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A chromosome-scale reference genome and genome-wide genetic variations elucidate adaptation in yak.

染色体尺度参考基因组和全基因组遗传变异阐明了牦牛的适应。

  • 影响因子:7.01
  • DOI:10.1111/1755-0998.13236
  • 作者列表:"Ji QM","Xin JW","Chai ZX","Zhang CF","Dawa Y","Luo S","Zhang Q","Pingcuo Z","Peng MS","Zhu Y","Cao HW","Wang H","Han JL","Zhong JC
  • 发表时间:2021-01-01
Abstract

: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.

摘要

牦牛是严酷的、氧气有限的青藏高原和喜马拉雅山兴都库什山脉当地人民的重要家畜。牦牛基因组在2012年进行了测序,但由于用于分析它的Illumina测序技术的固有局限性,其组装被碎片化。准确和完整的参考基因组对于该物种的遗传变异研究至关重要。长读序列比它们的短读序列更完整,并且已经成功地应用于各种物种的高质量基因组组装。在这项研究中,我们提出了一个高质量的染色体规模牦牛基因组组装 (BosGru_PB_v1.0) 与长读测序和染色质相互作用技术构建。与现有牦牛基因组组装 (BosGru_v2.0) 相比,BosGru_PB_v1.0表现出显著改善的染色体序列连续性、降低的重复结构模糊性和基因模型完整性。为了表征牦牛的遗传变异,我们基于Illumina短读产生了西藏和四川7个公认的国内牦牛品种和一个来自可可西里的野牦牛的从头基因组组装。我们将这8个组装体与BosGru_PB_v1.0基因组进行了比较,在全基因组水平上获得了牦牛遗传多样性的综合图谱,并鉴定了BosGru_PB_v1.0组装体中缺失的几个蛋白编码基因。尽管野牦牛经历了遗传瓶颈,但其多样性仍高于国内牦牛。在此,我们通过全基因组比对鉴定了品种特异性序列和基因,这可能有助于牦牛品种鉴定。

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