A gap-free telomere-to-telomere pig reference genome provides insight in centromere evolution and breed-specific selection

Li, D.; Wang, Y.; Yuan, T.; Li, X.; Quan, Y.; Liu, W.; Schachtschneider, K. M.; Schook, L. B.; Crooijmans, R. P. M. A.; Groenen, M. A. M.; Derks, M. F. L.; Yu, T.

doi:10.1101/2025.10.02.679976

bioRxiv · 10.1101/2025.10.02.679976

A gap-free telomere-to-telomere pig reference genome provides insight in centromere evolution and breed-specific selection

Li, D.·Wang, Y.·Yuan, T.·Li, X.·Quan, Y.·Liu, W.·Schachtschneider, K. M.·Schook, L. B.·Crooijmans, R. P. M. A.·Groenen, M. A. M.·Derks, M. F. L.·Yu, T.

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Abstract

The domestic pig is a key agricultural species and biomedical model, yet its reference genome has remained incomplete. Using PacBio HiFi, Oxford Nanopore reads, and Hi-C sequencing, we assembled the first telomere-to-telomere (T2T), gap-free pig genome (T2T-Sscrofa). 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 reveal a Robertsonian translocation in the western European wild boar and extensive structural variation across global pig populations. T2T-Sscrofa provides a comprehensive genomic foundation for agricultural, evolutionary, and biomedical research.

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Li, D., Wang, Y., Yuan, T., Li, X., Quan, Y., Liu, W., Schachtschneider, K. M., Schook, L. B., Crooijmans, R. P. M. A., Groenen, M. A. M., Derks, M. F. L., Yu, T.. 2025-10-03. A gap-free telomere-to-telomere pig reference genome provides insight in centromere evolution and breed-specific selection. https://doi.org/10.1101/2025.10.02.679976

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