Telomere-to-telomere genome assembly of a male goat reveals variants associated with cashmere traits
A complete goat (Capra hircus) reference genome enhances analyses of genetic variation, thus providing insights into domestication and selection in goats and related species. Here, we assemble a telomere-to-telomere (T2T) gap-free genome (2.86 Gb) from a cashmere goat (T2T-goat1.0), including a Y chromosome of 20.96 Mb. With a base accuracy of >99.999%, T2T-goat1.0 corrects numerous genome-wide structural and base errors in previous assemblies and adds 288.5 Mb of previously unresolved regions and 446 newly assembled genes to the reference genome. We sequence the genomes of five representative goat breeds for PacBio reads, and use T2T-goat1.0 as a reference to identify a total of 63,417 structural variations (SVs) with up to 4711 (7.42%) in the previously unresolved regions. T2T-goat1.0 was applied in population analyses of global wild and domestic goats, which revealed 32,419 SVs and 25,397,794 SNPs, including 870 SVs and 545,026 SNPs in the previously unresolved regions. Also, our analyses reveal a set of selective variants and genes associated with domestication (e.g., NKG2D and ABCC4) and cashmere traits (e.g., ABCC4 and ASIP).
Authors
- Xingtang Dou
- Chumeng Zhang (ORCID: https://orcid.org/0000-0003-3391-9390)
- Meng-Hua Li (ORCID: https://orcid.org/0000-0001-5194-2506)
- Yanling Ren (ORCID: https://orcid.org/0000-0003-3310-2225)
- Renqing Dingkao
- EEr Hehua
- Bai Wenlin
- Yichuan Wang (ORCID: https://orcid.org/0000-0003-2554-6686)
- Jiahui Huang (ORCID: https://orcid.org/0000-0002-8522-5430)
- Shangang Jia (ORCID: https://orcid.org/0000-0002-3306-7637)
- Dong-Xin Mo
- Hailiang Chen (ORCID: https://orcid.org/0000-0002-5802-2670)
- Zhihong Liu (ORCID: https://orcid.org/0000-0001-5237-7772)
- Liming Zhao (ORCID: https://orcid.org/0000-0002-6731-0279)
- Zhixin Wang (ORCID: https://orcid.org/0000-0003-0895-3853)
- Yahui Zhang (ORCID: https://orcid.org/0000-0003-3281-9830)
- Xijun Wang (ORCID: https://orcid.org/0000-0002-0949-3492)
- Yong Ye (ORCID: https://orcid.org/0000-0002-9535-8800)
- Di Han
- Ling-Yun Luo
- Hui Wu (ORCID: https://orcid.org/0000-0001-8748-9176)
- Zhao Zhi-gang
- Hai-Dong Du
Institutions
- Inner Mongolia Agricultural University (CN)
- Binzhou Medical University (CN)
- Shenyang Agricultural University (CN)
- Animal Science Research Institute (CN)
- Ningxia Academy of Agriculture and Forestry Sciences (CN)
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences (CN)
- Chinese Academy of Agricultural Sciences (CN)
- China Agricultural University (CN)
- Lanzhou University (CN)
Publication Details
- Journal
- Nature Communications
- Published
- 2024-11-20
- DOI
- https://doi.org/10.1038/s41467-024-54188-z
- Citations
- 18
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 4.21
Funders
- National Natural Science Foundation of China
- China Agricultural University
- Chinese Academy of Sciences
- Ministry of Science and Technology of the People's Republic of China
- Chinese Academy of Agricultural Sciences
- National Science and Technology Major Project
- National Key Research and Development Program of China