Polymorphisms at the 3’end of the movement protein (MP) gene of grapevine Pinot gris virus (GPGV) affect virus titre and small interfering RNA accumulation in GLMD disease

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.

Section: Family: Betaflexiviridaementioning

confidence: 99%

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

Shvets

Porotikova

Sandomirsky

et al. 2022

“…We carried out an analysis of the 3 region of the movement protein (MP) gene which may play a role in the manifestation of symptoms of GPGV infection [62]. It was previously found that the MP gene may have C to T substitutions at position 6685 and at position 6688 [63,64].…”

Section: Grapevine Pinot Gris Virusmentioning

confidence: 99%

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

Shvets

Sandomirsky

Porotikova

et al. 2022

In this study, we analyzed the virome of 73 grape samples from two Dagestan ampelographic collections in Russia using high-throughput sequencing of total RNAs. Fourteen viruses and four viroids were identified, with one to eleven of them detected in each plant. For the first time in Russia, we identified grapevine leafroll-associated virus 7 and grapevine Kizil Sapak virus. A total of 206 genomes of viruses and viroids were obtained, and their phylogenetic analysis was carried out. The de novo assembly and tblastx analysis allowed us to obtain contigs of a novel (+) ssRNA genome of a plant virus from the genus Umbravirus, which was tentatively named grapevine umbra-like virus (GULV), as well as contigs of a novel dsDNA pararetrovirus from the genus Caulimovirus, which was tentatively named grapevine pararetrovirus (GPRV). Complete genomes of these viruses were obtained and used for Sequence Demarcation Tool (SDT) analysis and phylogeny studies. GULV and GPRV were detected in 16 and 33 germplasm samples from the Dagestan collections, respectively.

“…Furthermore, in 2019, a full genome analysis of 20 GPGV isolates from a variety of grape cultivars (Pinot gris, Glera, Tocai Friulano, Tannat, Merlot, Riesling, Vetliner and Touriga Nacional) and an herbaceous host ( Silene latifolia ) with various countries of origin (Italy, Uruguay, France, Canada, the USA, Germany and Slovakia) revealed that they could be segregated into at least two groups, one of which is exclusively composed of asymptomatic isolates [ 33 ]. It was not until 2021 that the putative involvement of genetic variability on symptom expression was experimentally demonstrated by Tarquini et al [ 38 ]. In their study, a chimeric clone was synthesized by replacing a 356 bp segment at the end of the MP gene of a symptom-inducing strain (or virulent strain, fvg-Is12, accession number MH087443, Table S1 ) with the same segment derived from a non-symptom-inducing strain (or latent strain, fvg-Is15, accession number MH087446, Table S1 ).…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic and Evolutionary Studies of Grapevine Pinot Gris Virus Isolates from Canada

Vemulapati

McFadden-Smith

et al. 2023

This study investigated the phylogenetic relationship of grapevine Pinot gris virus (GPGV) isolates from Canada with GPGV isolates reported worldwide. Full-length genomes of 25 GPGV isolates representing the main four grape-growing regions in Canada (British Columbia, Ontario, Nova Scotia and Quebec) were sequenced and compared to genomes of 43 GPGV isolates representing eight countries and three continents. Phylogenetic analysis based on full genome sequences revealed an unambiguous separation of North American GPGV isolates with isolates from Europe and Asia. Within the North American clade, GPGV isolates from the USA segregated into a distinct subclade, whereas the relationships amongst GPGV isolates from different regions of Canada were not clearly defined. The phylogenetic analysis of the overlapping regions of MP and CP genes involving 169 isolates from 14 countries resulted in two distinctive clades, which were seemingly independent of their country of origin. Clade 1 included the majority of asymptomatic isolates (81% asymptomatic), whereas clade 2 was predominantly formed of symptomatic isolates (78% symptomatic). This research is the first study focused on the genetic variability and origin of GPGV in Canada.