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Archives of Virology

, Volume 163, Issue 11, pp 2937–2946 | Cite as

A complex virome unveiled by deep sequencing analysis of RNAs from a French Pinot Noir grapevine exhibiting strong leafroll symptoms.

  • Monique Beuve
  • Jean-Michel Hily
  • Antoine Alliaume
  • Catherine Reinbold
  • Jean Le Maguet
  • Thierry Candresse
  • Etienne Herrbach
  • Olivier Lemaire
Original Article

Abstract

We have characterized the virome of a grapevine Pinot Noir accession (P70) that displayed, over the year, very stable and strong leafroll symptoms. For this, we have used two extraction methods (dsRNA and total RNA) coupled with the high throughput sequencing (HTS) Illumina technique. While a great disparity in viral sequences were observed, both approaches gave similar results, revealing a very complex infection status. Five virus and viroid isolates [Grapevine leafroll-associated viruse-1 (GLRaV-1), Grapevine virus A (GVA), Grapevine rupestris stem pitting-associated virus (GRSPaV), Hop stunt viroid (HSVd) and Grapevine yellow speckle viroid 1 (GYSVd1)] were detected in P70 with a grand total of eleven variants being identified and de novo assembled. A comparison between both extraction methods regarding their power to detect viruses and the ease of genome assembly is also provided.

Notes

Acknowledgements

This work was supported by the Institut National de la Recherche Agronomique (INRA) and FranceAgriMer. JLM and AA were supported by Ph.D. grants respectively from the French National Association of Research and Technology and from Department SPE of INRA. Additional funds were kindly provided by three French professional committees for viticulture (the Interprofessional Committee of Champagne Wine, CIVC, Epernay; the Interprofessional Office of Burgundy Wines, BIVB, Beaune and the Interprofessional Committee of Wines from Alsace, CIVA, Colmar). This work was also partially supported by the Agence Nationale pour la Recherche, ANR Vinobodies contract: ANR- 14-CE19-0018-02. The authors acknowledge Jacky Misbach and the greenhouse team for technical support, Lionel Ley and the members of the experimental unit of INRA-Colmar for the production of plants, Emmanuelle Vigne and Shahinez Garcia for useful input into creating a more readable manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare there are no conflicts of interest.

Research involving human participants and/or animals

The research did not involve human participants or animals.

Informed consent

The research did not involve human participants or animals.

Supplementary material

705_2018_3949_MOESM1_ESM.pdf (681 kb)
Supplementary material 1 (PDF 680 kb)
705_2018_3949_MOESM2_ESM.pptx (2.2 mb)
Supplementary material 2 (PPTX 2301 kb)

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Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2018

Authors and Affiliations

  1. 1.SVQV, Université de StrasbourgColmarFrance
  2. 2.Institut Français des Productions Cidricoles (IFPC)SéesFrance
  3. 3.UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. BordeauxVillenave d’Ornon CedexFrance

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