Complete Nucleotide Sequence of an Isolate of Grapevine Satellite Virus and Evidence for the Presence of Multimeric Forms in an Infected Grapevine

Candresse, Thierry; Marais, Armelle; Theil, Sébastien; Faure, Chantal; Lacombe, Thierry; Boursiquot, Jean Michel

doi:10.1128/genomea.01703-16

Cited by 7 publications

(5 citation statements)

References 8 publications

(11 reference statements)

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“…Grapevine satellite virus was first described in California by deep sequencing of dsRNAs (Al Rwahnih et al, 2013 ) and later from Iran by the same technique (Candresse et al, 2017b ). During our survey we found its presence in two of our libraries (Supplementary Table 4 ).…”

Section: Resultsmentioning

confidence: 99%

NGS of Virus-Derived Small RNAs as a Diagnostic Method Used to Determine Viromes of Hungarian Vineyards

et al. 2018

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As virus diseases cannot be controlled by traditional plant protection methods, the risk of their spread have to be minimized on vegetatively propagated plants, such as grapevine. Metagenomic approaches used for virus diagnostics offer a unique opportunity to reveal the presence of all viral pathogens in the investigated plant, which is why their application can reduce the risk of using infected material for a new plantation. Here we used a special branch, deep sequencing of virus-derived small RNAs, of this high-throughput method for virus diagnostics, and determined viromes of vineyards in Hungary. With NGS of virus-derived small RNAs we could detect not only the viruses tested routinely, but also new ones, which had never been described in Hungary before. Virus presence did not correlate with the age of the plantation, moreover phylogenetic analysis of the identified virus isolates suggests that infections are mostly caused by the use of infected propagating material. Our results, validated by other molecular methods, raised further questions to be answered before this method can be introduced as a routine, reliable test for grapevine virus diagnostics.

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Section: Resultsmentioning

confidence: 99%

NGS of Virus-Derived Small RNAs as a Diagnostic Method Used to Determine Viromes of Hungarian Vineyards

et al. 2018

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“…It has first been discovered in California in the vineyards of the Davis Grapevine Virus Collection (DGVC) and the USDA National Clonal Germplasm Repository (NCGR) [134]. GV-Sat has also been found on the cultivar Askeri in the INRA collection in France [135], in the ampelographic collection in Slovenia [136,137] and in the vineyards of Hungary [138]. GV-Sat has not been previously detected on the territory of Russia.…”

Section: Family: Unassignedmentioning

confidence: 99%

Virome of Grapevine Germplasm from the Anapa Ampelographic Collection (Russia)

Shvets

Porotikova

Sandomirsky

et al. 2022

Viruses

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Grapevine germplasm collections are unique repositories of grape cultivars; therefore, it is necessary to minimize their infection with pathogens, including viruses, and develop various programs to maintain them in a virus-free state. In our study, we examined the virome of the largest Russian grapevine germplasm collection, the Anapa Ampelographic Collection, using high-throughput sequencing of total RNAs. As a result of bioinformatics analysis and validation of its results by reverse transcription PCR (RT-PCR) and quantitative RT-PCR (RT-qPCR), we identified 20 viruses and 3 viroids in 47 libraries. All samples were infected with 2 to 12 viruses and viroids, including those that cause economically significant diseases: leafroll, fleck, and rugose wood complex. For the first time in Russia, we detected Grapevine virus B (GVB), Grapevine virus F (GVF), Grapevine asteroid mosaic-associated virus (GAMaV), Grapevine Red Globe virus (GRGV), Grapevine satellite virus (GV-Sat), Grapevine virga-like virus (GVLV), Grapevine-associated jivivirus 1 (GaJV-1) and Vitis cryptic virus (VCV). A new putative representative of the genus Umbravirus with the provisional name Grapevine umbra-like virus (GULV) was also identified in Russian grape samples.

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“…GV-Sat (genus Virtovirus) was discovered in 2013 in the USA [95], then it was detected on grapevines from Iran [96], Hungary [97], Slovenia [98], and Russia [21]. GV-Sat was identified in three samples (Supplementary Table S7), but the number of reads was too small to assemble whole-genome sequences.…”

Section: Family: Unassigned Grapevine Satellite Virusmentioning

confidence: 99%

Grapevine Virome of the Don Ampelographic Collection in Russia Has Concealed Five Novel Viruses

Belkina,

Karpova,

Porotikova

et al. 2023

Viruses

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In this study, an analysis of the virome of 51 grapevines from the Don ampelographic collection named after Ya. I. Potapenko (Russia) was performed using high-throughput sequencing of total RNA. A total of 20 previously described grapevine viruses and 4 viroids were identified. The most detected were grapevine rupestris stem pitting-associated virus (98%), hop stunt viroid (98%), grapevine Pinot gris virus (96%), grapevine yellow speckle viroid 1 (94%), and grapevine fleck virus (GFkV, 80%). Among the economically significant viruses, the most present were grapevine leafroll-associated virus 3 (37%), grapevine virus A (24%), and grapevine leafroll-associated virus 1 (16%). For the first time in Russia, a grapevine-associated tymo-like virus (78%) was detected. After a bioinformatics analysis, 123 complete or nearly complete viral genomes and 64 complete viroid genomes were assembled. An analysis of the phylogenetic relationships with reported global isolates was performed. We discovered and characterized the genomes of five novel grapevine viruses: bipartite dsRNA grapevine alphapartitivirus (genus Alphapartitivirus, family Partitiviridae), bipartite (+) ssRNA grapevine secovirus (genus Fabavirus, family Secoviridae) and three (+) ssRNA grapevine umbra-like viruses 2, -3, -4 (which phylogenetically occupy an intermediate position between representatives of the genus Umbravirus and umbravirus-like associated RNAs).

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Complete Nucleotide Sequence of an Isolate of Grapevine Satellite Virus and Evidence for the Presence of Multimeric Forms in an Infected Grapevine

Cited by 7 publications

References 8 publications

NGS of Virus-Derived Small RNAs as a Diagnostic Method Used to Determine Viromes of Hungarian Vineyards

NGS of Virus-Derived Small RNAs as a Diagnostic Method Used to Determine Viromes of Hungarian Vineyards

Virome of Grapevine Germplasm from the Anapa Ampelographic Collection (Russia)

Grapevine Virome of the Don Ampelographic Collection in Russia Has Concealed Five Novel Viruses

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