1
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Galbács ZN, Agyemang ED, Pásztor G, Takács AP, Várallyay É. Viromes of Monocotyledonous Weeds Growing in Crop Fields Reveal Infection by Several Viruses Suggesting Their Virus Reservoir Role. PLANTS (BASEL, SWITZERLAND) 2024; 13:2664. [PMID: 39339638 PMCID: PMC11435186 DOI: 10.3390/plants13182664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Revised: 09/09/2024] [Accepted: 09/18/2024] [Indexed: 09/30/2024]
Abstract
In 2019, random samples of Panicum miliaceum growing as a weed were surveyed to uncover their virus infections at two locations in Hungary. This pilot study revealed infection with three viruses, two appearing for the first time in the country. As follow-up research, in the summer of 2021, we collected symptomatic leaves of several monocotyledonous plants in the same locations and determined their viromes using small RNA high-throughput sequencing (HTS). As a result, we have identified the presence of wheat streak mosaic virus (WSMV), barley yellow striate mosaic virus (BYSMV), barley virus G (BVG), and two additional viruses, namely Aphis glycines virus 1 (ApGlV1) and Ljubljana dicistrovirus 1 (LDV1), which are described for the first time in Hungary. New hosts of the viruses were identified: Cynodon dactylon is a new host of BYSMV and LDV1, Echinocloa crus-galli is a new host of BVG, ApGlV1 and LDV1, Sorghum halepense is a new host of ApGlV1, and Panicum miliaceum is a new host of LDV1. At the same time, Zea mays is a new host of ApGlV1 and LDV1. Small RNA HTS diagnosed acute infections but failed to detect persistent ones, which could be revealed using RT-PCR. The infection rates at the different locations and plant species were different. The phylogenetic analyses of the sequenced virus variants suggest that the tested monocotyledonous weeds can host different viruses and play a virus reservoir role. Viral spread from the reservoir species relies on the activity of insect vectors, which is why their management requires an active role in plant protection strategies, which need careful planning in the changing environment.
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Affiliation(s)
- Zsuzsanna N Galbács
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi Albert Street 4, H-2100 Godollo, Hungary
| | - Evans Duah Agyemang
- Department of Plant Protection, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, H-8360 Keszthely, Hungary
| | - György Pásztor
- Department of Plant Protection, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, H-8360 Keszthely, Hungary
| | - András Péter Takács
- Department of Plant Protection, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, H-8360 Keszthely, Hungary
| | - Éva Várallyay
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi Albert Street 4, H-2100 Godollo, Hungary
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2
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Lee GE, Lee HJ, Jeong RD. Comprehensive Metatranscriptomic Analysis of Plant Viruses in Imported Frozen Cherries and Blueberries. THE PLANT PATHOLOGY JOURNAL 2024; 40:377-389. [PMID: 39117336 PMCID: PMC11309839 DOI: 10.5423/ppj.oa.06.2024.0088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/08/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024]
Abstract
The possibility of new viruses emerging in various regions worldwide has increased due to a combination of factors, including climate change and the expansion of international trading. Plant viruses spread through various transmission routes, encompassing well-known avenues such as pollen, seeds, and insects. However, research on potential transmission routes beyond these known mechanisms has remained limited. To address this gap, this study employed metatranscriptomic analysis to ascertain the presence of plant viruses in imported frozen fruits, specifically cherries and blueberries. This analysis aimed to identify pathways through which plant viruses may be introduced into countries. Virome analysis revealed the presence of six species of plant viruses in frozen cherries and blueberries: cherry virus A (CVA), prunus necrotic ringspot virus (PNRSV), prune dwarf virus (PDV), prunus virus F (PrVF), blueberry shock virus (BlShV), and blueberry latent virus (BlLV). Identifying these potential transmission routes is crucial for effectively managing and preventing the spread of plant viruses and crop protection. This study highlights the importance of robust quality control measures and monitoring systems for frozen fruits, emphasizing the need for proactive measures to mitigate the risk associated with the potential spread of plant viruses.
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Affiliation(s)
- Ga-Eun Lee
- Department of Applied Biology, Chonnam National University, Gwangju 61185, Korea
| | - Hyo-Jeong Lee
- Department of Applied Biology, Chonnam National University, Gwangju 61185, Korea
| | - Rae-Dong Jeong
- Department of Applied Biology, Chonnam National University, Gwangju 61185, Korea
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3
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Komínková M, Ben Mansour K, Komínek P, Brožová J, Střalková R. Multiple Infections with Viruses of the Family Tymoviridae in Czech Grapevines. Viruses 2024; 16:343. [PMID: 38543709 PMCID: PMC10975331 DOI: 10.3390/v16030343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/07/2024] [Accepted: 02/21/2024] [Indexed: 05/23/2024] Open
Abstract
This study focused on the viruses of the Tymoviridae family that infect grapevines in the Czech Republic. Complete sequences of GFkV (grapevine fleck virus) and GRGV (grapevine red globe virus) from the genus Maculavirus and GRVFV (grapevine rupestris vein feathering virus) and GSyV-1 (grapevine Syrah virus 1) from the genus Marafivirus were obtained using high-throughput sequencing of small RNAs and total RNAs. Mixed infections with these viruses were observed, as well as several variants of these viruses in the same plant. Phylogenetic analysis showed the position of the newly obtained virus isolates within the Tymoviridae family. Recombinant analysis provided evidence of single and multiple intraspecific recombinations in GRGV, GSyV-1, and GRVFV. Additionally, GAMaV, a grapevine virus from the genus Marafivirus, was reported for the first time in the Czech Republic.
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Affiliation(s)
- Marcela Komínková
- Ecology, Diagnostics and Genetic Resources of Agriculturally Important Viruses, Fungi and Phytoplasmas, Crop Research Institute, Drnovská 507, 161 06 Prague, Czech Republic; (M.K.); or (K.B.M.); (J.B.)
- Department of Plant Protection, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic
| | - Karima Ben Mansour
- Ecology, Diagnostics and Genetic Resources of Agriculturally Important Viruses, Fungi and Phytoplasmas, Crop Research Institute, Drnovská 507, 161 06 Prague, Czech Republic; (M.K.); or (K.B.M.); (J.B.)
