Theoretical and Applied Genetics

, Volume 127, Issue 5, pp 1223–1235 | Cite as

The Tvv1 retrotransposon family is conserved between plant genomes separated by over 100 million years

  • Cédric Moisy
  • Alan H. Schulman
  • Ruslan Kalendar
  • Jan P. Buchmann
  • Frédérique Pelsy
Original Paper

Abstract

Key message

Combining several different approaches, we have examined the structure, variability, and distribution of Tvv1 retrotransposons. Tvv1 is an unusual example of a low-copy retrotransposon metapopulation dispersed unevenly among very distant species and is promising for the development of molecular markers.

Abstract

Retrotransposons are ubiquitous throughout the genomes of the vascular plants, but individual retrotransposon families tend to be confined to the level of plant genus or at most family. This restricts the general applicability of a family as molecular markers. Here, we characterize a new plant retrotransposon named Tvv1_Sdem, a member of the Copia superfamily of LTR retrotransposons, from the genome of the wild potato Solanum demissum. Comparative analyses based on structure and sequence showed a high level of similarity of Tvv1_Sdem with Tvv1-VB, a retrotransposon previously described in the grapevine genome Vitis vinifera. Extending the analysis to other species by in silico and in vitro approaches revealed the presence of Tvv1 family members in potato, tomato, and poplar genomes, and led to the identification of full-length copies of Tvv1 in these species. We were also able to identify polymorphism in UTL sequences between Tvv1_Sdem copies from wild and cultivated potatoes that are useful as molecular markers. Combining different approaches, our results suggest that the Tvv1 family of retrotransposons has a monophyletic origin and has been maintained in both the rosids and the asterids, the major clades of dicotyledonous plants, since their divergence about 100 MYA. To our knowledge, Tvv1 represents an unusual plant retrotransposon metapopulation comprising highly similar members disjointedly dispersed among very distant species. The twin features of Tvv1 presence in evolutionarily distant genomes and the diversity of its UTL region in each species make it useful as a source of robust molecular markers for diversity studies and breeding.

Notes

Acknowledgments

This work was supported by funding from Région Alsace, INRA, and the Academy of Finland (Project 123074). We thank Emilie Haegy and Romain Guyot (IRD, Montpellier) for technical assistance, and the members of the experimental unit of INRA-Colmar for the production of plants in the greenhouse. We also thank Véronique Lefebvre (INRA, Avignon), Gilles Pilate (INRA, Orléans), Veronique Brault (INRA-Colmar), Florence Lahogue-Esnault, Michel Renard and Jean-Paul Dantec (INRA, Rennes) who kindly provided us DNA and plant samples.

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards

The experiments comply with the current laws of the countries in which they were performed.

Supplementary material

122_2014_2293_MOESM1_ESM.pdf (1.9 mb)
Online resource Figure S1 (PDF 1963 kb)
122_2014_2293_MOESM2_ESM.pdf (340 kb)
Online resource Figure S2 (PDF 339 kb)
122_2014_2293_MOESM3_ESM.pdf (1.1 mb)
Online resource Figure S3: Multiple alignment of Tvv1 LTR sequences (PDF 1153 kb)
122_2014_2293_MOESM4_ESM.docx (17 kb)
Online resource Table S1 (DOCX 16 kb)
122_2014_2293_MOESM5_ESM.docx (27 kb)
Online resource Table S2 (DOCX 27 kb)
122_2014_2293_MOESM6_ESM.docx (25 kb)
Online resource Table S3 (DOCX 25 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Cédric Moisy
    • 1
    • 2
    • 5
  • Alan H. Schulman
    • 1
    • 2
  • Ruslan Kalendar
    • 1
  • Jan P. Buchmann
    • 1
  • Frédérique Pelsy
    • 3
    • 4
  1. 1.MTT/BI Plant Genomics Lab, Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
  2. 2.Biotechnology and Food ResearchMTT Agrifood Research FinlandJokioinenFinland
  3. 3.INRA, UMR1131ColmarFrance
  4. 4.Université de Strasbourg, UMR1131StrasbourgFrance
  5. 5.INRA, UMR AGAP 1334, DAVEMMontpellier Cedex 1France

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