ArticleBMC genomics2017
Comprehensive survey and evolutionary analysis of genome-wide miRNA genes from ten diploid Oryza species.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers, 1 of them a synthesis that pooled it.
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13 citing papers in PubMed, 1 synthesis or guideline pooled it, 27 citations in OpenAlex.
- Transcriptomic Alterations Induced by Tetrahydrocannabinol in SIV/HIV Infection: A Systematic Review.International journal of molecular sciences · 2025Pooled it
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- The Distribution of Average Pairwise Distances Among Human Pre-miRNAs for Disease Association Analysis.International journal of molecular sciences · 2026Article
- Genome-wide profiling of rice Double-stranded RNA-Binding Protein 1-associated RNAs by targeted RNA editing.Plant physiology · 2023Article
- Genomic diversity of aquaporins across genus Oryza provides a rich genetic resource for development of climate resilient rice cultivars.BMC plant biology · 2023Article
- Miniature Inverted-Repeat Transposable Elements: Small DNA Transposons That Have Contributed to PlantPlants (Basel, Switzerland) · 2023Review
- Clustering pattern and evolution characteristic of microRNAs in grass carp (Ctenopharyngodon idella).BMC genomics · 2023Article
- Analysis of Homologous Regions of Small RNAsCells · 2022Article
- Characterization and Comparative Analysis of MicroRNAs in 3 Representative Red Algae.Iranian journal of biotechnology · 2021Article
- Dynamics of cell wall structure and related genomic resources for drought tolerance in rice.Plant cell reports · 2021Review
- Plant microRNAs: biogenesis, gene silencing, web-based analysis tools and their use as molecular markers.3 Biotech · 2019Review
- Advances in Molecular Genetics and Genomics of African Rice (Plants (Basel, Switzerland) · 2019Review
- Advances in understanding salt tolerance in rice.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Review
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMicroRNAs (miRNAs) are non-coding RNAs that play versatile roles in post-transcriptional gene regulation. Although much is known about their biogenesis, and gene regulation very little is known about their evolutionary relation among the closely related species.
resultAll the orthologous miRNA genes of Oryza sativa (japonica) from 10 different Oryza species were identified, and the evolutionary changes among these genes were analysed. Significant differences in the expansion of miRNA gene families were observed across the Oryza species. Analysis of the nucleotide substitution rates indicated that the mature sequences show the least substitution rates among the different regions of miRNA genes, and also show a very much less substitution rates as compared to that of all protein-coding genes across the Oryza species. Evolution of miRNA genes was also found to be contributed by transposons. A non-neutral selection was observed at 80 different miRNA loci across Oryza species which were estimated to have lost ~87% of the sequence diversity during the domestication. The phylogenetic analysis revealed that O. longistaminata diverged first among the AA-genomes, whereas O. brachyantha and O. punctata appeared as the eminent out-groups. The miR1861 family organised into nine distinct compact clusters in the studied Oryza species except O. brachyantha. Further, the expression analysis showed that 11 salt-responsive miRNAs were differentially regulated between O. coarctata and O. glaberrima.
conclusionOur study provides the evolutionary dynamics in the miRNA genes of 10 different Oryza species which will support more investigations about the structural and functional organization of miRNA genes of Oryza species.
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