Evolutionary Genomics of Structural Variation in Asian Rice (Oryza sativa) Domestication.
Evolutionary Genomics of Structural Variation in Asian Rice (Oryza sativa) Domestication.
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亚洲大米（Oryza sativa）驯化的结构变化的进化基因组学。
DOI：
10.1093/molbev/msaa185
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发表时间：
2020-12-16
影响因子：
10.7
通讯作者：
Zhou Y
中科院分区：
文献类型：
--
作者：
Kou Y;Liao Y;Toivainen T;Lv Y;Tian X;Emerson JJ;Gaut BS;Zhou Y
尽管结构变异 (SV) 对表型有很大贡献，但结构变异 (SV) 是植物基因组进化的一个很大程度上未被研究的特征。在这项研究中，我们在亚洲水稻 (Oryza sativa) 及其野生祖先 (O. rufipogon) 的 347 个高覆盖度、重新测序的基因组样本中发现了 SV。除了这个短读数据集之外，我们还从全基因组组装和长读数据中推断出 SV。数据集之间的比较揭示了基因组变异的不同特征。例如，基因组比对发现籼稻品种相对于粳稻品种存在较大的倒位（∼4.3 Mb），长读分析表明来自外类群（O. longistaminata）的约 9% 的基因是半合子。然而，我们重点关注重测序样本以研究 SV 的群体基因组学。 SV 聚类分析概括了同样从 SNP 推断出的水稻品种组。然而，每种 SV 类型的位点频谱（包括倒位、重复、缺失、易位和移动元件插入）比同义 SNP 偏向频率较低的变异，这表明 SV 可能主要是有害的。在转座元件中，正弦和水手插入的频率特别低。我们还使用 SV 通过对比水稻和 O. rufipogon 来研究驯化。栽培基因组中衍生的 SV 和移动元件插入量比 O. rufipogon 多约 25%，这表明 SV 增加了水稻驯化的成本。 SV 分歧的峰值因已知的驯化基因而富集，但我们还检测到驯化过程中获得和丢失的数百个基因，其中一些因农艺利益性状而富集。
Structural variants (SVs) are a largely unstudied feature of plant genome evolution, despite the fact that SVs contribute substantially to phenotypes. In this study, we discovered SVs across a population sample of 347 high-coverage, resequenced genomes of Asian rice (Oryza sativa) and its wild ancestor (O. rufipogon). In addition to this short-read data set, we also inferred SVs from whole-genome assemblies and long-read data. Comparisons among data sets revealed different features of genome variability. For example, genome alignment identified a large (∼4.3 Mb) inversion in indica rice varieties relative to japonica varieties, and long-read analyses suggest that ∼9% of genes from the outgroup (O. longistaminata) are hemizygous. We focused, however, on the resequencing sample to investigate the population genomics of SVs. Clustering analyses with SVs recapitulated the rice cultivar groups that were also inferred from SNPs. However, the site-frequency spectrum of each SV type—which included inversions, duplications, deletions, translocations, and mobile element insertions—was skewed toward lower frequency variants than synonymous SNPs, suggesting that SVs may be predominantly deleterious. Among transposable elements, SINE and mariner insertions were found at especially low frequency. We also used SVs to study domestication by contrasting between rice and O. rufipogon. Cultivated genomes contained ∼25% more derived SVs and mobile element insertions than O. rufipogon, indicating that SVs contribute to the cost of domestication in rice. Peaks of SV divergence were enriched for known domestication genes, but we also detected hundreds of genes gained and lost during domestication, some of which were enriched for traits of agronomic interest.
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影响因子：
10.7
作者：
Choi JY;Platts AE;Fuller DQ;Hsing YI;Wing RA;Purugganan MD
通讯作者：
Purugganan MD
DOI：
10.1111/nph.12247
发表时间：
2013-07
期刊：
The New phytologist
影响因子：
--
作者：
Díez CM;Gaut BS;Meca E;Scheinvar E;Montes-Hernandez S;Eguiarte LE;Tenaillon MI
通讯作者：
Tenaillon MI
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.
影响因子：
30.8
作者：
Chia, Jer-Ming;Song, Chi;Ware, Doreen
通讯作者：
Ware, Doreen
影响因子：
10.7
作者：
Hamala, Tuomas;Savolainen, Outi
通讯作者：
Savolainen, Outi