- Department of Plant Protection, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic
| | - Petr Komínek
- Ecology, Diagnostics and Genetic Resources of Agriculturally Important Viruses, Fungi and Phytoplasmas, Crop Research Institute, Drnovská 507, 161 06 Prague, Czech Republic; (M.K.); or (K.B.M.); (J.B.)
| | - Jana Brožová
- Ecology, Diagnostics and Genetic Resources of Agriculturally Important Viruses, Fungi and Phytoplasmas, Crop Research Institute, Drnovská 507, 161 06 Prague, Czech Republic; (M.K.); or (K.B.M.); (J.B.)
| | - Radomíra Střalková
- Crop Research Institute, Prague, Research Station for Viticulture Karlštejn, Karlštejn 98, 267 18 Karlštejn, Czech Republic;
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4
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Tarquini G, Maestri S, Ermacora P, Martini M. The Oxford Nanopore MinION as a Versatile Technology for the Diagnosis and Characterization of Emerging Plant Viruses. Methods Mol Biol 2024; 2732:235-249. [PMID: 38060129 DOI: 10.1007/978-1-0716-3515-5_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
The emergence of novel viral epidemics that could affect major crops represents a serious threat to global food security. The early and accurate identification of the causative viral agent is the most important step for a rapid and effective response to disease outbreaks. Over the last years, the Oxford Nanopore Technologies (ONT) MinION sequencer has been proposed as an effective diagnostic tool for the early detection and identification of emerging viruses in plants, providing many advantages compared with different high-throughput sequencing (HTS) technologies. Here, we provide a step-by-step protocol that we optimized to obtain the virome of "Lamon bean" plants (Phaseolus vulgaris L.), an agricultural product with Protected Geographical Indication (PGI) in North-East of Italy, which is frequently subjected to multiple infections caused by different RNA viruses. The conversion of viral RNA in ds-cDNA enabled the use of Genomic DNA Ligation Sequencing Kit and Native Barcoding DNA Kit, which have been originally developed for DNA sequencing. This allowed the simultaneous diagnosis of both DNA- and RNA-based pathogens, providing a more versatile alternative to the use of direct RNA and/or direct cDNA sequencing kits.
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Affiliation(s)
- Giulia Tarquini
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Simone Maestri
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milano, Italy
| | - Paolo Ermacora
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Marta Martini
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy.
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5
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Jaksa-Czotter N, Nagyné Galbács Z, Jahan A, Demián E, Várallyay É. Viromes of Plants Determined by High-Throughput Sequencing of Virus-Derived siRNAs. Methods Mol Biol 2024; 2732:179-198. [PMID: 38060126 DOI: 10.1007/978-1-0716-3515-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Plants growing in open airfields can be infected by several viruses even as a multiple infection. Virus infection in crops can lead to a serious damage to the harvest. In addition, virus presence in grapevine, fruit trees, and tuberous vegetables, propagated vegetatively affects the phytosanitary status of the propagation material (both the rootstock and the variety) having profound effect on the lifetime and health of the new plantations. The fast evolution of sequencing techniques provides a new opportunity for metagenomics-based viral diagnostics. Small interfering (si) RNAs produced by the RNA silencing-based host immune system during viral infection can be sequenced by high-throughput techniques and analyzed for the presence of viruses, revealing the presence of all known viral pathogens in the sample and therefore opening new avenues in virus diagnostics. This method is based on Illumina sequencing and bioinformatics analysis of virus-derived siRNAs in the host. Here we describe a protocol for this challenging technique step by step with notes, to ensure success for every user.
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Affiliation(s)
- Nikoletta Jaksa-Czotter
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, MATE, Gödöllő, Hungary
| | - Zsuzsanna Nagyné Galbács
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, MATE, Gödöllő, Hungary
| | - Almash Jahan
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, MATE, Gödöllő, Hungary
| | - Emese Demián
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, MATE, Gödöllő, Hungary
| | - Éva Várallyay
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, MATE, Gödöllő, Hungary.
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6
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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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7
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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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Vinogradova S, Porotikova E, Navrotskaya E, Galbacs ZN, Massart S, Varallyay E. The First Virome of a Russian Vineyard. PLANTS (BASEL, SWITZERLAND) 2023; 12:3292. [PMID: 37765456 PMCID: PMC10534617 DOI: 10.3390/plants12183292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023]
Abstract
Among other pathogens, more than 80 viruses infect grapevine. The aim of this work was to study the virome diversity of grapevine viruses and mycoviruses of a vineyard using high-throughput sequencing technologies. The grapevine virome was studied in symptomatic vines of the Rkatsiteli cultivar (V. vinifera) collected at the vineyards of the Krasnodar Krai in Russia. Ribosomal-depleted total RNA and isolated small RNAs were used for library preparation and high-throughput sequencing. Six grapevine-infecting viruses and two viroids were validated by RT-PCR and analyzed phylogenetically. We identified the presence of grapevine leafroll-associated virus 3, grapevine Pinot gris virus, grapevine virus T, grapevine rupestris stem-pitting-associated virus, grapevine fleck virus, and grapevine rupestris vein feathering virus, as well as two viroids, grapevine yellow speckle viroid 1 and hop stunt viroid. We also studied the mycovirome of the vineyard and identified nine viruses with single-stranded positive-sense RNA genomes: alternaria arborescens mitovirus 1, botrytis cinerea mitovirus 1, botrytis cinerea mitovirus 2, botrytis cinerea mitovirus 3, botrytis cinerea mitovirus 4, sclerotinia sclerotiorum mitovirus 3, botrytis cinerea hypovirus 1, grapevine-associated narnavirus 1, and botrytis virus F. In addition, we identified botrytis cinerea hypovirus 1 satellite-like RNA and two single-stranded negative-sense RNA viruses. This is the first study of grapevine mycoviruses in Russia. The obtained result will contribute to the development of biocontrol strategies in the future.
