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

Darya Shvets; Elena Porotikova; Kirill Sandomirsky; Svetlana Vinogradova

doi:10.3390/v14061314

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

Viruses. 2022 Jun 15;14(6):1314. doi: 10.3390/v14061314.

Authors

Darya Shvets¹, Elena Porotikova¹, Kirill Sandomirsky¹, Svetlana Vinogradova¹

Affiliation

¹ Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky, Prospect 33, 119071 Moscow, 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.

Keywords: Anapa Ampelographic Collection; germplasm; grapevine; high-throughput sequencing; novel virus; total RNA; validation; virome.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Plant Diseases
RNA Viruses*
Tymoviridae*
Viroids*
Virome
Vitis*

Grants and funding

This research was partially funded by the Russian Science Foundation under grant no. 19-76-10029. Sanger sequencing was performed using scientific equipment from the Core Research Facility of Center “Bioengineering”, and the experimental climate control facility U-73547 and was partially funded by the Ministry of Education and Science of Russian Federation.