ArticleProceedings of the National Academy of Sciences of the United States of America2014
Rapid diversification of five Oryza AA genomes associated with rice adaptation.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers.
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91 citing papers in PubMed, 199 citations in OpenAlex.
- Genomic Footprints of Historical Introgression Between Ancient Lineages of Wild Oryza AA-Genome Species With Widely Separated Contemporary Distributions.Genome biology and evolution · 2026Article
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- Pangenome analyses of tea plants reveal structural variations driving gene expression alterations and agronomic trait diversification.Nature communications · 2025Article
- Epigenetic Regulation of Salt Stress Responses in Rice: Mechanisms and Prospects for Enhancing Tolerance.Epigenomes · 2025Review
- Toward improving multiomic research in understudied cereals.Nature genetics · 2025Review
- Construction of the super pan-genome for the genusHorticulture research · 2025Article
- Chromosome Ordinal Number-Related Genomic Stability Revealed AmongInternational journal of molecular sciences · 2025Article
- Evolutionary Dynamics and Expression Divergence of thePlants (Basel, Switzerland) · 2025Article
- Genome-Wide Dissection of Selection on microRNA Target Genes Involved in Rice Flower Development.Plants (Basel, Switzerland) · 2024Article
- Long Noncoding RNAs in Response to Hyperosmolarity Stress, but Not Salt Stress, Were Mainly Enriched in the Rice Roots.International journal of molecular sciences · 2024Article
- Seed abortion caused by the combination of two duplicate genes in the progeny from the cross betweenBreeding science · 2024Article
- Complete Mitochondrial Genome Assembly of an Upland Wild Rice Species,Life (Basel, Switzerland) · 2023Article
- Analysis of Homologous Regions of Small RNAsCells · 2022Article
- Chromosome-Level Genome Assembly of a FragrantInternational journal of molecular sciences · 2022Article
- Whole-genome DNA methylation patterns ofPlant direct · 2022Article
- Combining nucleotide variations and structure variations for improving astaxanthin biosynthesis.Microbial cell factories · 2022Article
- Evolution and co-evolution: insights into the divergence of plant heat shock factor genes.Physiology and molecular biology of plants : an international journal of functional plant biology · 2022Article
- New Hybrid Spikelet Sterility Gene Found in Interspecific Cross betweenPlants (Basel, Switzerland) · 2022Article
- Comparison of the pathway structures influencing the temporal response of salicylate and jasmonate defence hormones inFrontiers in plant science · 2022Review
- Genome Size Variation and Evolution Driven by Transposable Elements in the GenusFrontiers in plant science · 2022Article
31 more citing papers are in PubMed but not listed here.
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Authors and funding
22 authors at 7 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, and Oryza meridionalis. Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation. Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adaptations to their ecological niches in Asia, South America, Africa and Australia. Extensive variation in noncoding RNA gene numbers, function enrichment, and rates of sequence divergence might also help account for the different genetic adaptations of these rice species. Collectively, these resources provide new opportunities for evolutionary genomics, numerous insights into recent speciation, a valuable database of functional variation for crop improvement, and tools for efficient conservation of wild rice germplasm.
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