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LTR-TEs abundance, timing and mobility in Solanum commersonii and S. tuberosum genomes following cold-stress conditions

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Abstract

Main conclusion

Copia/Ale is the youngest lineage in both Solanum tuberosum and S. commersonii. Within it, we identified nightshade, a new LTR element active in the cultivated potato.

Abstract

From an evolutionary perspective, long-terminal repeat retrotransposons (LTR-RT) activity during stress may be viewed as a mean by which organisms can keep up rates of genetic adaptation to changing conditions. Potato is one of the most important crop consumed worldwide, but studies on LTR-RT characterization are still lacking. Here, we assessed the abundance, insertion time and activity of LTR-RTs in both cultivated Solanum tuberosum and its cold-tolerant wild relative S. commersonii genomes. Gypsy elements were more abundant than Copia ones, suggesting that the former was somehow more successful in colonizing potato genomes. However, Copia elements, and in particular, the Ale lineage, are younger than Gypsy ones, since their insertion time was in average ~ 2 Mya. Due to the ability of LTR-RTs to be circularized by the host DNA repair mechanisms, we identified via mobilome-seq a Copia/Ale element (called nightshade, informal name used for potato family) active in S. tuberosum genome. Our analyses represent a valuable resource for comparative genomics within the Solanaceae, transposon-tagging and for the design of cultivar-specific molecular markers in potato.

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Fig. 1
Fig. 2

Abbreviations

LTR-RTs:

Long-terminal repeat retrotransposons

TE:

Transposable element

DOC:

Depth of coverage

eccDNA:

Extrachromosomal circular DNA

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Acknowledgements

This work was carried out within the project “Development of potato genetic resources for sustainable agriculture” (PORES) funded by the University of Naples Federico II (Project ID: E76J17000010001). We are grateful to Mr. Raffaele Garramone for his technical assistance. No conflict of interest declared.

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Authors and Affiliations

  1. Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy

    Salvatore Esposito, Domenico Carputo & Riccardo Aversano

  2. Center for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona, Universitat de Barcelona, Campus Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain

    Fabio Barteri & Josep Casacuberta

  3. Institut de Recherche pour le Développement, IRD DIADE, Université de Perpignan, Plant Genome and Development Laboratory, Perpignan, France

    Marie Mirouze

Authors
  1. Salvatore Esposito
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  2. Fabio Barteri
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  3. Josep Casacuberta
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  4. Marie Mirouze
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  5. Domenico Carputo
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  6. Riccardo Aversano
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Correspondence to Domenico Carputo or Riccardo Aversano.

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Esposito, S., Barteri, F., Casacuberta, J. et al. LTR-TEs abundance, timing and mobility in Solanum commersonii and S. tuberosum genomes following cold-stress conditions . Planta 250, 1781–1787 (2019). https://doi.org/10.1007/s00425-019-03283-3

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