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Affiliation(s)
- Svetlana Vinogradova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Elena Porotikova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Emiliya Navrotskaya
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, 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
| | - Sébastien Massart
- Laboratory of Integrated and Urban Phytopathology, TERRA, Gembloux Agro-Bio Tech, Liège University, 5030 Gembloux, Belgium
| | - 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
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9
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Kolchenko M, Kapytina A, Kerimbek N, Pozharskiy A, Nizamdinova G, Khusnitdinova M, Taskuzhina A, Gritsenko D. Genetic Characterization of Raspberry Bushy Dwarf Virus Isolated from Red Raspberry in Kazakhstan. Viruses 2023; 15:v15040975. [PMID: 37112955 PMCID: PMC10143182 DOI: 10.3390/v15040975] [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: 03/13/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Raspberry bushy dwarf virus (RBDV) is an economically significant pathogen of raspberry and grapevine, and it has also been found in cherry. Most of the currently available RBDV sequences are from European raspberry isolates. This study aimed to sequence genomic RNA2 of both cultivated and wild raspberry in Kazakhstan and compare them to investigate their genetic diversity and phylogenetic relationships, as well as to predict their protein structure. Phylogenetic and population diversity analyses were performed on all available RBDV RNA2, MP and CP sequences. Nine of the isolates investigated in this study formed a new, well-supported clade, while the wild isolates clustered with the European isolates. Predicted protein structure analysis revealed two regions that differed between α- and β-structures among the isolates. For the first time, the genetic composition of Kazakhstani raspberry viruses has been characterized.
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Affiliation(s)
- Mariya Kolchenko
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan
| | - Anastasiya Kapytina
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan
| | - Nazym Kerimbek
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan
| | - Alexandr Pozharskiy
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan
- Department of Molecular Biology and Genetics, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Gulnaz Nizamdinova
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan
| | - Marina Khusnitdinova
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan
| | - Aisha Taskuzhina
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan
| | - Dilyara Gritsenko
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan
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10
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Shvets D, Sandomirsky K, Porotikova E, Vinogradova S. Metagenomic Analysis of Ampelographic Collections of Dagestan Revealed the Presence of Two Novel Grapevine Viruses. Viruses 2022; 14:2623. [PMID: 36560627 PMCID: PMC9781968 DOI: 10.3390/v14122623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/21/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
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.
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Affiliation(s)
| | | | | | - Svetlana Vinogradova
- Skryabin Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, 119071 Moscow, Russia
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11
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Complete Genome Sequences of Grapevine Red Globe Virus in Japan. Microbiol Resour Announc 2022; 11:e0043422. [DOI: 10.1128/mra.00434-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two complete and three partial genome sequences of grapevine red globe virus (GRGV) from grapevines (
Vitis
spp.) in Japan were determined.
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Kubina J, Hily JM, Mustin P, Komar V, Garcia S, Martin IR, Poulicard N, Velt A, Bonnet V, Mercier L, Lemaire O, Vigne E. Characterization of Grapevine Fanleaf Virus Isolates in ‘Chardonnay’ Vines Exhibiting Severe and Mild Symptoms in Two Vineyards. Viruses 2022; 14:v14102303. [PMID: 36298857 PMCID: PMC9609649 DOI: 10.3390/v14102303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 12/03/2022] Open
Abstract
Fanleaf degeneration is a complex viral disease of Vitis spp. that detrimentally impacts fruit yield and reduces the productive lifespan of most vineyards worldwide. In France, its main causal agent is grapevine fanleaf virus (GFLV). In the past, field experiments were conducted to explore cross-protection as a management strategy of fanleaf degeneration, but results were unsatisfactory because the mild virus strain negatively impacted fruit yield. In order to select new mild GFLV isolates, we examined two old ‘Chardonnay’ parcels harbouring vines with distinct phenotypes. Symptoms and agronomic performances were monitored over the four-year study on 21 individual vines that were classified into three categories: asymptomatic GFLV-free vines, GFLV-infected vines severely diseased and GFLV-infected vines displaying mild symptoms. The complete coding genomic sequences of GFLV isolates in infected vines was determined by high-throughput sequencing. Most grapevines were infected with multiple genetically divergent variants. While no specific molecular features were apparent for GFLV isolates from vines displaying mild symptoms, a genetic differentiation of GFLV populations depending on the vineyard parcel was observed. The mild symptomatic grapevines identified during this study were established in a greenhouse to recover GFLV variants of potential interest for cross-protection studies.
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Affiliation(s)
- Julie Kubina
- INRAE, SVQV UMR-A 1131, Université de Strasbourg, 68000 Colmar, France
| | - Jean-Michel Hily
- INRAE, SVQV UMR-A 1131, Université de Strasbourg, 68000 Colmar, France
- IFV, 30240 Le Grau-Du-Roi, France
| | - Pierre Mustin
- INRAE, SVQV UMR-A 1131, Université de Strasbourg, 68000 Colmar, France
| | - Véronique Komar
- INRAE, SVQV UMR-A 1131, Université de Strasbourg, 68000 Colmar, France
| | - Shahinez Garcia
- INRAE, SVQV UMR-A 1131, Université de Strasbourg, 68000 Colmar, France
| | | | - Nils Poulicard
- PHIM, Université Montpellier, IRD, INRAE, Cirad, SupAgro, 34000 Montpellier, France
| | - Amandine Velt
- INRAE, SVQV UMR-A 1131, Université de Strasbourg, 68000 Colmar, France
| | - Véronique Bonnet
- Maison Moët & Chandon, 20 Avenue de Champagne, 51200 Épernay, France
| | - Laurence Mercier
- Maison Moët & Chandon, 20 Avenue de Champagne, 51200 Épernay, France
| | - Olivier Lemaire
- INRAE, SVQV UMR-A 1131, Université de Strasbourg, 68000 Colmar, France
| | - Emmanuelle Vigne
- INRAE, SVQV UMR-A 1131, Université de Strasbourg, 68000 Colmar, France
- Correspondence:
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Grapevine Pinot Gris Virus Is Present in Different Non-Vitis Hosts. PLANTS 2022; 11:plants11141830. [PMID: 35890463 PMCID: PMC9315623 DOI: 10.3390/plants11141830] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 11/25/2022]
Abstract
Grapevine Pinot gris virus (GPGV) was described in Italy using a metagenomic approach: next-generation sequencing of the virus-derived small RNAs. Since that time, it has been reported all over the world. The presence of GPGV is associated with grapevine disease, but most of the time, the disease is asymptomatic. Although the host range of this virus has not been investigated, it has been found in the non-Vitis hosts, Silene latifolia and Chenopodium album. We investigated the presence of GPGV in grapevine and other plant species growing as weeds in the vineyard. Using RT-PCR, we identified GPGV in seven non-Vitis hosts: Ailanthus, Asclepias, Crataegus, Fraxinus, Rosa, Rubus, and Sambucus. In the case of Rosa and Rubus, this finding was supported by Northern blot detection of the virus. GPGV strains in non-Vitis hosts belong to the asymptomatic clade, and are clustered according to their original geographic locations. The presence of GPGV in species other than grapevine shows that besides well-known vector and propagating material-based infections, other possible entry sites for the virus can exist, which have to be taken into consideration when developing reliable regulation strategies.
