ArticleFrontiers in plant science2020
What Can Long Terminal Repeats Tell Us About the Age of LTR Retrotransposons, Gene Conversion and Ectopic Recombination?
Article in Frontiers in plant science, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed.
- Hide and seek: de novo identification in sugar beet reveals impact of non-autonomous LTR retrotransposons.Mobile DNA · 2026Article
- A pangenome of tetraploid wheat reveals the genetic architecture underlying domestication and genomic diversity for breeding.Nature genetics · 2026Article
- Wild tomato genome assemblies reveal structural variants and repeat content act as recombination barriers.Nature communications · 2026Article
- panHiTE: A comprehensive and accurate pipeline for TE detection in large-scale population genomes.Plant communications · 2026Article
- Comparison of Genomes of Species fromInternational journal of molecular sciences · 2025Article
- Resolving the Stasis-Dynamism Paradox: Genome Evolution in Tree Ferns.Molecular biology and evolution · 2025Article
- Dynamic patterns of repeats and retrotransposons in the centromeres of Humulus lupulus L.The New phytologist · 2025Article
- Genome-wide association study of Northern corn leaf blight (NCLB) resistance using temperate and subtropical maize recombinant inbred lines.BMC genomics · 2025Article
- Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning.BioData mining · 2024Article
- ZW sex chromosome structure in Amborella trichopoda.Nature plants · 2024Article
- Comparative genome analysis and the genome-shaping role of long terminal repeat retrotransposons in the evolutionary divergence of fungal pathogens Blastomyces dermatitidis and Blastomyces gilchristii.G3 (Bethesda, Md.) · 2024Article
- The gap-free genome ofHorticulture research · 2024Article
- A reference-grade genome of the xerophyte Ammopiptanthus mongolicus sheds light on its evolution history in legumes and drought-tolerance mechanisms.Plant communications · 2024Article
- High Diversity of Long Terminal Repeat Retrotransposons in Compact Vertebrate Genomes: Insights from Genomes ofAnimals : an open access journal from MDPI · 2024Article
- Article
- Genomic decoding of Theobroma grandiflorum (cupuassu) at chromosomal scale: evolutionary insights for horticultural innovation.GigaScience · 2024Article
- Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion.PLoS genetics · 2023Article
- Intraspecific Variation of Transposable Elements Reveals Differences in the Evolutionary History of Fungal Phytopathogen Pathotypes.Genome biology and evolution · 2023Article
- All families of transposable elements were active in the recent wheat genome evolution and polyploidy had no impact on their activity.The plant genome · 2023Article
- The nature and genomic landscape of repetitive DNA classes in Chrysanthemum nankingense shows recent genomic changes.Annals of botany · 2023Article
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3 authors.
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Abstract
LTR retrotransposons constitute a significant part of plant genomes and their evolutionary dynamics play an important role in genome size changes. Current methods of LTR retrotransposon age estimation are based only on LTR (long terminal repeat) divergence. This has prompted us to analyze sequence similarity of LTRs in 25,144 LTR retrotransposons from fifteen plant species as well as formation of solo LTRs. We found that approximately one fourth of nested retrotransposons showed a higher LTR divergence than the pre-existing retrotransposons into which they had been inserted. Moreover, LTR similarity was correlated with LTR length. We propose that gene conversion can contribute to this phenomenon. Gene conversion prediction in LTRs showed potential converted regions in 25% of LTR pairs. Gene conversion was higher in species with smaller genomes while the proportion of solo LTRs did not change with genome size in analyzed species. The negative correlation between the extent of gene conversion and the abundance of solo LTRs suggests interference between gene conversion and ectopic recombination. Since such phenomena limit the traditional methods of LTR retrotransposon age estimation, we recommend an improved approach based on the exclusion of regions affected by gene conversion.
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