ArticleMolecular biology and evolution2022
Miniature Inverted-repeat Transposable Elements Drive Rapid MicroRNA Diversification in Angiosperms.
Article in Molecular biology and evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 27 citations in OpenAlex.
- Transposon expansion is associated with reorganization of small RNA and DNA methylation landscapes in the morphologically minimal angiosperm Wolffia brasiliensis.The Plant journal : for cell and molecular biology · 2026Article
- Stones in genomic storms: transposable element-driven variation in Prunus fruit trees.Mobile DNA · 2026Review
- Inhibition of miR-224-5p promotes osteogenesis in dental pulp stem cells by targeting the PTEN/PI3K/AKT axis.Journal of orthopaedic surgery and research · 2026Article
- Genome-Wide Identification of miRNAs and Pollen-Associated miRNA-Target Relationships inPlants (Basel, Switzerland) · 2026Article
- Plant MITEs: miniature transposable elements with major impacts.Mobile DNA · 2025Review
- MITE Annotation and Landscape in 207 Plant Genomes Reveal Their Evolutionary Dynamics and Functional Roles.Molecular ecology resources · 2025Article
- Article
- Trans-Kingdom RNA Dialogues: miRNA and milRNA Networks as Biotechnological Tools for Sustainable Crop Defense and Pathogen Control.Plants (Basel, Switzerland) · 2025Review
- Evolution of Plant Conserved microRNAs After Whole-Genome Duplications.Genome biology and evolution · 2025Article
- The microRNA408-plantacyanin module balances plant growth and drought resistance by regulating reactive oxygen species homeostasis in guard cells.The Plant cell · 2024Article
- Impact of Chromosomal Fusion and Transposable Elements on the Genomic Evolution and Genetic Diversity ofPlants (Basel, Switzerland) · 2024Article
- Species-Specific miRNAs Contribute to the Divergence between Deciduous and Evergreen Species inPlants (Basel, Switzerland) · 2024Article
- Identification of miRNA858 long-loop precursors in seed plants.The Plant cell · 2024Article
- Review
- Genome-wide characterization and evolution analysis of miniature inverted-repeat transposable elements in Barley (Frontiers in plant science · 2024Article
- Conserved structured domains in plant non-coding RNA enod40, their evolution and recruitment of sequences from transposable elements.NAR genomics and bioinformatics · 2023Article
- Selection signatures and population dynamics of transposable elements in lima bean.Communications biology · 2023Article
- Insertion sequence transposition inactivates CRISPR-Cas immunity.Nature communications · 2023Article
- Differences in the intraspecies copy number variation of Arabidopsis thaliana conserved and nonconserved miRNA genes.Functional & integrative genomics · 2023Article
- Miniature Inverted-Repeat Transposable Elements: Small DNA Transposons That Have Contributed to PlantPlants (Basel, Switzerland) · 2023Review
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Authors and funding
9 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
MicroRNAs (miRNAs) are fast evolving endogenous small RNAs that regulate organism function and behavior in both animals and plants. Although models for de novo miRNA biogenesis have been proposed, the genomic mechanisms driving swift diversification of the miRNA repertoires in plants remain elusive. Here, by comprehensively analyzing 21 phylogenetically representative plant species, ranging from green algae to angiosperms, we systematically identified de novo miRNA events associated with 8,649 miRNA loci. We found that 399 (4.6%), 466 (5.4%), and 1,402 (16.2%) miRNAs were derived from inverted gene duplication events, long terminal repeats of retrotransposons, and miniature inverted-repeat transposable elements (MITEs), respectively. Among the miRNAs of these origins, MITEs, especially those belonging to the Mutator, Tc1/Mariner, and PIF/Harbinger superfamilies, were the predominant genomic source for de novo miRNAs in the 15 examined angiosperms but not in the six non-angiosperms. Our data further illustrated a transposition-transcription process by which MITEs are converted into new miRNAs (termed MITE-miRNAs) whereby properly sized MITEs are transcribed and therefore become potential substrates for the miRNA processing machinery by transposing into introns of active genes. By analyzing the 58,038 putative target genes for the 8,095 miRNAs, we found that the target genes of MITE-miRNAs were preferentially associated with response to environmental stimuli such as temperature, suggesting that MITE-miRNAs are pertinent to plant adaptation. Collectively, these findings demonstrate that molecular conversion of MITEs is a genomic mechanism leading to rapid and continuous changes to the miRNA repertoires in angiosperm.
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