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Shvets D, Porotikova E, Sandomirsky K, Vinogradova S. Virome of Grapevine Germplasm from the Anapa Ampelographic Collection (Russia). Viruses 2022; 14:1314. [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] [MESH Headings] [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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Affiliation(s)
| | | | | | - Svetlana Vinogradova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky, Prospect 33, 119071 Moscow, Russia; (D.S.); (E.P.); (K.S.)
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Lee HJ, Jeong RD. Metatranscriptomic Analysis of Plant Viruses in Imported Pear and Kiwifruit Pollen. THE PLANT PATHOLOGY JOURNAL 2022; 38:220-228. [PMID: 35678055 PMCID: PMC9343911 DOI: 10.5423/ppj.oa.03.2022.0047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/28/2022] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
Pollen is a vector for viral transmission. Pollen-mediated viruses cause serious economic losses in the fruit industry. Despite the commercial importance of pollen-associated viruses, the diversity of such viruses is yet to be fully explored. In this study, we performed metatranscriptomic analyses using RNA sequencing to investigate the viral diversity in imported apple and kiwifruit pollen. We identified 665 virus-associated contigs, which corresponded to four different virus species. We identified one virus, the apple stem grooving virus, from pear pollen and three viruses, including citrus leaf blotch virus, cucumber mosaic virus, and lychnis mottle virus in kiwifruit pollen. The assembled viral genome sequences were analyzed to determine phylogenetic relationships. These findings will expand our knowledge of the virosphere in fruit pollen and lead to appropriate management of international pollen trade. However, the pathogenic mechanisms of pollen-associated viruses in fruit trees should be further investigated.
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Affiliation(s)
| | - Rae-Dong Jeong
- Corresponding author. Phone) +82-62-530-2075, FAX) +82-62-530-2069, E-mail)
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16
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Miljanić V, Jakše J, Rusjan D, Škvarč A, Štajner N. Small RNA Sequencing and Multiplex RT-PCR for Diagnostics of Grapevine Viruses and Virus-Like Organisms. Viruses 2022; 14:v14050921. [PMID: 35632662 PMCID: PMC9145883 DOI: 10.3390/v14050921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 12/18/2022] Open
Abstract
Metagenomic approaches used for virus diagnostics allow for rapid and accurate detection of all viral pathogens in the plants. In order to investigate the occurrence of viruses and virus-like organisms infecting grapevine from the Ampelographic collection Kromberk in Slovenia, we used Ion Torrent small RNA sequencing (sRNA-seq) and the VirusDetect pipeline to analyze the sRNA-seq data. The used method revealed the presence of: Grapevine leafroll-associated virus 1 (GLRaV-1), Grapevine leafroll-associated virus 2 (GLRaV-2), Grapevine leafroll-associated virus 3 (GLRaV-3), Grapevine rupestris stem pitting-associated virus (GRSPaV), Grapevine fanleaf virus (GFLV) and its satellite RNA (satGFLV), Grapevine fleck virus (GFkV), Grapevine rupestris vein feathering virus (GRVFV), Grapevine Pinot gris virus (GPGV), Grapevine satellite virus (GV-Sat), Hop stunt viroid (HSVd), and Grapevine yellow speckle viroid 1 (GYSVd-1). Multiplex reverse transcription-polymerase chain reaction (mRT-PCR) was developed for validation of sRNA-seq predicted infections, including various combinations of viruses or viroids and satellite RNA. mRT-PCR could further be used for rapid and cost-effective routine molecular diagnosis, including widespread, emerging, and seemingly rare viruses, as well as viroids which testing is usually overlooked.
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Affiliation(s)
- Vanja Miljanić
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Denis Rusjan
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Andreja Škvarč
- Chamber of Agriculture and Forestry of Slovenia, Agriculture and Forestry Institute Nova Gorica, 5000 Nova Gorica, Slovenia
| | - Nataša Štajner
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
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Shvets D, Vinogradova S. Occurrence and Genetic Characterization of Grapevine Pinot Gris Virus in Russia. PLANTS (BASEL, SWITZERLAND) 2022; 11:1061. [PMID: 35448789 PMCID: PMC9028157 DOI: 10.3390/plants11081061] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/06/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
Grapevine Pinot gris virus (GPGV) is a widespread grapevine pathogen associated with symptoms of leaf mottling and deformation. In order to study the distribution and genetic diversity of GPGV in Russia, we tested 1347 grapevine samples from 3 regions of Russia-the Krasnodar Krai, Stavropol Krai, and Republic of Crimea-using duplex real-time RT-PCR. GPGV was detected in 993 grapevines, both symptomatic and asymptomatic. In 119 isolates, we sequenced complete movement protein (MP) and coat protein (CP) genes of the GPGV genome. The percentage of identity of the obtained nucleotide MP/CP sequences with the closest isolates from the GenBank was 97.75-99.56%. A phylogenetic analysis showed that these Russian GPGV isolates are mainly grouped with previously described representative asymptomatic isolates. New post-translational modifications of the MP and CP at the positions of polymorphisms in the genomes of Russian isolates were predicted. The present work is the first study on the distribution and genetic diversity of GPGV in Russia.
