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Analysis of institutional authors

Castanera, RCorresponding Author

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June 17, 2025
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Article

Tandem LTR-retrotransposon structures are common and highly polymorphic in plant genomes

Publicated to: Mobile DNA. 16 (1): 10- - 2025-03-12 16(1), DOI: 10.1186/s13100-025-00347-y

Authors:

Morales-Diaz, N; Sushko, S; Campos-Dominguez, L; Kopalli, V; Golicz, AA; Castanera, R; Casacuberta, JM
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Affiliations

CRAG CSIC IRTA UAB UB, Ctr Res Agr Genom, Campus UAB - Author
IRTA Genom & Biotechnol, Edifici CRAG,Campus UAB, Bellaterra 08193 - Author
Justus Liebig Univ Giessen, Dept Plant Breeding - Author
Max Planck Inst Biol Tubingen, Dept Mol Biol - Author
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Abstract

BackgroundLTR-retrotransposons (LTR-RT) are a major component of plant genomes and important drivers of genome evolution. Most LTR-RT copies in plant genomes are defective elements found as truncated copies, nested insertions or as part of more complex structures. The recent availability of highly contiguous plant genome assemblies based on long-read sequences now allows to perform detailed characterization of these complex structures and to evaluate their importance for plant genome evolution.ResultsThe detailed analysis of two rice loci containing complex LTR-RT structures showed that they consist of tandem arrays of LTR copies sharing internal LTRs. Our analyses suggests that these LTR-RT tandems are the result of a single insertion and not of the recombination of two independent LTR-RT elements. Our results also suggest that gypsy elements may be more prone to form these structures. We show that these structures are highly polymorphic in rice and therefore have the potential to generate genetic variability. We have developed a computational pipeline (IDENTAM) that scans genome sequences and identifies tandem LTR-RT candidates. Using this tool, we have detected 266 tandems in a pangenome built from the genomes of 76 accessions of cultivated and wild rice, showing that tandem LTR-RT structures are frequent and highly polymorphic in rice. Running IDENTAM in the Arabidopsis, almond and cotton genomes showed that LTR-RT tandems are frequent in plant genomes of different size, complexity and ploidy level. The complexity of differentiating intra-element variations at the nucleotide level among haplotypes is very high, and we found that graph-based pangenomic methodologies are appropriate to resolve these structures.ConclusionsOur results show that LTR-RT elements can form tandem arrays. These structures are relatively abundant and highly polymorphic in rice and are widespread in the plant kingdom. Future studies will contribute to understanding how these structures originate and whether the variability that they generate has a functional impact.
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Keywords

DnaEvolutionProvidesRecombinationSizeTransposable elements

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Mobile DNA due to its progression and the good impact it has achieved in recent years, according to the agency Scopus (SJR), it has become a reference in its field. In the year of publication of the work, 2025, it was in position , thus managing to position itself as a Q1 (Primer Cuartil), in the category Molecular Biology.

Independientemente del impacto esperado determinado por el canal de difusión, es importante destacar el impacto real observado de la propia aportación.

Según las diferentes agencias de indexación, el número de citas acumuladas por esta publicación hasta la fecha 2026-04-03:

  • WoS: 6
  • Europe PMC: 5
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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 2026-04-03:

  • 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: 8.
  • 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: 8 (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: 1.
  • 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/20.500.12327/4589
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Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: Germany.

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 (Morales-Díaz, N) and Last Author (Casacuberta, JM).

the authors responsible for correspondence tasks have been CASTANERA ANDRES, RAUL 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/; MICIU/Programa Estatal de generación del conocimiento y fortalecimiento científico y tecnológico del sistema I+D+I/CEX2019-000902-S/ES/ /; MICINN/Programa Estatal de promoción del talento y su empleabilidad en I+D+I/IJC2020-045949-I/ES/ /; MICINN/ /RYC2022-037459-I/ES/ /
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Awards linked to the item

Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature. The work done at CRAG was funded by grant PID2022-143167NB-I00 funded by MICIU/AEI/ 10.13039/50110001103 and by “ERDF/EU” and grant CEX2019-000902-S funded by MICIU/AEI /10.13039/501100011033. NMD is funded by Grant PRE2020-095111 Funded by MCIU/AEI /10.13039/501100011033 and by “ESF Investing in your future”, and RC was partially funded by a Juan de la Cierva contract, grant IJC2020-045949-I funded by MICIU/AEI /10.13039/501100011033 and by European Union NextGenerationEU/PRTR”, and is now a Ramón y Cajal contract holder, RYC2022-037459-I funded by MICIU/AEI/ 10.13039/501100011033 and by FSE+. AAG was supported by the LOEWE Start Professorship from the Hessian Ministry for Science and the Arts. VK was supported by GRK 2843 from the German Research Foundation (DFG).
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