葡萄驯化中结构变异的种群遗传学。,Nature Plants

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葡萄驯化中结构变异的种群遗传学。
Nature Plants ( IF 15.8 ) Pub Date : 2019-09-09 , DOI: 10.1038/s41477-019-0507-8
Yongfeng Zhou ₁ , Andrea Minio ₂ , Mélanie Massonnet ₂ , Edwin Solares ₁ , Yuanda Lv ₁ , Tengiz Beridze ₃ , Dario Cantu ₂ , Brandon S Gaut ₁

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结构变异 (SV) 是植物基因组中一个很大程度上未被探索的特征。人们对 SV 的类型和大小、它们在个体中的分布，尤其是它们的种群动态知之甚少。了解这些动态对于理解 SV 对表型的贡献以及将它们识别为全基因组关联中的因果遗传变异的可能性至关重要。在这里，我们识别 SV 并研究它们在克隆繁殖的葡萄栽培品种及其异交野生祖细胞中的进化基因组学。为了对 SV 进行分类，我们组装了高度杂合的霞多丽基因组，其中七分之一的基因是基于 SV 的半合子。通过全基因组、长读和短读比对，对霞多丽和赤霞珠基因组进行综合比较，我们将 SV 检测扩展到群体样本。我们发现强烈的净化选择对 SV 起作用，但特别是对倒置和易位事件起作用。然而，SV 在克隆繁殖的谱系中作为隐性杂合子累积。他们还定义了野生和栽培葡萄藤之间基因组差异的离群区域，表明在驯化中的作用。离群区域包括性别决定区域和浆果颜色位点，其中独立的大型复杂倒置驱动了趋同表型进化。

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The population genetics of structural variants in grapevine domestication.

Structural variants (SVs) are a largely unexplored feature of plant genomes. Little is known about the type and size of SVs, their distribution among individuals and, especially, their population dynamics. Understanding these dynamics is critical for understanding both the contributions of SVs to phenotypes and the likelihood of identifying them as causal genetic variants in genome-wide associations. Here, we identify SVs and study their evolutionary genomics in clonally propagated grapevine cultivars and their outcrossing wild progenitors. To catalogue SVs, we assembled the highly heterozygous Chardonnay genome, for which one in seven genes is hemizygous based on SVs. Using an integrative comparison between Chardonnay and Cabernet Sauvignon genomes by whole-genome, long-read and short-read alignment, we extended SV detection to population samples. We found that strong purifying selection acts against SVs but particularly against inversion and translocation events. SVs nonetheless accrue as recessive heterozygotes in clonally propagated lineages. They also define outlier regions of genomic divergence between wild and cultivated grapevines, suggesting roles in domestication. Outlier regions include the sex-determination region and the berry colour locus, where independent large, complex inversions have driven convergent phenotypic evolution.

更新日期：2019-09-09

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