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Elimination of Eight Viruses and Two Viroids from Preclonal Candidates of Six Grapevine Varieties (Vitis vinifera L.) through In Vivo Thermotherapy and In Vitro Meristem Tip Micrografting. PLANTS 2022; 11:plants11081064. [PMID: 35448791 PMCID: PMC9029751 DOI: 10.3390/plants11081064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 11/17/2022]
Abstract
Viruses and virus-like organisms are a major problem in viticulture worldwide. They cannot be controlled by standard plant protection measures, and once infected, plants remain infected throughout their life; therefore, the propagation of healthy vegetative material is crucial. In vivo thermotherapy at 36–38 °C for at least six weeks, followed by meristem tip micrografting (0.1–0.2 mm) onto in vitro-growing seedling rootstocks of Vialla (Vitis labrusca × Vitis riparia), was successfully used to eliminate eight viruses (grapevine rupestris stem pitting-associated virus (GRSPaV), grapevine Pinot gris virus (GPGV), grapevine fanleaf virus (GFLV), grapevine leafroll-associated virus 3 (GLRaV-3), grapevine fleck virus (GFkV), grapevine rupestris vein feathering virus (GRVFV), grapevine Syrah virus-1 (GSyV-1), and raspberry bushy dwarf virus (RBDV)), as well as two viroids (hop stunt viroid (HSVd) and grapevine yellow speckle viroid 1 (GYSVd-1)) from preclonal candidates of six grapevine varieties (Vitis vinifera L.). A half-strength MS medium including vitamins supplemented with 30 g/L of sucrose and solidified with 8 g/L of agar, without plant growth regulators, was used for the growth and root development of micrografts and the subsequently micropropagated plants; no callus formation, hyperhydricity, or necrosis of shoot tips was observed. Although the overall regeneration was low (higher in white than in red varieties), a 100% elimination was achieved for all eight viruses, whereas the elimination level for viroids was lower, reaching only 39.2% of HSVd-free and 42.6% GYSVd-1-free vines. To the best of our knowledge, this is the first report of GPGV, GRVFV, GSyV-1, HSVd, and GYSVd-1 elimination through combining in vivo thermotherapy and in vitro meristem tip micrografting, and the first report of RBDV elimination from grapevines. The virus-free vines were successfully acclimatized in rockwool plugs and then transferred to soil.
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Tarquini G, Martini M, Maestri S, Firrao G, Ermacora P. The Virome of ‘Lamon Bean’: Application of MinION Sequencing to Investigate the Virus Population Associated with Symptomatic Beans in the Lamon Area, Italy. PLANTS 2022; 11:plants11060779. [PMID: 35336661 PMCID: PMC8951528 DOI: 10.3390/plants11060779] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/10/2022] [Accepted: 03/12/2022] [Indexed: 11/23/2022]
Abstract
‘Lamon bean’ is a protected geographical indication (PGI) for a product of four varieties of bean (Phaseolus vulgaris L.) grown in a specific area of production, which is located in the Belluno district, Veneto region (N.E. of Italy). In the last decade, the ‘Lamon bean’ has been threatened by severe virus epidemics that have compromised its profitability. In this work, the full virome of seven bean samples showing different foliar symptoms was obtained by MinION sequencing. Evidence that emerged from sequencing was validated through RT-PCR and ELISA in a large number of plants, including different ecotypes of Lamon bean and wild herbaceous hosts that may represent a virus reservoir in the field. Results revealed the presence of bean common mosaic virus (BCMV), cucumber mosaic virus (CMV), peanut stunt virus (PSV), and bean yellow mosaic virus (BYMV), which often occurred as mixed infections. Moreover, both CMV and PSV were reported in association with strain-specific satellite RNAs (satRNAs). In conclusion, this work sheds light on the cause of the severe diseases affecting the ‘Lamon bean’ by exploitation of MinION sequencing.
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Affiliation(s)
- Giulia Tarquini
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, I-33100 Udine, Italy; (G.T.); (M.M.); (G.F.)
| | - Marta Martini
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, I-33100 Udine, Italy; (G.T.); (M.M.); (G.F.)
| | - Simone Maestri
- Department of Biotechnology, University of Verona, I-37134 Verona, Italy;
| | - Giuseppe Firrao
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, I-33100 Udine, Italy; (G.T.); (M.M.); (G.F.)
| | - Paolo Ermacora
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, I-33100 Udine, Italy; (G.T.); (M.M.); (G.F.)
- Correspondence:
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20
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Miljanić V, Jakše J, Kunej U, Rusjan D, Škvarč A, Štajner N. Virome Status of Preclonal Candidates of Grapevine Varieties ( Vitis vinifera L.) From the Slovenian Wine-Growing Region Primorska as Determined by High-Throughput Sequencing. Front Microbiol 2022; 13:830866. [PMID: 35265062 PMCID: PMC8899541 DOI: 10.3389/fmicb.2022.830866] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022] Open
Abstract
Diseases caused by viruses and virus-like organisms are one of the major problems in viticulture and grapevine marketing worldwide. Therefore, rapid and accurate diagnosis and identification is crucial. In this study, we used HTS of virus- and viroid-derived small RNAs to determine the virome status of Slovenian preclonal candidates of autochthonous and local grapevine varieties (Vitis vinifera L.). The method applied to the studied vines revealed the presence of nine viruses and two viroids. All viral entities were validated and more than 160 Sanger sequences were generated and deposited in NCBI. In addition, a complete description into the co-infections in each plant studied was obtained. No vine was found to be virus- and viroid-free, and no vine was found to be infected with only one virus or viroid, while the highest number of viral entities in a plant was eight.
