2026-04-14T08:11:08Zhttps://recercat.cat/oai/request

oai:recercat.cat:20.500.12327/49022026-02-24T00:35:11Zcom_2072_4428com_2072_4427col_2072_487898

2026-02-24T00:35:11Z urn:hdl:20.500.12327/4902 Differential LTR‑retrotransposon dynamics across polyploidization, speciation, domestication, and improvement of cotton (Gossypium) Campos-Dominguez, Lucía Castanera, Raúl Grover, Corrine E. Wendel, Jonathan F. Casacuberta, Josep M. Producció Vegetal Genòmica i Biotecnologia Background Transposable 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. Results We 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. Conclusions Our 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. 2026-02-24T00:35:11Z 2026-02-24T00:35:11Z 2025-10-27 info:eu-repo/semantics/article 1474-7596 https://hdl.handle.net/20.500.12327/4902 https://doi.org/10.1186/s13059-025-03837-7 eng Genome Biology MICINN/Programa Estatal para impulsar la investigación científico-técnica y su transferencia/PID2022-143167NB-I00/ES/Los Transposones, un motor de la evolución de los genomas de plantas/ FEDER/ / /EU/ / EC/H2020/945043/EU/Agricultural Genomics Transversal Postdoctoral Program/AgenT MICIU/Programa Estatal de generación del conocimiento y fortalecimiento científico y tecnológico del sistema I+D+I/CEX2019-000902-S/ES/ / MICINN/ /RYC2022-037459-I/ES/ / ESF+/ / /EU/ / http://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess Attribution 4.0 International Springer