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

Darya Shvets; Kirill Sandomirsky; Elena Porotikova; Svetlana Vinogradova

doi:10.3390/v14122623

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

Viruses. 2022 Nov 24;14(12):2623. doi: 10.3390/v14122623.

Authors

Darya Shvets¹, Kirill Sandomirsky¹, Elena Porotikova¹, Svetlana Vinogradova¹

Affiliation

¹ Skryabin Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, 119071 Moscow, Russia.

Abstract

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.

Keywords: RNA-seq; Vitis vinifera; diagnostics; dsDNA grapevine virus; grapevine germplasm; grapevine pararetrovirus; grapevine umbra-like virus; novel grapevine viruses; virome.

Publication types

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

MeSH terms

Dagestan
Genome, Viral
Phylogeny
Plant Diseases
Plant Viruses* / genetics
Viroids* / genetics

Grants and funding

The article was made possible with support from the Ministry of Science and Higher Education of the Russian Federation in accordance with agreement № 075-15-2022-318 date 20 April 2022 on providing a grant in the form of subsidies from the Federal budget of Russian Federation. The grant was provided for state support for the creation and development of a World-class Scientific Center “Agrotechnologies for the Future”.