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

Abstract

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.

Metagenomic Analysis of Ampelographic Collections of Dagestan Revealed the Presence of Two Novel Grapevine Viruses

“…The blastn analysis showed that the Russian isolate D1371o had a 79.83% identity at the nucleotide level with an isolate from South Africa (MW309530.1), while the isolate D1357o had an 87.92% identity with a French isolate (MG925333.1). In previous studies, we have also shown a rather low (at the level of 81.41-85.97%) identity of Russian isolates with the world's isolates [30]. On the dendrogram, the Russian GVA isolates were grouped with representative isolates of molecular group I (Supplementary Figure S7), clustering with isolates from France, South Africa and Russia.…”

“…Co-infection of GLRaV-7 with other closteroviruses prevents GLRaV-7 from being identified as the etiological agent of GLRD [67]. GLRaV-1, GLRaV-2, GLRaV-3 and GLRaV-4 have previously been detected in Russia [30,53,54,68,69].…”

“…The Betaflexiviridae family currently includes four genera (Fivirus, Foveavirus, Trichovirus and Vitivirus), the representatives of which infect grapes worldwide [7]. Grapevine rupestris stem pitting-associated virus (GRSPaV), grapevine virus T (GVT) (genus Foveavirus), GPGV (genus Trichovirus) and grapevine virus A (GVA,genus Vitivirus) have been detected in most vineyards in Russia [30,53,54,60]. In 2019, a novel member of the proposed genus "Fivivirus", GKSV, was identified on an asymptomatic grapevine cv.…”

“…The most widespread viruses are grapevine rupestris vein feathering virus (GRVFV), grapevine asteroid mosaic-associated virus (GAMaV), grapevine Syrah virus 1 (GSyV-1) (genus Marafivirus), grapevine fleck virus (GFkV) and grapevine red globe virus (GRGV) (genus Maculavirus). At present, all these viruses have been detected in Russian vineyards, including the Anapa ampelographic collection [30,53,54].…”

“…Ampelographic collections grow all over the world [29,30]. Russia hosts an important portion of the total number of the world's grapevine genetic resources, which are located in various regions of the country: the Rostov Oblast, the Krasnodar Krai, the Republic of Crimea and the Republic of Dagestan [31].…”