Whole Genome Characterization of Prunus Necrotic Ringspot Virus and Prune Dwarf Virus Infecting Stone Fruits in Russia

We conducted a survey of the phytosanitary status of the Prunus germplasm collection in the Nikita Botanical Gardens, Yalta, Russia. The virome of plants displaying virus-like symptoms was studied using Illumina MiSeq high-throughput sequencing. Reads related to prunus necrotic ringspot virus (PNRSV...

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Bibliographic Details
Published in:Horticulturae 2023-08, Vol.9 (8), p.941
Main Authors: Chirkov, Sergei, Sheveleva, Anna, Tsygankova, Svetlana, Slobodova, Natalia, Sharko, Fedor, Petrova, Kristina, Mitrofanova, Irina
Format: Article
Language:English
Subjects:
Botanical gardens
Clusters
Cultivars
Diseases and pests
Evolution
Flowers & plants
Fruits
full-length genomes
Genetic aspects
Genetic diversity
Genomes
Geographical distribution
Germplasm
high-throughput sequencing
Next-generation sequencing
Open reading frames
Phylogenetics
Phylogeny
Physiological aspects
Plant viruses
Polymerase chain reaction
Proteins
prune dwarf virus
Prunus
prunus necrotic ringspot virus
Prunus spp
RNA polymerase
RNA sequencing
virome
Virus diseases of plants
Viruses
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Summary:We conducted a survey of the phytosanitary status of the Prunus germplasm collection in the Nikita Botanical Gardens, Yalta, Russia. The virome of plants displaying virus-like symptoms was studied using Illumina MiSeq high-throughput sequencing. Reads related to prunus necrotic ringspot virus (PNRSV), prune dwarf virus (PDV), and ourmia-like virus 1 (OuLV1) were generated in a number of samples. Near complete genomes of two divergent PNRSV isolates, PDV isolate, and a contig partly covered OuLV1 genome were assembled de novo using the metaSPAdes program. The structure of the genomic RNA1, RNA2, and RNA3 of the new ilarvirus isolates was shown to be typical of PNRSV and PDV. This is the first report and characterization of the PNRSV and PDV full-length genomes from Russia, expanding the information on their geographical distribution and genetic diversity. An open reading frames (ORF)-based phylogeny of all full-length PNRSV and PDV genomes available in GenBank divided each ORF into two or three main clusters. A number of isolates migrated from one cluster to another cluster, depending on the analyzed genome segment. The different branching order may indicate reassortment in the evolutionary history of some PDV and PNRSV isolates.
ISSN:2311-7524
2311-7524
DOI:10.3390/horticulturae9080941