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Belkina D, Karpova D, Porotikova E, Lifanov I, Vinogradova S. Grapevine Virome of the Don Ampelographic Collection in Russia Has Concealed Five Novel Viruses. Viruses 2023; 15:2429. [PMID: 38140672 PMCID: PMC10747563 DOI: 10.3390/v15122429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
In this study, an analysis of the virome of 51 grapevines from the Don ampelographic collection named after Ya. I. Potapenko (Russia) was performed using high-throughput sequencing of total RNA. A total of 20 previously described grapevine viruses and 4 viroids were identified. The most detected were grapevine rupestris stem pitting-associated virus (98%), hop stunt viroid (98%), grapevine Pinot gris virus (96%), grapevine yellow speckle viroid 1 (94%), and grapevine fleck virus (GFkV, 80%). Among the economically significant viruses, the most present were grapevine leafroll-associated virus 3 (37%), grapevine virus A (24%), and grapevine leafroll-associated virus 1 (16%). For the first time in Russia, a grapevine-associated tymo-like virus (78%) was detected. After a bioinformatics analysis, 123 complete or nearly complete viral genomes and 64 complete viroid genomes were assembled. An analysis of the phylogenetic relationships with reported global isolates was performed. We discovered and characterized the genomes of five novel grapevine viruses: bipartite dsRNA grapevine alphapartitivirus (genus Alphapartitivirus, family Partitiviridae), bipartite (+) ssRNA grapevine secovirus (genus Fabavirus, family Secoviridae) and three (+) ssRNA grapevine umbra-like viruses 2, -3, -4 (which phylogenetically occupy an intermediate position between representatives of the genus Umbravirus and umbravirus-like associated RNAs).
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Affiliation(s)
- Daria Belkina
- Skryabin Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, 119071 Moscow, Russia; (D.B.)
- North Caucasian Federal Scientific Center of Horticulture, Viticulture, Wine-Making, 40 Years of Victory Street, Build. 39, 350901 Krasnodar, Russia
| | - Daria Karpova
- Skryabin Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, 119071 Moscow, Russia; (D.B.)
- North Caucasian Federal Scientific Center of Horticulture, Viticulture, Wine-Making, 40 Years of Victory Street, Build. 39, 350901 Krasnodar, Russia
| | - Elena Porotikova
- Skryabin Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, 119071 Moscow, Russia; (D.B.)
| | - Ilya Lifanov
- Skryabin Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, 119071 Moscow, Russia; (D.B.)
| | - Svetlana Vinogradova
- Skryabin Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, 119071 Moscow, Russia; (D.B.)
- North Caucasian Federal Scientific Center of Horticulture, Viticulture, Wine-Making, 40 Years of Victory Street, Build. 39, 350901 Krasnodar, Russia
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Salamon P, Nagyne-Galbacs Z, Demian E, Achs A, Alaxin P, Predajňa L, Agyemang ED, Desiderio F, Takacs AP, Menzel W, Škorić D, Glasa M, Varallyay E. Clematis vitalba Is a Natural Host of the Novel Ilarvirus, Prunus Virus I. Viruses 2023; 15:1964. [PMID: 37766370 PMCID: PMC10536899 DOI: 10.3390/v15091964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
Clematis vitalba L. is a climbing shrub and a pioneer plant in abandoned orchards or vineyards that are widespread in temperate climate zones. In past years, several viruses infecting the Clematis species have been identified, including different ilarviruses. Prunus virus I (PrVI) is a recently described ilarvirus, which has been shown to infect sweet cherries and peaches in Greece. Moreover, its presence has been detected in ornamental Clematis in Russia. In the present work, we analyzed the virome of wildly growing C. vitalba plants from Hungary, Slovakia and Croatia showing different kinds of symptoms using high-throughput sequencing (HTS) of small RNAs or ribodepleted RNAs. Applying HTS enabled us to identify the presence of PrVI in C. vitalba, and the bioinformatic analyses were further validated with RT-PCR using PrVI-specific primers and Sanger dideoxy sequencing. Nearly full genome sequences of all three viral RNAs of one Hungarian, two Slovak and one Croatian isolate were determined. Their phylogenetic analysis showed high similarity to each other and to other PrVI isolates described from Central Europe. As the sampled plants were co-infected with other viruses, it is not possible to determine a direct correlation between the infection with PrVI and the observed symptoms. Analyses of different Prunus species in stock collection showed infection of several peach and sweet cherry varieties in Hungary. Our results expand the knowledge on the natural host range of PrVI and highlight the necessity to evaluate alternative plant hosts (even non-Prunus) of PrVI and the role of the virus in the etiology of the potential diseases.
