The domestic pig is a key agricultural species and biomedical model, yet its reference genome has been incomplete for a long time. Using PacBio HiFi, Oxford Nanopore reads, and Hi-C sequencing, we assembled the telomere-to-telomere (T2T), gap-free new pig reference genome (T2T-Sscrofa, GCA_000003025.7). Importantly, this assembly derives from the same individual pig that provided the original reference genome, thereby completing the long-standing foundation of pig genomics. This assembly resolves 274.8 Mb of previously unassembled sequence, including centromeres, segmental duplications, and ribosomal DNA arrays, and identifies 255 new protein-coding genes. Comparative analyses further uncovered a Robertsonian translocation in Western European wild boar and extensive structural variation across global pig populations. By integrating the newly assembled Asian pig genome (T2T-Bamei) into a pangenome framework, we evaluated the advantages of these complete T2T references and highlighted potential (reference) biases in Eurasian pig genomes. Furthermore, we predicted structural divergence of homologous proteins across humans, mouse, and different pig breeds, revealing breed-specific molecular features that enhance the utility of pigs as models for human biomedical research. Together, T2T-Sscrofa and the pangenome provide a comprehensive genomic foundation that will advance agricultural, evolutionary, and biomedical research.
T2T-Sscrofa: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_000003025.7
The code utilized in this research is provided here. For any inquiries or technical support, please do not hesitate to contact us or submit an issue. Email: lidong9866@nwsuaf.edu.cn