characterized the hierarchical structure of REs evolution in pigs, consisting of cross-species conserved, Suidae-specific, and Sus scrofa-specific regulatory elements. Only 2.86% of REs were conserved across species, whereas 16.35% were Suidae-specific, suggesting lineage-specific regu