The first near-complete genome assembly of pig: enabling more accurate genetic research

Pigs are crucial sources of meat and protein, valuable animal models, and potential donors for xenotransplantation. However, the existing reference genome for pigs is incomplete, with thousands of segments and missing centromeres and telomeres, which limits our understanding of the genetic mechanisms underlying important traits in these genomic regions. To address this issue, we present a near complete chromosome telomere-to-telomere gap-free genome assembly for the Jinhua pig (JH-T2T), constructed using PacBio HiFi and ONT long reads. This assembly includes all 18 autosomes and the X and Y sex chromosomes, with only six gaps. It features annotations of 46.90% repetitive sequences, 35 telomeres, 17 centromeres on 16 chromosomes, and 23,924 high-confident genes. Compared to the Sscrofa11.1 reference genome, JH-T2T closes nearly all gaps, extends sequences by 177 Mb, predicts a greater number of more intact telomeres and centromeres, and gains 799 more genes and loses 114 genes. Moreover, it enhances the mapping rate for both Western and Chinese local pigs, outperforming Sscrofa11.1 as a reference genome. Additionally, this comprehensive genome assembly will facilitate large-scale variant detection and enable the exploration of genes associated with pig domestications, such as GPAM, CYP2C18, LY9, ITLN2, and CHIA. Our findings represent a significant advancement in pig genomics, providing a robust resource that enhances genetic research, breeding programs, and biomedical applications.