ArticleMolecular biology and evolution2020
Evolutionary Genomics of Structural Variation in Asian Rice (Oryza sativa) Domestication.
Article in Molecular biology and evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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63 citing papers in PubMed.
- Whole-Genome Variants Resource of 144 Oryza rufipogon Accessions.Scientific data · 2026Article
- What has population genomics told us about the dynamics of selection and plant adaptation?Molecular biology and evolution · 2026Review
- Haplotype-resolved T2T genome and population resequencing provide insights into the domestication and mogroside biosynthesis ofHorticulture research · 2026Article
- Integration of structural variation enhances the resolution of population structure and helps delineate conservation units.Annals of botany · 2026Article
- Both semi-dwarf and photoperiod-insensitive traits in rice were important for the Green Revolution.Botanical studies · 2026Article
- The Genome of the Rice Variety Mowanggu Provides Insight Into Resistance to Magnaporthe oryzae.Molecular plant pathology · 2026Article
- Population genomics reveals association of transposable elements variants with climatic adaptation in wild Amur grape.Nature communications · 2026Article
- Sub-pangenome analysis reveals structural variants associated with fruit color and bacterial wilt resistance in eggplant.Nature communications · 2026Article
- Article
- The Evolutionary Dynamics of Genetic Mutational Load Throughout Tomato Domestication History.Molecular ecology · 2025Article
- Pan-genome identification and expression analysis of the ARF gene family in potato.BMC plant biology · 2025Article
- Transposon Dynamics Drive Genome Evolution and Regulate Genetic Mechanisms of Agronomic Traits in Cotton.Plants (Basel, Switzerland) · 2025Article
- Accurate, Scalable Structural Variant Genotyping in Complex Genomes at Population Scales.Molecular biology and evolution · 2025Article
- Topologically associating domains and the evolution of three-dimensional genome architecture in rice.The Plant journal : for cell and molecular biology · 2025Article
- Genome assembly of pomegranate highlights structural variations driving population differentiation and key loci underpinning cold adaption.Horticulture research · 2025Article
- Identification of quantitative trait loci (QTLs) for key cheese making phenotypes in the blue-cheese mold Penicillium roqueforti.PLoS genetics · 2025Article
- The genomic and epigenomic landscapes of hemizygous genes across crops with contrasting reproductive systems.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Benchmarking, detection, and genotyping of structural variants in a population of whole-genome assemblies using the SVGAP pipeline.bioRxiv : the preprint server for biology · 2025Article
- Pangenome Reveals Gene Content Variations and Structural Variants Contributing to Pig Characteristics.Genomics, proteomics & bioinformatics · 2025Article
- Grapevine pangenome facilitates trait genetics and genomic breeding.Nature genetics · 2024Article
3 more citing papers are in PubMed but not listed here.
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8 authors.
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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 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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