Telomere-to-telomere genome assembly of a male goat reveals variants associated with cashmere traits
Hui Wu,
Ling-Yun Luo,
Ya-Hui Zhang,
Chong-Yan Zhang,
Jia-Hui Huang,
Dong-Xin Mo,
Li-Ming Zhao,
Zhi-Xin Wang,
Yi-Chuan Wang,
EEr He-Hua,
Wen-Lin Bai,
Di Han,
Xing-Tang Dou,
Yan-Ling Ren,
Renqing Dingkao,
Hai-Liang Chen,
Yong Ye,
Hai-Dong Du,
Zhan-Qiang Zhao,
Xi-Jun Wang,
Shan-Gang Jia (shangang.jia@cau.edu.cn),
Zhi-Hong Liu (liuzh7799@163.com) and
Meng-Hua Li (menghua.li@cau.edu.cn)
Additional contact information
Hui Wu: China Agricultural University
Ling-Yun Luo: China Agricultural University
Ya-Hui Zhang: China Agricultural University
Chong-Yan Zhang: Inner Mongolia Agricultural University
Jia-Hui Huang: China Agricultural University
Dong-Xin Mo: China Agricultural University
Li-Ming Zhao: Lanzhou University
Zhi-Xin Wang: Inner Mongolia Agricultural University
Yi-Chuan Wang: Inner Mongolia Agricultural University
EEr He-Hua: NingXia Academy of Agriculture and Forestry Sciences
Wen-Lin Bai: Shenyang Agricultural University
Di Han: Modern Agricultural Production Base Construction Engineering Center of Liaoning Province
Xing-Tang Dou: Ltd.
Yan-Ling Ren: Shandong Binzhou Academy of Animal Science and Veterinary Medicine
Renqing Dingkao: Gannan Institute of Animal Husbandry Science
Hai-Liang Chen: Ltd.
Yong Ye: Zhongwei Goat Breeding Center of Ningxia Province
Hai-Dong Du: Zhongwei Goat Breeding Center of Ningxia Province
Zhan-Qiang Zhao: Zhongwei Goat Breeding Center of Ningxia Province
Xi-Jun Wang: Jiaxiang Animal Husbandry and Veterinary Development Center
Shan-Gang Jia: China Agricultural University
Zhi-Hong Liu: Inner Mongolia Agricultural University
Meng-Hua Li: China Agricultural University
Nature Communications, 2024, vol. 15, issue 1, 1-20
Abstract:
Abstract 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).
Date: 2024
References: Add references at CitEc
Citations:
Downloads: (external link)
https://www.nature.com/articles/s41467-024-54188-z Abstract (text/html)
Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.
Export reference: BibTeX
RIS (EndNote, ProCite, RefMan)
HTML/Text
Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-54188-z
Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/
DOI: 10.1038/s41467-024-54188-z
Access Statistics for this article
Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie
More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla (sonal.shukla@springer.com) and Springer Nature Abstracting and Indexing (indexing@springernature.com).