ArticleThe Plant cell2008
Dynamic evolution of oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set.
Article in The Plant cell, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed.
- Telomere-to-telomere genome assembly of Oryza australiensis reveals transposon-driven centromere repositioning and shared EE-DD ancestry.Nature communications · 2026Article
- Genus-Wide Pan-Genome Analysis ofPlants (Basel, Switzerland) · 2025Article
- Oryza genome evolution through a tetraploid lens.Nature genetics · 2025Article
- Fine-mapping and evolutionary history of R-BPMV, a dominant resistance gene to Bean pod mottle virus in Phaseolus vulgaris L.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Article
- The International Oryza Map Alignment Project (IOMAP): the Americas-past achievements and future directions.Journal of experimental botany · 2023Article
- Analysis of Homologous Regions of Small RNAsCells · 2022Article
- The ties of brotherhood between japonica and indica rice for regional adaptation.Science China. Life sciences · 2022Article
- Evolutionary alterations in gene expression and enzymatic activities of gibberellin 3-oxidase 1 in Oryza.Communications biology · 2022Article
- Dynamic differential evolution schemes of WRKY transcription factors in domesticated and wild rice.Scientific reports · 2021Article
- Xa7, a Small Orphan Gene Harboring Promoter Trap for AvrXa7, Leads to the Durable Resistance to Xanthomonas oryzae Pv. oryzae.Rice (New York, N.Y.) · 2021Article
- Article
- Genetics and Genomics of African Rice (Oryza glaberrima Steud) Domestication.Rice (New York, N.Y.) · 2021Review
- StAR-Related Lipid Transfer (START) Domains Across the Rice Pangenome Reveal How Ontogeny Recapitulated Selection Pressures During Rice Domestication.Frontiers in genetics · 2021Article
- Wild and Cultivated Species of Rice Have Distinctive Proteomic Responses to Drought.International journal of molecular sciences · 2020Article
- Back to the Wild: On a Quest for Donors Toward Salinity Tolerant Rice.Frontiers in plant science · 2020Review
- Introgression of the chromosomal region with the Pi-cd locus from Oryza meridionalis into O. sativa L. during rice domestication.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Article
- Lateral transfers of large DNA fragments spread functional genes among grasses.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Potential of Oryza officinalis to augment the cold tolerance genetic mechanisms of Oryza sativa by network complementation.Scientific reports · 2018Article
- Transcriptome Analysis and Functional Identification ofThe plant genome · 2018Article
8 more citing papers are in PubMed but not listed here.
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19 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Oryza (23 species; 10 genome types) contains the world's most important food crop - rice. Although the rice genome serves as an essential tool for biological research, little is known about the evolution of the other Oryza genome types. They contain a historical record of genomic changes that led to diversification of this genus around the world as well as an untapped reservoir of agriculturally important traits. To investigate the evolution of the collective Oryza genome, we sequenced and compared nine orthologous genomic regions encompassing the Adh1-Adh2 genes (from six diploid genome types) with the rice reference sequence. Our analysis revealed the architectural complexities and dynamic evolution of this region that have occurred over the past approximately 15 million years. Of the 46 intact genes and four pseudogenes in the japonica genome, 38 (76%) fell into eight multigene families. Analysis of the evolutionary history of each family revealed independent and lineage-specific gain and loss of gene family members as frequent causes of synteny disruption. Transposable elements were shown to mediate massive replacement of intergenic space (>95%), gene disruption, and gene/gene fragment movement. Three cases of long-range structural variation (inversions/deletions) spanning several hundred kilobases were identified that contributed significantly to genome diversification.
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