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Affiliation(s)
- Vanja Miljanić
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Urban Kunej
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Denis Rusjan
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Andreja Škvarč
- Chamber of Agriculture and Forestry of Slovenia, Agriculture and Forestry Institute Nova Gorica, Nova Gorica, Slovenia
| | - Nataša Štajner
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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Čarija M, Radić T, Černi S, Mucalo A, Zdunić G, Vončina D, Jagunić M, Hančević K. Prevalence of Virus Infections and GLRaV-3 Genetic Diversity in Selected Clones of Croatian Indigenous Grapevine Cultivar Plavac Mali. Pathogens 2022; 11:pathogens11020176. [PMID: 35215120 PMCID: PMC8876015 DOI: 10.3390/pathogens11020176] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/11/2022] [Accepted: 01/26/2022] [Indexed: 12/04/2022] Open
Abstract
The cultivar Plavac Mali (Vitis vinifera L.), the most important indigenous red grapevine cultivar in Croatia, was tested for the presence of 16 grapevine viruses. Thirty-five samples from the collection vineyard were tested for the presence of grapevine leafroll-associated viruses-1, -2, and -3 (GLRaV-1, GLRaV-2 and GLRaV-3, respectively), grapevine fanleaf virus (GFLV), arabis mosaic virus (ArMV), grapevine virus-A (GVA), -B (GVB), -G (GVG), -H (GVH), -I (GVI), -J (GVJ), grapevine fleck virus (GFkV), grapevine rupestris stem pitting associated virus (GRSPaV), and grapevine pinot gris virus (GPGV) by reverse transcription–polymerase chain reaction (RT-PCR). Furthermore, standard PCR was conducted for grapevine badnavirus 1 (GBV-1) and grapevine red blotch virus (GRBV). Mixed infections were most common and GLRaV-3, the most abundant virus found in 85.71% of the vines tested, was further molecularly characterised. Different genomic variants of the heat shock protein homologue (HSP70h) were separated by cloning, detected by single-strand conformation polymorphism (SSCP) analysis, sequenced, and phylogenetically analysed. The presence of phylogenetic groups I and II was only confirmed. This study demonstrates the high virus infection rate of Plavac Mali vines and the heterogeneity of GLRaV-3 present nowadays in a collection vineyard.
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Affiliation(s)
- Mate Čarija
- Institute for Adriatic Crops, 21000 Split, Croatia; (M.Č.); (T.R.); (A.M.); (G.Z.)
| | - Tomislav Radić
- Institute for Adriatic Crops, 21000 Split, Croatia; (M.Č.); (T.R.); (A.M.); (G.Z.)
| | - Silvija Černi
- Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia;
| | - Ana Mucalo
- Institute for Adriatic Crops, 21000 Split, Croatia; (M.Č.); (T.R.); (A.M.); (G.Z.)
| | - Goran Zdunić
- Institute for Adriatic Crops, 21000 Split, Croatia; (M.Č.); (T.R.); (A.M.); (G.Z.)
| | - Darko Vončina
- Department of Plant Pathology, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia; (D.V.); (M.J.)
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), 10000 Zagreb, Croatia
| | - Martin Jagunić
- Department of Plant Pathology, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia; (D.V.); (M.J.)
| | - Katarina Hančević
- Institute for Adriatic Crops, 21000 Split, Croatia; (M.Č.); (T.R.); (A.M.); (G.Z.)
- Correspondence: ; Tel.: +385-21434435
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Fowkes AR, McGreig S, Pufal H, Duffy S, Howard B, Adams IP, Macarthur R, Weekes R, Fox A. Integrating High throughput Sequencing into Survey Design Reveals Turnip Yellows Virus and Soybean Dwarf Virus in Pea ( Pisum Sativum) in the United Kingdom. Viruses 2021; 13:2530. [PMID: 34960799 PMCID: PMC8707713 DOI: 10.3390/v13122530] [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: 11/18/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 12/28/2022] Open
Abstract
There is only limited knowledge of the presence and incidence of viruses in peas within the United Kingdom, therefore high-throughput sequencing (HTS) in combination with a bulk sampling strategy and targeted testing was used to determine the virome in cultivated pea crops. Bulks of 120 leaves collected from twenty fields from around the UK were initially tested by HTS, and presence and incidence of virus was then determined using specific real-time reverse-transcription PCR assays by testing smaller mixed-bulk size samples. This study presents the first finding of turnip yellows virus (TuYV) in peas in the UK and the first finding of soybean dwarf virus (SbDV) in the UK. While TuYV was not previously known to be present in UK peas, it was found in 13 of the 20 sites tested and was present at incidences up to 100%. Pea enation mosaic virus-1, pea enation mosaic virus-2, pea seed-borne mosaic virus, bean yellow mosaic virus, pea enation mosaic virus satellite RNA and turnip yellows virus associated RNA were also identified by HTS. Additionally, a subset of bulked samples were re-sequenced at greater depth to ascertain whether the relatively low depth of sequencing had missed any infections. In each case the same viruses were identified as had been identified using the lower sequencing depth. Sequencing of an isolate of pea seed-borne mosaic virus from 2007 also revealed the presence of TuYV and SbDV, showing that both viruses have been present in the UK for at least a decade, and represents the earliest whole genome of SbDV from Europe. This study demonstrates the potential of HTS to be used as a surveillance tool, or for crop-specific field survey, using a bulk sampling strategy combined with HTS and targeted diagnostics to indicate both presence and incidence of viruses in a crop.
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Affiliation(s)
- Aimee R. Fowkes
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK; (S.M.); (I.P.A.); (R.M.); (R.W.); (A.F.)
| | - Sam McGreig
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK; (S.M.); (I.P.A.); (R.M.); (R.W.); (A.F.)
| | - Hollie Pufal
- School of Natural and Environmental Sciences, University of Newcastle, Newcastle NE1 7RU, UK;
| | - Shona Duffy
- Processors & Growers Research Organisation (PGRO), Peterborough PE8 6HJ, UK; (S.D.); (B.H.)
| | - Becky Howard
- Processors & Growers Research Organisation (PGRO), Peterborough PE8 6HJ, UK; (S.D.); (B.H.)
| | - Ian P. Adams
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK; (S.M.); (I.P.A.); (R.M.); (R.W.); (A.F.)
| | - Roy Macarthur
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK; (S.M.); (I.P.A.); (R.M.); (R.W.); (A.F.)
| | - Rebecca Weekes
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK; (S.M.); (I.P.A.); (R.M.); (R.W.); (A.F.)
| | - Adrian Fox
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK; (S.M.); (I.P.A.); (R.M.); (R.W.); (A.F.)
