ArticleBMC genomics2008
Selection and mutation on microRNA target sequences during rice evolution.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- How Binding Affinity and Binding Specificity Map to Sequence Space.Journal of molecular evolution · 2026Article
- Bacterial gene 5' ends have unusual mutation rates that can mislead tests of selection.PLoS biology · 2025Article
- Functional synonymous mutations and their evolutionary consequences.Nature reviews. Genetics · 2025Review
- miR398 targets a CuBMC plant biology · 2025Article
- Genome-Wide Dissection of Selection on microRNA Target Genes Involved in Rice Flower Development.Plants (Basel, Switzerland) · 2024Article
- Systematic analysis reveals cis and trans determinants affecting C-to-U RNA editing in Arabidopsis thaliana.BMC genetics · 2020Article
- Fine-Tuning the Expression of Duplicate Genes by Translational Regulation inFrontiers in plant science · 2019Article
- Major Domestication-Related Phenotypes inThe Plant cell · 2018Article
- Adenine Enrichment at the Fourth CDS Residue in Bacterial Genes Is Consistent with Error Proofing for +1 Frameshifts.Molecular biology and evolution · 2017Article
- microRNAs and Their Targets in Apple (Frontiers in plant science · 2017Article
- Abiotic Stress Responsive miRNA-Target Network and Related Markers (SNP, SSR) inFrontiers in plant science · 2017Article
- Functional Roles of microRNAs in Agronomically Important Plants-Potential as Targets for Crop Improvement and Protection.Frontiers in plant science · 2017Review
- Impacts of Whole-Genome Triplication on MIRNA Evolution in Brassica rapa.Genome biology and evolution · 2015Article
- Decoding mechanisms by which silent codon changes influence protein biogenesis and function.The international journal of biochemistry & cell biology · 2015Review
- Comparative analysis of the Dicer-like gene family reveals loss of miR162 target site in SmDCL1 from Salvia miltiorrhiza.Scientific reports · 2015Article
- Genome-wide identification and evolutionary analysis of positively selected miRNA genes in domesticated rice.Molecular genetics and genomics : MGG · 2015Article
- Duplicate gene divergence by changes in microRNA binding sites in Arabidopsis and Brassica.Genome biology and evolution · 2015Article
- Post-transcriptional and post-translational regulations of drought and heat response in plants: a spider's web of mechanisms.Frontiers in plant science · 2015Article
- The miR9863 family regulates distinct Mla alleles in barley to attenuate NLR receptor-triggered disease resistance and cell-death signaling.PLoS genetics · 2014Article
- Comparative expression profiling of miRNA during anther development in genetic male sterile and wild type cotton.BMC plant biology · 2013Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMicroRNAs (miRNAs) posttranscriptionally down-regulate gene expression by binding target mRNAs. Analysis of the evolution of miRNA binding sites is helpful in understanding the co-evolution between miRNAs and their targets. To understand this process in plants a comparative analysis of miRNA-targeted duplicated gene pairs derived from a well-documented whole genome duplication (WGD) event in combination with a population genetics study of six experimentally validated miRNA binding sites in rice (O. sativa) was carried out.
resultsOf the 1,331 pairs of duplicate genes from the WGD, 41 genes (29 pairs) were computationally predicted to be miRNA targets. Sequence substitution analysis indicated that the synonymous substitution rate was significantly lower in the miRNA binding sites than their 5' and 3' flanking regions. Of the 29 duplicated gene pairs, 17 have only one paralog been targeted by a miRNA. This could be due to either gain of a miRNA binding site after the WGD or because one of the duplicated genes has escaped from being a miRNA target after the WGD (loss of miRNA binding site). These possibilities were distinguished by separating miRNAs conserved in both dicots and monocot plants from rice-specific miRNAs and by phylogenetic analysis of miRNA target gene families. The gain/loss rate of miRNA binding sites was estimated to be 3.0 x 10(-9) gain/loss per year. Most (70.6%) of the gains/losses were due to nucleotide mutation. By analysis of cultivated (O. sativa; n = 30) and wild (O. rufipogon; n = 15) rice populations, no segregating site was observed in six miRNA binding sites whereas 0.12-0.20 SNPs per 21-nt or 1.53-1.80 x 10(-3) of the average pairwise nucleotide diversity (pi) were found in their flanking regions.
conclusionBoth molecular evolution and population genetics support the hypothesis that conservation of miRNA binding sites is maintained by purifying selection through elimination of deleterious alleles. Nucleotide mutations play a major role in the gain/loss of miRNA binding sites during evolution.
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