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

Beuve, Monique; Hily, Jean-Michel; Alliaume, Antoine; Reinbold, Catherine; Maguet, Jean Le; Candresse, Thierry; Herrbach, Étienne; Lemaire, Olivier

doi:10.1007/s00705-018-3949-9

Cited by 31 publications

(39 citation statements)

References 48 publications

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“…As expected, all samples displayed reads corresponding to ubiquitous grapevine viral pathogens: grapevine rupestris stem pitting-associated virus (GRSPaV) as well as two viroids (HSVd and GYSVd1) (Table 2). From each sample, two to four genomes of GRSPaV were assembled, confirming the fact that multiple GRSPaV variants can infect a single grapevine (Beuve et al, 2018). All 11 GRSPaV genomes thus obtained were part of a genome-wide diversity study of GRSPaV (Hily et al, 2018a).…”

Section: Discussionmentioning

confidence: 71%

“…Grapevine research also improved with HTS, with many new viruses being identified all over the world, belonging to different families such as Betaflexiviridae (Al Rwahnih et al, 2012; Giampetruzzi et al, 2012; Jo et al, 2017a,b; Blouin et al, 2018a,b; Candresse et al, 2018; Diaz-Lara et al, 2018), Caulimoviridae (Zhang et al, 2011), Luteoviridae (Silva et al, 2017), Secoviridae (Al Rwahnih et al, 2016), or Tymoviridae (Al Rwahnih et al, 2009; Beuve et al, 2015; Cretazzo and Velasco, 2017; Vargas-Asencio et al, 2017). HTS technologies have been confirmed to be a powerful diagnostic tool allowing for an exhaustive description of viral species present in many grapevine sample (Coetzee et al, 2010; Al Rwahnih et al, 2011; Jo et al, 2015; Beuve et al, 2018). Depending on the chosen methodology, complete (to near complete) viral genome can be also be assembled, re-shaping the viral evolution field (Simmonds et al, 2017) with genome-wide studies made easily achievable (Hily et al, 2018a).…”

Section: Discussionmentioning

confidence: 99%

“…In order to take into account viral diversity, many extraction methods have been perfected, focusing on the viral genetic make-up at different stages of the viral cycle: (i) total RNA or total DNA, with or without specific enrichment steps (Dayaram et al, 2012; Beuve et al, 2018), (ii) double-stranded RNA which targets viruses with dsRNA genomes as well as RNA viruses and viroids during their replication step (Coetzee et al, 2010; Blouin et al, 2016; Beuve et al, 2018), (iii) vsiRNA (viral small-interfering RNA) derived from the adaptive antiviral plant defense mechanism (Donaire et al, 2009; Kreuze et al, 2009), and (iv) encapsidated nucleic acid using the VANA (Virion-Associated Nucleic Acid) approach (Filloux et al, 2015). While each method may have some drawbacks (e.g., highly purified, DNAse-treated dsRNA not efficient for the detection of DNA viruses, non-encapsidated virus, or viruses with unstable particles missed by VANA), the large panel of HTS approaches available provides the investigator or diagnostician with the opportunity to fine-tune technical options to meet his specific objectives.…”

Section: Introductionmentioning

confidence: 99%

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High-Throughput Sequencing and the Viromic Study of Grapevine Leaves: From the Detection of Grapevine-Infecting Viruses to the Description of a New Environmental Tymovirales Member

et al. 2018

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In the past decade, high-throughput sequencing (HTS) has had a major impact on virus diversity studies as well as on diagnosis, providing an unbiased and more comprehensive view of the virome of a wide range of organisms. Rather than the serological and molecular-based methods, with their more “reductionist” view focusing on one or a few known agents, HTS-based approaches are able to give a “holistic snapshot” of the complex phytobiome of a sample of interest. In grapevine for example, HTS is powerful enough to allow for the assembly of complete genomes of the various viral species or variants infecting a sample of known or novel virus species. In the present study, a total RNAseq-based approach was used to determine the full genome sequences of various grapevine fanleaf virus (GFLV) isolates and to analyze the eventual presence of other viral agents. From four RNAseq datasets, a few complete grapevine-infecting virus and viroid genomes were de-novo assembled: (a) three GFLV genomes, 11 grapevine rupestris stem-pitting associated virus (GRSPaV) and six viroids. In addition, a novel viral genome was detected in all four datasets, consisting of a single-stranded, positive-sense RNA molecule of 6033 nucleotides. This genome displays an organization similar to Tymoviridae family members in the Tymovirales order. Nonetheless, the new virus shows enough differences to be considered as a new species defining a new genus. Detection of this new agent in the original grapevines proved very erratic and was only consistent at the end of the growing season. This virus was never detected in the spring period, raising the possibility that it might not be a grapevine-infecting virus, but rather a virus infecting a grapevine-associated organism that may be transiently present on grapevine samples at some periods of the year. Indeed, the Tymoviridae family comprises isometric viruses infecting a wide range of hosts in different kingdoms (Plantae, Fungi, and Animalia). The present work highlights the fact that even though HTS technologies produce invaluable data for the description of the sanitary status of a plant, in-depth biological studies are necessary before assigning a new virus to a particular host in such metagenomic approaches.

