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<p>Ongoing efforts to improve sheep reference genome assemblies still leave many gaps and incomplete regions, resulting in a few common failures and errors in genomic studies. Here, we report a 2.85-Gb gap-free telomere-to-telomere genome of a ram (<i>T2T-sheep1.0</i>), including all autosomes and the X and Y chromosomes. This genome adds 220.05 Mb of previously unresolved regions and 754 new genes to the most updated reference assembly <i>ARS-UI_Ramb_v3.0</i>; it contains four types of repeat units (SatI, SatII, SatIII and CenY) in centromeric regions. <i>T2T-sheep1.0</i> has a base accuracy of more than 99.999%, corrects several structural errors in previous reference assemblies and improves structural variant detection in repetitive sequences. Alignment of whole-genome short-read sequences of global domestic and wild sheep against <i>T2T-sheep1.0</i> identifies 2,664,979 new single-nucleotide polymorphisms in previously unresolved regions, which improves the population genetic analyses and detection of selective signals for domestication (for example, <i>ABCC4</i>) and wool fineness (for example, <i>FOXQ1</i>).</p>

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Telomere-to-telomere sheep genome assembly identifies variants associated with wool fineness

  • 期刊论文

  • 发表日期：

    2025年1月8日

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  • Ling-Yun Luo,
  • Hui Wu,
  • Li-Ming Zhao,
  • Ya-Hui Zhang,
  • Jia-Hui Huang,
  • Qiu-Yue Liu,
  • Hai-Tao Wang,
  • Dong-Xin Mo,
  • He-Hua EEr,
  • Lian-Quan Zhang,
  • Hai-Liang Chen,
  • Shan-Gang Jia,
  • Wei-Min Wang,
  • Meng-Hua Li

摘要

Ongoing efforts to improve sheep reference genome assemblies still leave many gaps and incomplete regions, resulting in a few common failures and errors in genomic studies. Here, we report a 2.85-Gb gap-free telomere-to-telomere genome of a ram (T2T-sheep1.0), including all autosomes and the X and Y chromosomes. This genome adds 220.05 Mb of previously unresolved regions and 754 new genes to the most updated reference assembly ARS-UI_Ramb_v3.0; it contains four types of repeat units (SatI, SatII, SatIII and CenY) in centromeric regions. T2T-sheep1.0 has a base accuracy of more than 99.999%, corrects several structural errors in previous reference assemblies and improves structural variant detection in repetitive sequences. Alignment of whole-genome short-read sequences of global domestic and wild sheep against T2T-sheep1.0 identifies 2,664,979 new single-nucleotide polymorphisms in previously unresolved regions, which improves the population genetic analyses and detection of selective signals for domestication (for example, ABCC4) and wool fineness (for example, FOXQ1).