ArticleNature communications2023
Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers, 1 of them a synthesis that pooled it.
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Who cites it
52 citing papers in PubMed, 1 synthesis or guideline pooled it, 81 citations in OpenAlex.
- Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome.Journal of proteome research · 2024Pooled it
- Inversion characterization inbioRxiv : the preprint server for biology · 2026Article
- The Rise of Plant Pan-Genomes: From Genome Variation to Predictive Breeding.Advanced genetics (Hoboken, N.J.) · 2026Article
- Cross incompatibility restricting genome exchange and diversification of primary gene pool in plants: challenges and opportunities.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Empowering Plant Biotechnology Research: Super-Pangenomes as a Novel Arsenal for Crop Breeding and Improvement.Molecular biotechnology · 2026Review
- Whole-Genome Variants Resource of 144 Oryza rufipogon Accessions.Scientific data · 2026Article
- Interhaplotype Inversions and Repeat Expansion in the Sexually Deceptive Orchid Chiloglottis trapeziformis.Genome biology and evolution · 2026Article
- Review
- Challenges in Bringing Pangenome Research Into Breeding: A Case Study in Rice.Plant biotechnology journal · 2026Review
- Ubiquitin-like SUMO protease expansion in rice (Oryza sativa L.).The plant genome · 2026Article
- Sub-pangenome analysis reveals structural variants associated with fruit color and bacterial wilt resistance in eggplant.Nature communications · 2026Article
- Dynamics of genome evolution in the era of pangenome analysis.Cell genomics · 2026Review
- Fine mapping and cloning of an intersubspecific reproductive isolation locusMolecular breeding : new strategies in plant improvement · 2026Article
- Screening of Monokaryotic Strains ofJournal of fungi (Basel, Switzerland) · 2025Article
- Pangenomes as a framework for adaptive radiation, speciation, and adaptation.American journal of botany · 2025Article
- The Potential of NGTs to Overcome Constraints in Plant Breeding and Their Regulatory Implications.International journal of molecular sciences · 2025Review
- Pangenomic structural variant patterns reflect evolutionary diversification in Brassica napus.Genome biology · 2025Article
- Low-call-rate SNPs and presence-absence variation identified in the rice pan-genome can improve genomic prediction of rice gene bank accessions.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Genome Architecture and Speciation in Plants and Animals.Molecular ecology · 2025Review
- A Chromosome Inversion Creates a Supergene for Sex and Colour in Lake Malawi Cichlids.Molecular ecology · 2025Article
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Authors and funding
25 authors at 9 institutions in 6 countries.
Funding
Abstract
Understanding and exploiting genetic diversity is a key factor for the productive and stable production of rice. Here, we utilize 73 high-quality genomes that encompass the subpopulation structure of Asian rice (Oryza sativa), plus the genomes of two wild relatives (O. rufipogon and O. punctata), to build a pan-genome inversion index of 1769 non-redundant inversions that span an average of ~29% of the O. sativa cv. Nipponbare reference genome sequence. Using this index, we estimate an inversion rate of ~700 inversions per million years in Asian rice, which is 16 to 50 times higher than previously estimated for plants. Detailed analyses of these inversions show evidence of their effects on gene expression, recombination rate, and linkage disequilibrium. Our study uncovers the prevalence and scale of large inversions (≥100 bp) across the pan-genome of Asian rice and hints at their largely unexplored role in functional biology and crop performance.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.