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.

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

Figure 1

Frequency of distribution of grapevine viruses and viroids in Anapa Ampelographic Collection (percentage of the total number of collected samples).

Figure 2

Color-coded pairwise identity matrix performed for the Russian isolate of the Grapevine umbra-like virus and representatives of the genus Umbravirus for (a) nucleotide sequences, (b) amino acid sequences of RNA-dependent RNA polymerase (RdRp) gene. GenBank accession numbers for each isolate are presented in Supplementary Table S5.

Figure 3

Phylogenetic analysis of (a) nucleotide sequences, (b) amino acids sequences of RNA-dependent RNA polymerase (RdRp) gene of a Russian isolate of Grapevine umbra-like virus (marked with a green label), representatives of the genus Umbravirus (marked with an orange label) and unclassified Umbravirus (marked with a blue label). The tree was constructed using the Maximum Likelihood method. The numbers at the nodes indicate bootstrap values >60% (1000 replicates). GenBank accession numbers for each isolate are presented in Supplementary Table S5.