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 regulatory innovation in pigs. Cross-species constrained REs exhibited higher conservation and were preferentially located proximal to transcription start sites. Sus scrofa-specific REs exhibited lower conservation, higher TE content, and were mainly distributed in intergenic regions. These patterns suggest that TEs may contribute to regulatory sequence turnover during pig evolution. Functional enrichment analysis showed that conserved REs were associated with fundamental developmental and neurobiological processes, whereas Sus scrofa-specific REs were enriched in pathways related to lipid metabolism, immune response, and neural signaling. In addition, intra-species analysis across 35 pig genomes demonstrated high overall conservation of REs. Our study reveals distinct evolutionary patterns of regulatory elements in pigs and provide novel insights into regulatory innovation underlying phenotypic diversity and economically important traits in livestock.