ArticlePLoS genetics2019
Environmental and epigenetic regulation of Rider retrotransposons in tomato.
Article in PLoS genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers, 1 of them a synthesis that pooled it.
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Who cites it
43 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Nearby transposable elements impact plant stress gene regulatory networks: a meta-analysis in A. thaliana and S. lycopersicum.BMC genomics · 2022Pooled it
- Haplotype-resolved regulation of secondary metabolism in cannabis.Horticulture research · 2026Article
- Apoplastic pH modulates gene expression, the proteome, and ABA content in Vicia faba guard cells and is accompanied by reduced stomatal aperture under salt stress.Journal of experimental botany · 2026Article
- Wild tomato genome assemblies reveal structural variants and repeat content act as recombination barriers.Nature communications · 2026Article
- Extrachromosomal circular DNA are functional, heritable units that expand genomic plasticity and confer resilience.Frontiers in plant science · 2026Review
- Host Factors Promoting the LTR Retrotransposon Life Cycle in Plant Cells: Current Knowledge and Future Directions.International journal of molecular sciences · 2025Review
- Positive-Strand RNA Viruses Induce LTR Retrotransposon Transcription and Extrachromosomal Circular DNA Generation in Plants.International journal of molecular sciences · 2025Article
- DNA methylation contributes to plant acclimation to naturally fluctuating light.The New phytologist · 2025Article
- Transposable elements drive evolution and perturb gene expression in Brassica rapa and B. oleracea.The Plant journal : for cell and molecular biology · 2025Article
- The role of mobile DNA elements in the dynamics of plant genome plasticity.Journal of experimental botany · 2025Review
- Physiologic, Genetic and Epigenetic Determinants of Water Deficit Tolerance in Fruit Trees.Plants (Basel, Switzerland) · 2025Review
- Time-course transcriptome analysis reveals gene co-expression networks and transposable element responses to cold stress in cotton.BMC genomics · 2025Article
- Epigenetic odyssey to decrypt the hidden code for sustainable brassica production: enhancing yield, stress resilience and nutritional quality.Frontiers in plant science · 2025Review
- Review
- Horizontal transfer of plasmid-like extrachromosomal circular DNAs across graft junctions in Solanaceae.Molecular horticulture · 2024Article
- DNA Methylation Dynamics in Response to Drought Stress in Crops.Plants (Basel, Switzerland) · 2024Review
- Chromosome-level genome assembly of a cliff plant Taihangia rupestris var. ciliata provides insights into its adaptation and demographic history.BMC plant biology · 2024Article
- Jasmonate ZIM Domain Protein (Plants (Basel, Switzerland) · 2024Article
- Transposition of HOPPLA in siRNA-deficient plants suggests a limited effect of the environment on retrotransposon mobility in Brachypodium distachyon.PLoS genetics · 2024Article
- Transposon dynamics in the emerging oilseed crop Thlaspi arvense.PLoS genetics · 2024Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Transposable elements in crop plants are the powerful drivers of phenotypic variation that has been selected during domestication and breeding programs. In tomato, transpositions of the LTR (long terminal repeat) retrotransposon family Rider have contributed to various phenotypes of agronomical interest, such as fruit shape and colour. However, the mechanisms regulating Rider activity are largely unknown. We have developed a bioinformatics pipeline for the functional annotation of retrotransposons containing LTRs and defined all full-length Rider elements in the tomato genome. Subsequently, we showed that accumulation of Rider transcripts and transposition intermediates in the form of extrachromosomal DNA is triggered by drought stress and relies on abscisic acid signalling. We provide evidence that residual activity of Rider is controlled by epigenetic mechanisms involving siRNAs and the RNA-dependent DNA methylation pathway. Finally, we demonstrate the broad distribution of Rider-like elements in other plant species, including crops. Our work identifies Rider as an environment-responsive element and a potential source of genetic and epigenetic variation in plants.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.