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Structural variability of Tvv1 grapevine retrotransposons can be caused by illegitimate recombination

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Abstract

Structural variability of Tvv1, a grapevine retrotransposon Ty1 copia-like family, was investigated within the grape genome and the canonical sequence of Tvv1 determined. Then, two remarkable elements, Tvv1-Δ3001 and Tvv1-Δ3640, which had suffered large deletions 3,001 bp and 3,460 bp in length of their coding sequences were compared to the canonical copy. In both deleted elements, the deletion breakpoint was characterized by a stretch 13 bp-long in Tvv1-Δ3001 and 11 bp-long in Tvv1-Δ3640 found duplicated in the canonical copy at each bound of the deleted regions. Tvv1-Δ3001 and Tvv1-Δ3460 were both shown to be unique copies fixed at a single locus in the grapevine genome. Their presence was very variable in a set of 58 varieties and wild vines. These elements have most likely been dispersed through natural intermixing after their initial insertion whose chronology was estimated. The model that we propose to explain the structure of Tvv1-Δ3001 and Tvv1-Δ3640, implies illegitimate recombination involving template switching between two RNA molecules co-packaged in the VLP prior to the integration of the deleted daughter copy into the host genome.

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Acknowledgments

The authors thank Dr. Eva Zyprian and Dr. Reinhardt Töpfer from the Federal Centre for Breeding Research on Cultivated Plant, Institute for Grapevine Breeding Geilweilerhof (Siebeldingen, Germany) for kindly providing the partial sequence of the BAC clone A1-16, Riccardo Velasco from the Istituto Agrario San Michele all’Adige (Italy) for the pinot sequence (VV78X150312.9) and Anne Françoise Adam-Blondon (INRA-URGV, France) for the BAC clone 3E11. We thank Lucie Bevilacqua-Schehrer and Cindy Ponama for their valuable technical assistance, Vincent Dumas and the experimental domain staff for grapevine accessions, Malek Alioua (ULP-Strasbourg, France) for sequencing, and Pere Mestre for careful revision of the English. Cedric Moisy is a doctoral fellow supported by the Conseil Régional d’Alsace. All experiments described in this study comply with the current laws of France.

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Authors and Affiliations

  1. UMR 1131 Santé de la Vigne et Qualité du Vin, INRA, Université Louis Pasteur de Strasbourg, 68000, Colmar, France

    Cédric Moisy, Sophie Blanc, Didier Merdinoglu & Frédérique Pelsy

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  1. Cédric Moisy
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  2. Sophie Blanc
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  3. Didier Merdinoglu
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  4. Frédérique Pelsy
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Correspondence to Frédérique Pelsy.

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Communicated by C. Gebhardt.

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Moisy, C., Blanc, S., Merdinoglu, D. et al. Structural variability of Tvv1 grapevine retrotransposons can be caused by illegitimate recombination. Theor Appl Genet 116, 671–682 (2008). https://doi.org/10.1007/s00122-007-0700-4

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  • DOI: https://doi.org/10.1007/s00122-007-0700-4

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