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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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Evaluation of sensitivity and specificity in RNA-Seq-based detection of grapevine viral pathogens. J Virol Methods 2021; 300:114383. [PMID: 34843827 DOI: 10.1016/j.jviromet.2021.114383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/14/2021] [Accepted: 11/25/2021] [Indexed: 11/22/2022]
Abstract
Virus detection is a crucial step for the implementation of clean stock programs that preserve healthy crop species. Viral infections in grapevine, a vegetatively propagated perennial crop, cannot be eradicated from the vineyards by the application of agrochemicals and must be curtailed at the stage of nursery production during the propagation of planting material. Viral detection is routinely performed using enzyme-linked immunosorbent assays (ELISA) or Reverse Transcription-quantitative Polymerase Chain Reactions (RT-qPCR). High throughput sequencing (HTS) approaches have the potential to detect all viral pathogens in a plant specimen. However, to date, no published HTS-based study has used threshold selection based on ROC curves for discriminating positive from negative samples. To fill this gap, we assessed the specificity and sensitivity of different sequencing and bioinformatics approaches for nine common viruses, which were tested in the same specimens using ELISA and/or RT-qPCR. The normalized detection thresholds giving the best results were 19.28 Fragments Per Kilobase of transcript per Million mapped reads (FPKM) for alignment-based total RNA-Seq approaches, 386 Reads Per Million mapped reads (RPM) for metagenomics-based total RNA-Seq, 1572 FPKM for alignment-based small RNA-Seq analysis and 0.97 % of contigs for de novo analysis of small RNA-Seq data. Validation of the proposed thresholds using independent specimens collected over time from the same stocks and other specimens collected from nearby stocks that had derived from the same propagating material showed that HTS approaches are accurate, with RNA-Seq approaches showing better performance than small RNA-Seq.
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25
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Tarquini G, Pagliari L, Ermacora P, Musetti R, Firrao G. Trigger and Suppression of Antiviral Defenses by Grapevine Pinot Gris Virus (GPGV): Novel Insights into Virus-Host Interaction. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1010-1023. [PMID: 33983824 DOI: 10.1094/mpmi-04-21-0078-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Grapevine Pinot gris virus (GPGV) is an emerging trichovirus that has been putatively associated with a novel grapevine disease known as grapevine leaf mottling and deformation (GLMD). Yet the role of GPGV in GLMD disease is poorly understood, since it has been detected both in symptomatic and symptomless grapevines. We exploited a recently constructed GPGV infectious clone (pRI::GPGV-vir) to induce an antiviral response in Nicotiana benthamiana plants. In silico prediction of virus-derived small interfering RNAs and gene expression analyses revealed the involvement of DCL4, AGO5, and RDR6 genes during GPGV infection, suggesting the activation of the posttranscriptional gene-silencing (PTGS) pathway as a plant antiviral defense. PTGS suppression assays in transgenic N. benthamiana 16c plants revealed the ability of the GPGV coat protein to suppress RNA silencing. This work provides novel insights on the interaction between GPGV and its host, revealing the ability of the virus to trigger and suppress antiviral RNA silencing.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Giulia Tarquini
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine I-33100, Italy
| | - Laura Pagliari
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine I-33100, Italy
| | - Paolo Ermacora
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine I-33100, Italy
| | - Rita Musetti
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine I-33100, Italy
| | - Giuseppe Firrao
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine I-33100, Italy
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26
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Velasco L, Padilla CV. High-Throughput Sequencing of Small RNAs for the Sanitary Certification of Viruses in Grapevine. FRONTIERS IN PLANT SCIENCE 2021; 12:682879. [PMID: 34367209 PMCID: PMC8336637 DOI: 10.3389/fpls.2021.682879] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Biological indexing is the method generally recognized for the certification of propagative grapevines in many countries, and it is mandatory in the European Union. It consists of the evaluation of the plant material after grafting on indicators that are inspected for symptom development. This is a lengthy process that requires well-trained workers, testing field, etc. Alternative diagnostic methods such as serology and RT-qPCR have been discarded for certification because of their intrinsic drawbacks. In turn, high-throughput sequencing (HTS) of plant RNA has been proposed as a plausible alternative to bioassay, but before it is accepted, different aspects of this process must be evaluated. We have compared the HTS of small RNAs with bioassays and other diagnostic methods from a set of 40 grapevine plants submitted for certification. The results allowed the authors the identification of numerous grapevine viruses in the samples, as well as different variants. Besides, relationships between symptom expression and viromes were investigated, in particular leafroll-associated viruses. We compared HTS results using analytical and bioinformatics approaches in order to define minimum acceptable quality standards for certification schemes, resulting in a pipeline proposal. Finally, the comparison between HTS and bioassay resulted favorable for the former in terms of reliability, cost, and timing.
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Affiliation(s)
- Leonardo Velasco
- Instituto Andaluz de Investigación y Formación Agraria, Málaga, Spain
| | - Carlos V. Padilla
- Instituto Murciano de Investigación y Desarrollo Agrario y Alimentario, Murcia, Spain
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Demian E, Holczbauer A, Galbacs ZN, Jaksa-Czotter N, Turcsan M, Olah R, Varallyay E. Variable Populations of Grapevine Virus T Are Present in Vineyards of Hungary. Viruses 2021; 13:1119. [PMID: 34200935 PMCID: PMC8230486 DOI: 10.3390/v13061119] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/04/2021] [Accepted: 06/09/2021] [Indexed: 12/02/2022] Open
Abstract
Grapevine virus T (GVT) is a recently described foveavirus, which was identified from a transcriptome of a Teroldego grapevine cultivar in 2017. Recently, we surveyed vineyards and rootstock plantations in Hungary using small RNA (sRNA) high-throughput sequencing (HTS), at a time when GVT had not yet been described. A re-analysis of our sRNA HTS datasets and a survey of grapevines by RT-PCR revealed the presence of GVT in most of the vineyards tested, while at rootstock fields its presence was very rare. The presence and high variability of the virus in the country was confirmed by sequence analysis of strains originating from different vineyards. In this study, we demonstrate the presence of GVT in Hungary and show its high diversity, suggesting that GVT presence may not seriously affect grapevine health and that it could have been present in European vineyards for a long time as a latent infection.
