ArticleGenome biology2025
Differential LTR-retrotransposon dynamics across polyploidization, speciation, domestication, and improvement of cotton (Gossypium).
Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed.
- Hide and seek: de novo identification in sugar beet reveals impact of non-autonomous LTR retrotransposons.Mobile DNA · 2026Article
- Transposable elements and their epigenetic modifications mediate gene expression and subgenome dominance in Brassica carinata.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Genomic diversity and the domestication history of cotton (Proceedings of the National Academy of Sciences of the United States of America · 2026Article
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5 authors.
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Abstract
backgroundTransposable elements are major components of plant genomes and major drivers of plant genome evolution. The cotton genus (Gossypium) is an excellent evolutionary model for polyploidization, speciation, domestication, and crop improvement. Here, we implement genome and pangenome analyses to study in detail the dynamics of LTR-retrotransposons during the cotton evolution.
resultsWe show that some LTR-retrotransposon lineages amplified in tetraploid cotton compared to their diploid progenitors, whereas others stayed stable or amplified but were removed through solo-LTR formation. Using species-level pangenomes we show that only a few lineages (CRM, Tekay, Ivana, and Tork) remained active after polyploidization and are still transposing. Tekay and CRM elements have re-shaped the centromeric and pericentromeric regions of tetraploid cottons in a subgenome specific manner, through new insertions but also selective eliminations through solo-LTR formation. On the other hand, Ivana and Tork have actively inserted within or close to genes affecting their expression. Finally, population-level analyses using the two pangenomes and data from 283 and 223 varieties of G. hirsutum and G. barbadense reveal changes in Transposon Insertion Polymorphism frequencies accompanying domestication and improvement of both species, suggesting the possibility of selection on linked regions.
conclusionsOur findings reveal that LTR-retrotransposon lineages followed differential dynamics during cotton evolution, displaying differences among species and the two coresident genomes of allopolyploid cotton. A handful of the LTR-retrotransposon lineages that expanded after polyploidization helped shape the genomes of both G. hirsutum and G. barbadense, impacting their centromere and pericentromeric regions as well as protein-coding genes.
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