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Peer-reviewedCC BY 4.0G3: Genes, Genomes, Genetics

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

  • Yuwei Ren1
  • Feng Wang1
  • Xinjian Li1,2
  • Guangliang Liu2
  • Ruiping Sun1
  • Xinli Zheng1
  • Yan Zhang1
  • Ruiyi Lin3
  • Xuyang Lu1,3
  • Linlin Chen1
  • Wenshui Xin1,2
  • Zhe Chao1
  1. 1Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences , Haikou, Hainan 571100 ,
  2. 2Sanya Institute, Hainan Academy of Agricultural Sciences , Sanya, Hainan 572025 ,
  3. 3College of Animal Sciences, Fujian Agriculture and Forestry University , Fuzhou, Fujian 350002 ,
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Abstract

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.

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Cite

BibTeXRIS
BibTeX
@article{ren2026telomeretotelomere,
  title = {{A telomere-to-telomere (T2T) genome assembly of the Wuzhishan pig}},
  author = {Yuwei Ren and Feng Wang and Xinjian Li and Guangliang Liu and Ruiping Sun and Xinli Zheng and Yan Zhang and Ruiyi Lin and Xuyang Lu and Linlin Chen and Wenshui Xin and Zhe Chao},
  journal = {G3: Genes, Genomes, Genetics},
  year = {2026},
  month = oct,
  doi = {10.1093/g3journal/jkag295},
  url = {https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkag295/8979769},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - A telomere-to-telomere (T2T) genome assembly of the Wuzhishan pig
AU  - Yuwei Ren
AU  - Feng Wang
AU  - Xinjian Li
AU  - Guangliang Liu
AU  - Ruiping Sun
AU  - Xinli Zheng
AU  - Yan Zhang
AU  - Ruiyi Lin
AU  - Xuyang Lu
AU  - Linlin Chen
AU  - Wenshui Xin
AU  - Zhe Chao
PY  - 2026
DA  - 2026/10/22
JO  - G3: Genes, Genomes, Genetics
DO  - 10.1093/g3journal/jkag295
UR  - https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkag295/8979769
AB  - 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.
SN  - 2160-1836
ER  -