ArticlePloS one2013
Transcriptional activity, chromosomal distribution and expression effects of transposable elements in Coffea genomes.
Article in PloS one, 2013. 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, 56 citations in OpenAlex.
- Physiologic, Genetic and Epigenetic Determinants of Water Deficit Tolerance in Fruit Trees.Plants (Basel, Switzerland) · 2025Review
- Chromosome distribution of four LTR retrotransposons and 18 S rDNA in coffea eugenioides.Scientific reports · 2025Article
- LTR Retroelements and Bird Adaptation to Arid Environments.International journal of molecular sciences · 2023Article
- Transposable elements: multifunctional players in the plant genome.Frontiers in plant science · 2023Review
- MegaLTR: a web server and standalone pipeline for detecting and annotating LTR-retrotransposons in plant genomes.Frontiers in plant science · 2023Article
- Review
- Impact of polyploidy on plant tolerance to abiotic and biotic stresses.Frontiers in plant science · 2022Review
- Differential nuclease sensitivity profiling uncovers a drought responsive change in maize leaf chromatin structure for two large retrotransposon derivatives,Plant direct · 2021Article
- Comparative phylogenetics of repetitive elements in a diverse order of flowering plants (Brassicales).G3 (Bethesda, Md.) · 2021Article
- Diversity of repetitive sequences within compact genomes of Phaseolus L. beans and allied genera Cajanus L. and Vigna Savi.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2020Article
- Homology-Free Detection of Transposable Elements Unveils Their Dynamics in Three Ecologically DistinctGenes · 2020Article
- Genomics of Evolutionary Novelty in Hybrids and Polyploids.Frontiers in genetics · 2020Review
- The Role of Transposable Elements in Pongamia Unigenes and Protein Diversity.Molecular biotechnology · 2020Article
- Intraspecific Diversity in the Cold Stress Response of Transposable Elements in the DiatomGenes · 2019Article
- Structure and Distribution of Centromeric Retrotransposons at Diploid and AllotetraploidFrontiers in plant science · 2018Article
- Impact of transposable elements on polyploid plant genomes.Annals of botany · 2017Review
- Article
- Review
- Transcriptionally active LTR retrotransposons in Eucalyptus genus are differentially expressed and insertionally polymorphic.BMC plant biology · 2015Article
- RNA-Seq analysis identifies genes associated with differential reproductive success under drought-stress in accessions of wild barley Hordeum spontaneum.BMC plant biology · 2015Article
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Authors and funding
13 authors at 6 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Plant genomes are massively invaded by transposable elements (TEs), many of which are located near host genes and can thus impact gene expression. In flowering plants, TE expression can be activated (de-repressed) under certain stressful conditions, both biotic and abiotic, as well as by genome stress caused by hybridization. In this study, we examined the effects of these stress agents on TE expression in two diploid species of coffee, Coffea canephora and C. eugenioides, and their allotetraploid hybrid C. arabica. We also explored the relationship of TE repression mechanisms to host gene regulation via the effects of exonized TE sequences. Similar to what has been seen for other plants, overall TE expression levels are low in Coffea plant cultivars, consistent with the existence of effective TE repression mechanisms. TE expression patterns are highly dynamic across the species and conditions assayed here are unrelated to their classification at the level of TE class or family. In contrast to previous results, cell culture conditions per se do not lead to the de-repression of TE expression in C. arabica. Results obtained here indicate that differing plant drought stress levels relate strongly to TE repression mechanisms. TEs tend to be expressed at significantly higher levels in non-irrigated samples for the drought tolerant cultivars but in drought sensitive cultivars the opposite pattern was shown with irrigated samples showing significantly higher TE expression. Thus, TE genome repression mechanisms may be finely tuned to the ideal growth and/or regulatory conditions of the specific plant cultivars in which they are active. Analysis of TE expression levels in cell culture conditions underscored the importance of nonsense-mediated mRNA decay (NMD) pathways in the repression of Coffea TEs. These same NMD mechanisms can also regulate plant host gene expression via the repression of genes that bear exonized TE sequences.
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