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Planta

, Volume 250, Issue 5, pp 1781–1787 | Cite as

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

  • Salvatore Esposito
  • Fabio Barteri
  • Josep Casacuberta
  • Marie Mirouze
  • Domenico CarputoEmail author
  • Riccardo AversanoEmail author
Short Communication

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.

Keywords

Extrachromosomal circular DNA Insertion time Mobilome Potato Wild species 

Abbreviations

LTR-RTs

Long-terminal repeat retrotransposons

TE

Transposable element

DOC

Depth of coverage

eccDNA

Extrachromosomal circular DNA

Notes

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.

Supplementary material

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Supplementary material 1 (TIFF 408 kb)
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Supplementary material 3 (TIFF 190 kb)
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Supplementary material 4 (TIFF 370 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Agricultural SciencesUniversity of Naples Federico IIPorticiItaly
  2. 2.Center for Research in Agricultural GenomicsConsejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona, Universitat de Barcelona, Campus Universitat Autònoma de BarcelonaBellaterraSpain
  3. 3.Institut de Recherche pour le Développement, IRD DIADEUniversité de Perpignan, Plant Genome and Development LaboratoryPerpignanFrance

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