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Archives of Virology

, Volume 163, Issue 11, pp 3105–3111 | Cite as

A genome-wide diversity study of grapevine rupestris stem pitting-associated virus

  • Jean-Michel Hily
  • Monique Beuve
  • Emmanuelle Vigne
  • Gérard Demangeat
  • Thierry Candresse
  • Olivier Lemaire
Brief Report

Abstract

Over the last decade, many scientific disciplines have been impacted by the dawn of new sequencing techniques (HTS: high throughput sequencing). Plant pathology and more specifically virology have been greatly transformed by this ‘metagenomics’ paradigm shift. Such tools significantly facilitate disease diagnostics with tremendous sensitivity, providing invaluable information such as an exhaustive list of viruses being present in a sample as well as their relative concentration. In addition, many new plant viruses have been discovered. Using RNAseq technology, in silico reconstruction of complete viral genome sequences is easily attainable. This step is of importance for taxonomy, population structure analyses, phylogeography and viral evolution studies. Here, after assembling 81 new near-complete genome sequences of grapevine rupestris stem pitting-associated virus (GRSPaV), we performed a genome-wide diversity study of this ubiquitous virus of grapevine worldwide.

Notes

Acknowledgements

This work was supported by the Institut National de la Recherche Agronomique (INRA). Additional funds were kindly provided by three French professional committees for viticulture (Interprofessional Committee of Champagne Wine, CIVC, Epernay; Interprofessional Office of Burgundy Wines, CIVB, Beaune and Interprofessional Committee of Wines from Alsace, CIVA, Colmar) and by Moët & Chandon. 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.

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_3945_MOESM1_ESM.pdf (431 kb)
‘Per codon’ analysis of the average behavior of each codon for all pairwise comparisons for synonymous (blue line) and non-synonymous (orange) mutations along the replicase polyprotein (A), TGBp1 (B), TGBp2 (c), TGBp3 (D) and CP (E), using SNAP v2,1,1 software. Overlapping sequence between TGBp2 and TGBp3 is shown (blue background) and between CP and ORF6 (green background). Nucleotide diversity index (π) study was evaluated by sliding window analyses using DnaSP v. 5.10 between the 71 genomes for which ORF6 was predicted (orange) and the 32 genomes for which ORF6 was missing (blue). 1 (PDF 431 kb)

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Copyright information

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

Authors and Affiliations

  1. 1.SVQVUniversité de StrasbourgColmarFrance
  2. 2.UMR 1332 Biologie du Fruit et Pathologie, INRAUniversity of BordeauxVillenave d’Ornon CedexFrance

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