A telomere-to-telomere (T2T) genome assembly of the Wuzhishan pig
Yuwei Ren, Feng Wang, Xinjian Li, Guangliang Liu, Ruiping Sun, Xinli Zheng, Yan Zhang, Ruiyi Lin, Xuyang Lu, Linlin Chen, Wenshui Xin, Zhe ChaoAbstract
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.