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

by Biologie du fruit et pathologie (BFP) ; Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB) , Santé de la vigne et qualité du vin (SVQV) ; Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg (UNISTRA) , Reinbold, Catherine , Le Maguet, Jean , Lemaire, Olivier , Beuve, Monique , ANR-14-CE19-0018,VinoBodies,Nanobodies: le couteau Suisse de la virologie de la vigne , Hily, Jean-Michel , Alliaume, Antoine , Candresse, Thierry , Herrbach, Etienne

in Agricultural sciences / Biomedical and Life Sciences / Biomedicine / Double-stranded RNA / genome assembly / Genomes / Grapevine rupestris stem pitting-associated virus / Grapevine virus A / Grapevine yellow speckle viroid 1 / high-throughput nucleotide sequencing / Hop stunt viroid / Infectious Diseases / Life Sciences / Medical Microbiology / Microbiology and Parasitology / Next-generation sequencing / Original Article / Phytopathology and phytopharmacy / Ribonucleic acid / RNA / Stem pitting / Stunt / Vegetal Biology / Virology / Viruses / Vitis / Wines

2018

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

2018

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

2018

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Journal Article

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

Biologie du fruit et pathologie (BFP) ; Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB),

Santé de la vigne et qualité du vin (SVQV) ; Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg (UNISTRA),

Reinbold, Catherine,

Le Maguet, Jean,

Lemaire, Olivier,

Beuve, Monique,

ANR-14-CE19-0018,VinoBodies,Nanobodies: le couteau Suisse de la virologie de la vigne,

Hily, Jean-Michel,

Alliaume, Antoine,

Candresse, Thierry,

Herrbach, Etienne

2018

Overview

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.

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Publisher

Springer Verlag,CCSD,Springer Vienna,Springer Nature B.V

Subject

Agricultural sciences

/ Biomedical and Life Sciences

/ Biomedicine

/ Double-stranded RNA

/ genome assembly

/ Genomes

/ Grapevine rupestris stem pitting-associated virus