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

Molecular Biology and Evolution
Yixuan KouYongfeng S. Zhou

Abstract

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 ma...Continue Reading

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Citations

Jan 24, 2021·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Murukarthick JayakodiMartin Mascher
Apr 6, 2021·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Tejashree H ModakRachel S Schwartz
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Apr 19, 2021·The Plant Journal : for Cell and Molecular Biology·Raúl CastaneraJosep M Casacuberta
Jun 9, 2021·Plant Biotechnology Journal·Yuxuan YuanDavid Edwards

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Methods Mentioned

BETA
PCR

Software Mentioned

thetaStat
SVTyper
nucmer
F ST
Harbinger
MAFFT
Maker
ADMIXTURE
BWA
VCFtools

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