1. Telomere-to-telomere sheep genome assembly identifies variants associated with wool fineness
- Author
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Luo, Ling-Yun, Wu, Hui, Zhao, Li-Ming, Zhang, Ya-Hui, Huang, Jia-Hui, Liu, Qiu-Yue, Wang, Hai-Tao, Mo, Dong-Xin, EEr, He-Hua, Zhang, Lian-Quan, Chen, Hai-Liang, Jia, Shan-Gang, Wang, Wei-Min, and Li, Meng-Hua
- Abstract
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-sheep1.0has 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-sheep1.0identifies 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).
- Published
- 2025
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