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

Archives of Virology
Monique BeuveOlivier Lemaire

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.

References

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Citations

Jul 11, 2020·Critical Reviews in Food Science and Nutrition·Pierre LedormandMarion Dalmasso
Jul 26, 2018·Archives of Virology·Jean-Michel HilyOlivier Lemaire

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Datasets Mentioned

BETA
PRJNA448981
KU674797

Methods Mentioned

BETA
scrapings
PCR

Software Mentioned

RDP4
BlastX
BlastN
MEGA
MEGA7
MUSCLE
CLC Genomics Workbench
RDP
DnaSP

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