Evolutionary Genomics of Structural Variation in Asian Rice (Oryza sativa) Domestication

被引:66
作者
Kou, Yixuan [1 ,2 ]
Liao, Yi [1 ]
Toivainen, Tuomas [1 ,3 ]
Lv, Yuanda [1 ]
Tian, Xinmin [4 ]
Emerson, J. J. [1 ]
Gaut, Brandon S. [1 ]
Zhou, Yongfeng [1 ,5 ]
机构
[1] UC Irvine, Dept Ecol & Evolutionary Biol, Irvine, CA 92697 USA
[2] Jiangxi Agr Univ, Lab Subtrop Biodivers, Nanchang, Jiangxi, Peoples R China
[3] Univ Helsinki, Dept Agr Sci, Helsinki, Finland
[4] Xinjiang Univ, Coll Life Sci & Technol, Dept Biol Sci, Urumqi, Peoples R China
[5] Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Genome Anal Lab, Minist Agr, Shenzhen, Peoples R China
基金
美国国家卫生研究院; 美国国家科学基金会; 中国国家自然科学基金;
关键词
structural variation; rice; domestication; transposable element insertions; gene gain and loss; COPY-NUMBER POLYMORPHISM; DELETERIOUS MUTATIONS; TRANSPOSABLE ELEMENT; NATURAL-POPULATIONS; GENETIC-STRUCTURE; WIDE PATTERNS; PAIRED-END; MAIZE; SELECTION; ALIGNMENT;
D O I
10.1093/molbev/msaa185
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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 (similar to 4.3Mb) inversion in indica rice varieties relative to japonica varieties, and long-read analyses suggest that similar to 9% of genes from the out-group (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 similar to 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.
引用
收藏
页码:3507 / 3524
页数:18
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