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Affiliation(s)
- Pal Salamon
- Applied Plant Genomics Group, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, 2100 Godollo, Hungary;
| | - Zsuzsanna Nagyne-Galbacs
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, 2100 Godollo, Hungary; (Z.N.-G.); (E.D.); (F.D.)
| | - Emese Demian
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, 2100 Godollo, Hungary; (Z.N.-G.); (E.D.); (F.D.)
| | - Adam Achs
- Institute of Virology, Biomedical Research Center of the Slovak Academy of Sciences, Dúbravská Cesta 9, 84505 Bratislava, Slovakia; (A.A.); (P.A.); (L.P.); (M.G.)
| | - Peter Alaxin
- Institute of Virology, Biomedical Research Center of the Slovak Academy of Sciences, Dúbravská Cesta 9, 84505 Bratislava, Slovakia; (A.A.); (P.A.); (L.P.); (M.G.)
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Nám. J. Herdu 2, 91701 Trnava, Slovakia
| | - Lukáš Predajňa
- Institute of Virology, Biomedical Research Center of the Slovak Academy of Sciences, Dúbravská Cesta 9, 84505 Bratislava, Slovakia; (A.A.); (P.A.); (L.P.); (M.G.)
| | - Evans Duah Agyemang
- Department of Plant Protection, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Deák Ferenc Street 17, 8360 Keszthely, Hungary; (E.D.A.); (A.P.T.)
| | - Francesco Desiderio
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, 2100 Godollo, Hungary; (Z.N.-G.); (E.D.); (F.D.)
| | - Andras Peter Takacs
- Department of Plant Protection, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Deák Ferenc Street 17, 8360 Keszthely, Hungary; (E.D.A.); (A.P.T.)
| | - Wulf Menzel
- Plant Virus Department, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, 38124 Braunschweig, Germany;
| | - Dijana Škorić
- Department of Biology, Faculty of Science, University of Zagreb, Marulićev trg 9a, 10000 Zagreb, Croatia;
| | - Miroslav Glasa
- Institute of Virology, Biomedical Research Center of the Slovak Academy of Sciences, Dúbravská Cesta 9, 84505 Bratislava, Slovakia; (A.A.); (P.A.); (L.P.); (M.G.)
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Nám. J. Herdu 2, 91701 Trnava, Slovakia
| | - Eva Varallyay
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, 2100 Godollo, Hungary; (Z.N.-G.); (E.D.); (F.D.)
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Virome of Grapevine Germplasm from the Anapa Ampelographic Collection (Russia). Viruses 2022; 14:v14061314. [PMID: 35746784 PMCID: PMC9230720 DOI: 10.3390/v14061314] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/07/2022] [Accepted: 06/13/2022] [Indexed: 11/16/2022] Open
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.
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Navrotskaya E, Porotikova E, Yurchenko E, Galbacs ZN, Varallyay E, Vinogradova S. High-Throughput Sequencing of Small RNAs for Diagnostics of Grapevine Viruses and Viroids in Russia. Viruses 2021; 13:2432. [PMID: 34960701 PMCID: PMC8709451 DOI: 10.3390/v13122432] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 11/16/2022] Open
Abstract
The use of high-throughput sequencing (HTS) technology has led to significant progress in the identification of many viruses and their genetic variants. In this study, we used the HTS platform to sequence small RNAs (sRNAs) of grapevine to study the virome. Isolation of RNA was performed using symptomatic grapevines collected from commercial vineyards in Krasnodar Krai in 2017-2018. To determine the viromes of vineyards, we used an integrated approach that included a bioinformatic analysis of the results of sRNA HTS and the molecular method RT-PCR, which made it possible to identify 13 viruses and 4 viroids. Grapevine leafroll-associated virus 4 (GLRaV-4), Grapevine Syrah Virus-1 (GSyV-1), Raspberry bushy dwarf virus (RBDV), Australian grapevine viroid (AGVd), and Grapevine yellow speckle viroid 2 (GYSVd-2) were identified for the first time in Russia. Out of 38 samples analyzed, 37 had mixed infections with 4-11 viruses, indicating a high viral load. Analysis of the obtained sequences of fragments of virus genomes made it possible to identify recombination events in GLRaV-1, GLRaV-2, GLRaV-3, GLRaV-4, GVT, GPGV, GRSPaV, GVA, and GFLV. The obtained results indicate a wide spread of the viruses and a high genetic diversity in the vineyards of Krasnodar Krai and emphasize the urgent need to develop and implement long-term strategies for the control of viral grapevine diseases.
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Affiliation(s)
- Emiliya Navrotskaya
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia; (E.N.); (E.P.)
| | - Elena Porotikova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia; (E.N.); (E.P.)
| | - Eugeniya Yurchenko
- Federal State Budgetary Scientific Institution ‘North Caucasian Federal Scientific Horticulture and Viticulture Center’, Protection and Plant Biotechnology Scientific Center, Head, 40 Years of Victory Street 39, 350072 Krasnodar, Russia;
| | - Zsuzsanna Nagyne Galbacs
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, H-2100 Godollo, Hungary; (Z.N.G.); (E.V.)
| | - Eva Varallyay
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, H-2100 Godollo, Hungary; (Z.N.G.); (E.V.)
| | - Svetlana Vinogradova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia; (E.N.); (E.P.)
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