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Analysis of institutional authors

Castanera, RAuthor

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December 18, 2025
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Differential LTR-retrotransposon dynamics across polyploidization, speciation, domestication, and improvement of cotton (Gossypium)

Publicated to: Genome Biology. 26 (1): 369- - 2025-10-27 26(1), DOI: 10.1186/s13059-025-03837-7

Authors:

Campos-Dominguez, L; Castanera, R; Grover, CE; Wendel, JF; Casacuberta, JM
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Affiliations

Iowa State Univ, Dept Ecol Evolut & Organismal Biol - Author
IRTA, Genom & Biotechnol, Campus UAB,Edif CRAG, Bellaterra 08193 - Author
UB, UAB, Ctr Res Agr Genom, CSIC,IRTA,CRAG, Campus UAB, Cerdanyola del Valles - Author
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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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Keywords

Allopolyploid plantsEvolutionEvolutionary genomicsGenome expansionPangenomeRetrotransposonRevealsSizeSolo-ltrTip (transposon insertion polymorphism)Transposable elementsWild

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Genome Biology due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2025, it was in position 7/192, thus managing to position itself as a Q1 (Primer Cuartil), in the category Genetics & Heredity. Notably, the journal is positioned above the 90th percentile.

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Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2026-04-04:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 5.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 5 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 6.
  • The number of mentions on the social network X (formerly Twitter): 1 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.
  • Assignment of a Handle/URN as an identifier within the deposit in the Institutional Repository: http://hdl.handle.net/20.500.12327/4902
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Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: United States of America.

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (Campos-Dominguez, L) and Last Author (Casacuberta, JM).

the authors responsible for correspondence tasks have been Campos-Dominguez, L and Casacuberta, JM.

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Observations

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/ /
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Awards linked to the item

This work was supported by PID2022-143167NB-I00 grant funded by MICIU/AEI/10.13039/501100011033 and by ERDF/EU to JC. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 945043 through the Postdoctoral Fellowship awarded to L.C.-D. by the AGenT H2020-MSCA-COFUND-2019 programme co-funded by the grant CEX2019-000902-S funded by MICIU/AEI/10.13039/501100011033. RC’s work was supported by his Ramón y Cajal fellowship (RYC2022-037459-I) funded by MICIU/AEI/10.13039/501100011033 and by ESF +. We acknowledge support on cotton research and polyploidy from the National Science Foundation, and we would also like to acknowledge Iowa State University Research IT for computational support.
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