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

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 wer...

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Bibliographic Details
Published in:Viruses 2023-12, Vol.15 (12), p.2429
Main Authors: Belkina, Daria, Karpova, Daria, Porotikova, Elena, Lifanov, Ilya, Vinogradova, Svetlana
Format: Article
Language:English
Subjects:
alphapartitivirus
Bioinformatics
Cultivars
Diseases and pests
Double-stranded RNA
Environmental conditions
Flowers & plants
Genetic aspects
Genome, Viral
Genomes
Germplasm
Grapes
grapevine virome
Identification and classification
Infections
Next-generation sequencing
Pathogens
Phylogeny
Plant Diseases
Plant viruses
RNA-seq
secovirus
Stem pitting
umbra-like virus
Viral infections
Viroids
Virome
Virus diseases of plants
Viruses
Vitis
Vitis vinifera
Wineries & vineyards
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Summary: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 , family ), bipartite (+) ssRNA grapevine secovirus (genus , family ) and three (+) ssRNA grapevine umbra-like viruses 2, -3, -4 (which phylogenetically occupy an intermediate position between representatives of the genus and umbravirus-like associated RNAs).
ISSN:1999-4915
1999-4915
DOI:10.3390/v15122429