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Section: Discussionmentioning

confidence: 71%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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High-Throughput Sequencing and the Viromic Study of Grapevine Leaves: From the Detection of Grapevine-Infecting Viruses to the Description of a New Environmental Tymovirales Member

et al. 2018

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“…Eggs were sieved, then incubated in a box at room temperature until hatching. To estimate whether mobile nymphs blown away by wind could be infectious, newly hatched crawlers were placed on excised leaves of Pinot noir (P70 accession, infected with GLRaV‐1 and GVA, Beuve et al, ). Ten pools of 30 crawlers were analysed by RT‐PCR after an acquisition access period (AAP) of 1, 2, 6, 8 hr, and 1 to 5 days, picking up only mobile crawlers, since once crawlers fasten themselves to the leaves they display a lesser tendency to move.…”

Section: Methodsmentioning

confidence: 99%

Gone with the wind: Aerial dispersal of Parthenolecanium corni crawlers in a newly planted grapevine plot

Hommay¹,

Wiss²,

Maguet

et al. 2019

Annals of Applied Biology

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Soft scales nymphs are suspected to propagate grapevine leafroll viruses in the vineyard, while moving from vine to vine, but results of long distance dispersion, especially those due to wind, are poorly known. Thus, a net of sticky cylindrical traps was placed in a newly planted grapevine plot to evaluate aerial dispersal of Parthenolecanium corni (Hemiptera Coccidae) nymphs. The plot was surrounded by vine plots infested by this species. Number of crawlers collected on traps was generally higher on the trap side exposed downwind and depended on population density of neighbouring vines. Coloured glitters of size and weight similar to that of crawlers were used to simulate wind transport. The highest number of glitters was trapped at the prevailing wind sector. A majority of glitters was found on traps close to dispersion cups, and the most remote were collected up to 165 m away from glitter source. Wind dispersal of crawlers was confirmed by colonisation of the new vine plot by P. corni, 2 years after plantation. The settling of P. corni on the young plot displayed no significant structure, as expected from a wind dispersal. Although grapevine leafroll viruses and Grapevine virus A were detected by reverse transcription-polymerase chain reaction in several batches of trapped nymphs, these viruses were not found in vines colonised by P. corni in the new plot within the 4 years following plantation.

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“…HTS data in nectarine provided insight to the etiology of stem pitting disease [14]. Diseased grapevine plants infected by Grapevine Pinot gris virus are found based on HTS data to acquire very complex viromes [15]. The total RNA-Seq approach concretely in grapevine resulted in complete virus and viroid genomes through de-novo assembly [16–17].…”

Section: Introductionmentioning

confidence: 99%

Unravelling the virome in birch: RNA-Seq reveals a complex of known and novel viruses

Rumbou

Candresse

Marais

et al. 2019

Preprint

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25 High-throughput sequencing (HTS), combined with bioinformatics for de novo discovery and 26 assembly of plant virus or viroid genome reads, has promoted the discovery of abundant novel 27 DNA and RNA viruses and viroids. However, the elucidation of a viral population in a single plant is 28 rarely reported. In five birch trees of German and Finnish origin exhibiting symptoms of birch leaf-29 roll disease (BRLD), we identified in total five viruses, among which three are novel. The number of 30 identified virus variants in each transcriptome ranged from one to five. The novel species are 31 genetically -fully or partially -characterized, they belong to the genera Carlavirus, Idaeovirus and 32 Capillovirus and they are tentatively named birch carlavirus, birch idaeovirus, and birch 33 capillovirus, respectively. The only virus systematically detected by HTS in symptomatic trees 34 affected by the BRLD was the recently discovered birch leafroll-associated virus. The role of the 35 new carlavirus in BLRD etiology seems at best weak, as it was detected only in one of three 36 symptomatic trees. Continuing studies have to clarify the impact of the carlavirus to the BLRD. The 37 role of the Capillovirus and the Idaeovirus within the BLRD complex and whether they influence 38 plant vitality need to be investigated. Our study reveals the viral population in single birch trees and 39 provides a comprehensive overview for the diversities of the viral communities they harbor. 40 41 Keywords: Betula sp., virome, birch leaf-roll disease, birch carlavirus, birch idaeovirus, birch 42 capillovirus 3 44 Introduction 45 Symptoms in birch trees (Betula sp.) caused by various viruses and related to the birch 46 leaf-roll disease (BLRD) are observed throughout Europe [1-2]. Diseased birches exhibit foliar 47 disorders including vein banding, leaf roll, mottling, necrotic lesions and tip dieback. Based on 48 earlier studies on virus-diseased trees it is assumed that BLRD might significantly reduce the tree's 49 photosynthetic capacity and contribute to tree decline [3]. Due to lack of knowledge, risk analyses 50 and prevention measures, the disease has effectively spread throughout Europe and has until now 51 been reported in European countries with diverse climatic conditions such as Finland, Sweden, 52 Norway, Germany, Austria, UK and France, including stands of a Mediterranean island [2-5]. 53The initial hypothesis for the BLRD disease etiology implicated Cherry leaf roll virus (CLRV) 54 as the disease main causal agent [1-2; 4-5]. However, after long-lasting trials applying 55 conventional viral detection methods (virus purification, RT-PCR, double-stranded-RNA isolation, 56 virus mechanical transmission), this virus could not be convincingly associated with the 57 appearance of disease symptoms. To identify BLRD etiology, a birch metagenomic study was 58 therefore initiated. A RNA-Seq analysis revealed for the first time in diseased trees from Germany 59 and Finland birch leafroll-associated virus (BLRaV), the first reverse-tra...

show abstract

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

Cited by 31 publications

References 48 publications

High-Throughput Sequencing and the Viromic Study of Grapevine Leaves: From the Detection of Grapevine-Infecting Viruses to the Description of a New Environmental Tymovirales Member

High-Throughput Sequencing and the Viromic Study of Grapevine Leaves: From the Detection of Grapevine-Infecting Viruses to the Description of a New Environmental Tymovirales Member

Gone with the wind: Aerial dispersal of Parthenolecanium corni crawlers in a newly planted grapevine plot

Unravelling the virome in birch: RNA-Seq reveals a complex of known and novel viruses

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