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<p>A complete telomere-to-telomere (T2T) genome is essential for advancing pig genomic research. Here we assembled a pig T2T gap-free genome T2T-pig1.0 (2.63 Gb) for a boar in Wuzhishan, China, covering all 20 chromosomes. T2T-pig1.0 with an accuracy of &gt;99.999% uncovers 194.42 Mb of previously unresolved regions (PURs), and 1,189 new genes are added to the current reference genome Sscrofa11.1. We annotated 111 protein-coding genes with 11 male-specific conserved orthologous genes on chromosome Y (43.25 Mb). Pig-specific centromeric satellite repeat units are revealed. Centromeric regions of all telocentric chromosomes harbor a unique structure, ‘telomere-SAT1B-(mSAT)<i>ₙ</i>-SAT3-q_arm’, and a few young long terminal repeats. With the addition of 339,092 single-nucleotide polymorphisms in PURs, the population structure is updated with cross-continental introgression, and a selective sweep analysis reveals 280 new regions and 133 new genes potentially associated with body stature. <i>GALNT13</i>, with strong selection signals, has a role in inhibiting porcine chondrocyte proliferation while promoting chondrocyte differentiation.</p>

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Telomere-to-telomere genome assembly of a male pig provides insight into population structure and selection for body stature

  • 期刊论文

  • 发表日期：

    2025年12月12日

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  • Ya-Biao Luo,
  • Ning Huang,
  • Cheng-Wan Zha,
  • Li-Xian Yang,
  • Peng-Xiang Xue,
  • Qiao Xu,
  • Xiao-Yang Yang,
  • Long-Miao Zhang,
  • Yu-Bei Wang,
  • Zhe Chao,
  • Rui-Ping Sun,
  • Feng Wang,
  • Shan-Gang Jia,
  • Mei-Ying Fang

摘要

A complete telomere-to-telomere (T2T) genome is essential for advancing pig genomic research. Here we assembled a pig T2T gap-free genome T2T-pig1.0 (2.63 Gb) for a boar in Wuzhishan, China, covering all 20 chromosomes. T2T-pig1.0 with an accuracy of >99.999% uncovers 194.42 Mb of previously unresolved regions (PURs), and 1,189 new genes are added to the current reference genome Sscrofa11.1. We annotated 111 protein-coding genes with 11 male-specific conserved orthologous genes on chromosome Y (43.25 Mb). Pig-specific centromeric satellite repeat units are revealed. Centromeric regions of all telocentric chromosomes harbor a unique structure, ‘telomere-SAT1B-(mSAT)ₙ-SAT3-q_arm’, and a few young long terminal repeats. With the addition of 339,092 single-nucleotide polymorphisms in PURs, the population structure is updated with cross-continental introgression, and a selective sweep analysis reveals 280 new regions and 133 new genes potentially associated with body stature. GALNT13, with strong selection signals, has a role in inhibiting porcine chondrocyte proliferation while promoting chondrocyte differentiation.