气候变化领域集成服务门户(CCPortal): A chromosome-scale reference genome and genome-wide genetic variations elucidate adaptation in yak

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DOI	10.1111/1755-0998.13236
	A chromosome-scale reference genome and genome-wide genetic variations elucidate adaptation in yak
	Ji Q.-M.; Xin J.-W.; Chai Z.-X.; Zhang C.-F.; Dawa Y.; Luo S.; Zhang Q.; Pingcuo Z.; Peng M.-S.; Zhu Y.; Cao H.-W.; Wang H.; Han J.-L.; Zhong J.-C.
发表日期	2021
ISSN	1755098X
起始页码	201
结束页码	211
卷号	21 期号:1
英文摘要	Yak is an important livestock animal for the people indigenous to the harsh, oxygen-limited Qinghai-Tibetan Plateau and Hindu Kush ranges of the Himalayas. The yak genome was sequenced in 2012, but its assembly was fragmented because of the inherent limitations of the Illumina sequencing technology used to analyse it. An accurate and complete reference genome is essential for the study of genetic variations in this species. Long-read sequences are more complete than their short-read counterparts and have been successfully applied towards high-quality genome assembly for various species. In this study, we present a high-quality chromosome-scale yak genome assembly (BosGru_PB_v1.0) constructed with long-read sequencing and chromatin interaction technologies. Compared to an existing yak genome assembly (BosGru_v2.0), BosGru_PB_v1.0 shows substantially improved chromosome sequence continuity, reduced repetitive structure ambiguity, and gene model completeness. To characterize genetic variation in yak, we generated de novo genome assemblies based on Illumina short reads for seven recognized domestic yak breeds in Tibet and Sichuan and one wild yak from Hoh Xil. We compared these eight assemblies to the BosGru_PB_v1.0 genome, obtained a comprehensive map of yak genetic diversity at the whole-genome level, and identified several protein-coding genes absent from the BosGru_PB_v1.0 assembly. Despite the genetic bottleneck experienced by wild yak, their diversity was nonetheless higher than that of domestic yak. Here, we identified breed-specific sequences and genes by whole-genome alignment, which may facilitate yak breed identification. © 2020 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd
英文关键词	genetic introgression; regions of homozygosity; single-nucleotide polymorphisms; whole-genome sequencing; yak
语种	英语
scopus关键词	Molecular Ecology Resources
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/158371
作者单位	State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement; Lhasa; China; Institute of Animal Science and Veterinary Research; Tibet Academy of Agricultural and Animal Husbandry Sciences; Lhasa; China; Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization; Sichuan Province and Ministry of Education; Southwest Minzu University; Chengdu; China; State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals; Kunming Institute of Zoology; Chinese Academy of Sciences; Kunming; China; CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources; Institute of Animal Science; Chinese Academy of Agriculture Sciences (CAAS); Beijing; China
推荐引用方式 GB/T 7714	Ji Q.-M.,Xin J.-W.,Chai Z.-X.,et al. A chromosome-scale reference genome and genome-wide genetic variations elucidate adaptation in yak[J],2021,21(1).
APA	Ji Q.-M..,Xin J.-W..,Chai Z.-X..,Zhang C.-F..,Dawa Y..,...&Zhong J.-C..(2021).A chromosome-scale reference genome and genome-wide genetic variations elucidate adaptation in yak.,21(1).
MLA	Ji Q.-M.,et al."A chromosome-scale reference genome and genome-wide genetic variations elucidate adaptation in yak".21.1(2021).