ArticleMobile DNA2019
Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes.
Article in Mobile DNA, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 43 citations in OpenAlex.
- The Demographic History of Populations and Genomic Imprinting have Shaped the Transposon Patterns in Arabidopsis lyrata.Molecular biology and evolution · 2025Article
- Dynamics of transposable element accumulation in the non-recombining regions of mating-type chromosomes in anther-smut fungi.Nature communications · 2023Article
- Chromosome-level Genome Assembly of Euphorbia peplus, a Model System for Plant Latex, Reveals that Relative Lack of Ty3 Transposons Contributed to Its Small Genome Size.Genome biology and evolution · 2023Article
- Transposable elements maintain genome-wide heterozygosity in inbred populations.Nature communications · 2022Article
- Species-specific chromatin landscape determines how transposable elements shape genome evolution.eLife · 2022Article
- K-mer counting and curated libraries drive efficient annotation of repeats in plant genomes.The plant genome · 2021Article
- Parallel adaptation in autopolyploid Arabidopsis arenosa is dominated by repeated recruitment of shared alleles.Nature communications · 2021Article
- Genetic Context Significantly Influences the Maintenance and Evolution of Degenerate Pathways.Genome biology and evolution · 2021Article
- Transcriptional activity of transposable elements along an elevational gradient in Arabidopsis arenosa.Mobile DNA · 2021Article
- Integrated Genomic Analyses From Low-Depth Sequencing Help Resolve Phylogenetic Incongruence in the Bamboos (Poaceae: Bambusoideae).Frontiers in plant science · 2021Article
- Comparative analysis of genome-wide DNA methylation inEpigenetics · 2020Article
- Low Long Terminal Repeat (LTR)-Retrotransposon Expression in Leaves of the Marine PhanerogamLife (Basel, Switzerland) · 2020Article
- Relaxed purifying selection in autopolyploids drives transposable element over-accumulation which provides variants for local adaptation.Nature communications · 2019Article
- Article
- Substitutions Are Boring: Some Arguments about Parallel Mutations and High Mutation Rates.Trends in genetics : TIG · 2019Review
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Authors and funding
13 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTransposable elements (TEs) are genomic parasites with major impacts on host genome architecture and host adaptation. A proper evaluation of their evolutionary significance has been hampered by the paucity of short scale phylogenetic comparisons between closely related species. Here, we characterized the dynamics of TE accumulation at the micro-evolutionary scale by comparing two closely related plant species,
resultsJoint genome annotation in these two outcrossing species confirmed that both contain two distinct populations of TEs with either 'recent' or 'old' insertion histories. Identification of rare segregating insertions suggests that diverse TE families contribute to the ongoing dynamics of TE accumulation in the two species. Orthologous TE fragments (i.e. those that have been maintained in both species), tend to be located closer to genes than those that are retained in one species only. Compared to non-orthologous TE insertions, those that are orthologous tend to produce fewer short interfering RNAs, are less heavily methylated when found within or adjacent to genes and these tend to have lower expression levels. These findings suggest that long-term retention of TE insertions reflects their frequent acquisition of adaptive roles and/or the deleterious effects of removing nearly neutral TE insertions when they are close to genes.
conclusionOur results indicate a rapid evolutionary dynamics of the TE landscape in these two outcrossing species, with an important input of a diverse set of new insertions with variable propensity to resist deletion.
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