A telomere-to-telomere (T2T) genome assembly of the Wuzhishan pig

The Wuzhishan (WZS) minipig, native to Hainan Province, China, is valuable for both agriculture and biomedicine, creating a need for a telomere-to-telomere (T2T) genome assembly to support breeding and biomedical research. In this study, a gap-free, T2T genome assembly organized into 20 chromosomes was generated for the WZS pig (designated WZS-T2T) using a combination of PacBio HiFi, Oxford Nanopore ultra-long reads, and Hi-C data. The assembly spans approximately 2.68 Gb with a scaffold N50 of approximately 142.87 Mb. High completeness and accuracy were demonstrated by a Quality Value (QV) score of 70.2 and a BUSCO completeness score of 99.3%. A total of 23,100 protein-coding genes were predicted, and telomeres were fully assembled across all 20 chromosomes. Notably, the Y chromosome (ChrY) represents the longest assembled ChrY among published T2T pig genomes. Comparative analyses showed that sex differentiation-related genes (including SRY) and innate immune-related genes (PRKX and DDX3X) are conserved across most porcine Y chromosomes. Conversely, the energy metabolism gene SLC25A4 and the macrophage receptor-related gene CSF2RA were identified exclusively in the WZS-T2T assembly among the analyzed genomes. These gene-content variations on ChrY likely reflect both individual variation and differences in assembly completeness. Overall, a high-quality WZS reference genome was established to support agricultural and biomedical applications.