ArticleProceedings of the National Academy of Sciences of the United States of America2009
Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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47 citing papers in PubMed.
- Mapping the Molecular Evolution and Role of Wild Rice GLYIII Protein-Encoding Genes in Abiotic Stress Response.Biochemical genetics · 2026Article
- Telomere-to-telomere genome assembly of Oryza australiensis reveals transposon-driven centromere repositioning and shared EE-DD ancestry.Nature communications · 2026Article
- Oryza genome evolution through a tetraploid lens.Nature genetics · 2025Article
- Evolution and diversification of the momilactone biosynthetic gene cluster in the genus Oryza.The New phytologist · 2025Article
- Tracing the intraspecies expansion of glyoxalase genes and their expanding roles across the genus Oryza.Functional & integrative genomics · 2024Article
- Wild rice: unlocking the future of rice breeding.Plant biotechnology journal · 2024Review
- Comparative metabolite profiling of salt sensitivePlant-environment interactions (Hoboken, N.J.) · 2024Article
- Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages.Nature communications · 2024Article
- Population structure and genetic differentiation analyses reveal high level of diversity and allelic richness in crop wild relatives of AA genome species of rice (Oryza sativa L.) in India.Journal of applied genetics · 2023Article
- The International Oryza Map Alignment Project (IOMAP): the Americas-past achievements and future directions.Journal of experimental botany · 2023Article
- Measurements of Antibacterial Activity of Seed Crude Extracts in Cultivated Rice and Wild Oryza Species.Rice (New York, N.Y.) · 2022Article
- Mapping QTLs for yield component traits using overwintering cultivated rice.Journal of genetics · 2021Article
- Natural Diversity in Stomatal Features of Cultivated and Wild Oryza Species.Rice (New York, N.Y.) · 2020Article
- Potential of Platinum Standard Reference Genomes to Exploit Natural Variation in the Wild Relatives of Rice.Frontiers in plant science · 2020Review
- Back to the Wild: On a Quest for Donors Toward Salinity Tolerant Rice.Frontiers in plant science · 2020Review
- Intervention of molecular breeding in water saving rice production system: aerobic rice.3 Biotech · 2019Review
- Transcriptome Analysis and Functional Identification ofThe plant genome · 2018Article
- Draft genome sequence of first monocot-halophytic species Oryza coarctata reveals stress-specific genes.Scientific reports · 2018Article
- Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.Nature genetics · 2018Article
- Morphological and Molecular Data Reveal Three Distinct Populations of Indian Wild RiceFrontiers in plant science · 2018Article
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15 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Comparative genomics is a powerful tool to decipher gene and genome evolution. Placing multiple genome comparisons in a phylogenetic context improves the sensitivity of evolutionary inferences. In the genus Oryza, this comparative approach can be used to investigate gene function, genome evolution, domestication, polyploidy, and ecological adaptation. A large genomic region surrounding the MONOCULM1 (MOC1) locus was chosen for study in 14 Oryza species, including 10 diploids and 4 allotetraploids. Sequencing and annotation of 18 bacterial artificial chromosome clones for these species revealed highly conserved gene colinearity and structure in the MOC1 region. Since the Oryza radiation about 14 Mya, differences in transposon amplification appear to be responsible for the different current sizes of the Oryza genomes. In the MOC1 region, transposons were only conserved between genomes of the same type (e.g., AA or BB). In addition to the conserved gene content, several apparent genes have been generated de novo or uniquely retained in the AA lineage. Two different 3-gene segments have been inserted into the MOC1 region of O. coarctata (KK) or O. sativa by unknown mechanism(s). Large and apparently noncoding sequences flanking the MOC1 gene were observed to be under strong purifying selection. The allotetraploids Oryza alta and Oryza minuta were found to be products of recent polyploidization, less than 1.6 and 0.4 Mya, respectively. In allotetraploids, pseudogenization of duplicated genes was common, caused by large deletions, small frame-shifting insertions/deletions, or nonsense mutations.
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