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Affiliation(s)
- Emese Demian
- Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Ménesi Road 44, H-1118 Budapest, Hungary; (E.D.); (A.H.); (Z.N.G.); (N.J.-C.)
| | - Aliz Holczbauer
- Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Ménesi Road 44, H-1118 Budapest, Hungary; (E.D.); (A.H.); (Z.N.G.); (N.J.-C.)
| | - Zsuzsanna Nagyne Galbacs
- Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Ménesi Road 44, H-1118 Budapest, Hungary; (E.D.); (A.H.); (Z.N.G.); (N.J.-C.)
| | - Nikoletta Jaksa-Czotter
- Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Ménesi Road 44, H-1118 Budapest, Hungary; (E.D.); (A.H.); (Z.N.G.); (N.J.-C.)
| | - Mihaly Turcsan
- Institute for Viticulture and Oenology, Hungarian University of Agriculture and Life Sciences, Villányi Str. 29-43, H-1118 Budapest, Hungary; (M.T.); (R.O.)
| | - Robert Olah
- Institute for Viticulture and Oenology, Hungarian University of Agriculture and Life Sciences, Villányi Str. 29-43, H-1118 Budapest, Hungary; (M.T.); (R.O.)
| | - Eva Varallyay
- Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Ménesi Road 44, H-1118 Budapest, Hungary; (E.D.); (A.H.); (Z.N.G.); (N.J.-C.)
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28
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Survey of five major grapevine viruses infecting Blatina and Žilavka cultivars in Bosnia and Herzegovina. PLoS One 2021; 16:e0245959. [PMID: 33481949 PMCID: PMC7822351 DOI: 10.1371/journal.pone.0245959] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/11/2021] [Indexed: 11/23/2022] Open
Abstract
The sanitary status of grapevines has not yet been considered sufficiently in vineyards throughout Bosnia and Herzegovina (BiH). An extensive survey of five major grapevine viruses in the country was carried out in 2019. A total of 630 samples from the two dominant autochthonous cultivars, named Žilavka and Blatina, were tested by DAS-ELISA for the presence of grapevine leafroll-associated viruses (GLRaV-1 and 3), grapevine fleck virus (GFkV), grapevine fanleaf virus (GFLV) and Arabis mosaic virus (ArMV). Eighty-eight % of the samples were positive for at least one virus, and all five viruses were detected, thought with different incidence, i.e. GLRaV-3 (84%), GFLV (43%), GLRaV-1 (14%), GFkV (10%) and ArMV (0.2%). The majority of infected plants (about 75%) were asymptomatic. Specific virus symptoms were observed in the remaining infected plants, together with the reported GLRaV vectors, Planococcus ficus and Parthenolecanium corni, while nematodes of the Xiphinema genus were not found in the GFLV- or ArMV-infected vineyards. The GLRaV-3 CP phylogenetic analyses showed 75–100% nucleotide identity between the BiH and reference isolates, and the BiH isolates clustered into the major group. The dNS/dS ratio indicated a negative selection of the virus population, and the lack of geographical structuring within the population was observed. In addition, putative GLRaV-3 recombinants with breakpoints in the 5’ of the CP gene were detected, while no recombinant strains were identified for the other four viruses. The obtained results indicate a deteriorated sanitary status of the cultivated grapevines, the prevalence and intraspecies genetic diversity of GLRaV-3 throughout the country. The establishment of certified grapevine material and adequate virus vector control is therefore of primary importance to prevent further spread of these viruses. This study presents the results of the first molecular characterisation of grapevine viruses in Bosnia and Herzegovina.
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29
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HTS-Based Monitoring of the Efficiency of Somatic Embryogenesis and Meristem Cultures Used for Virus Elimination in Grapevine. PLANTS 2020; 9:plants9121782. [PMID: 33339181 PMCID: PMC7765609 DOI: 10.3390/plants9121782] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/12/2020] [Accepted: 12/14/2020] [Indexed: 11/17/2022]
Abstract
Meristem culture and somatic embryogenesis are effective tools for virus elimination of vegetatively propagated crops including grapevine (Vitis vinifera L.). While both have been shown to be useful to eliminate the main grapevine viruses, their efficiency differs depending on the virus and grapevine variety. In our work, we investigated the efficiency of these two virus elimination methods using small RNA high-throughput sequencing (HTS) and RT-PCR as virus diagnostics. Field grown mother plants of four clones representing three cultivars, infected with different viruses and viroids, were selected for elimination via somatic embryogenesis (SE) and meristem culture (ME). Our results show for the first time that using SE, elimination in mother plants was effective for all viruses, i.e., grapevine rupestris vein feathering virus (GRVFV), grapevine Syrah virus 1 (GSyV-1), Grapevine virus T (GVT) and grapevine Pinot gris virus (GPGV). This study also confirms previous studies showing that SE is a possible strategy for the elimination of GFkV, GRSPaV, HSVd, and GYSVd-1. Our results demonstrate that the efficacy of virus elimination via SE is relatively high while the purging of viroids is lower. Our work provides evidence that the efficiency of SE is comparable to that of the technically difficult ME technique, and that SE will offer a more effective strategy for the production of virus-free grapevine in the future.
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30
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Gaafar YZA, Herz K, Hartrick J, Fletcher J, Blouin AG, MacDiarmid R, Ziebell H. Investigating the Pea Virome in Germany-Old Friends and New Players in the Field(s). Front Microbiol 2020; 11:583242. [PMID: 33281777 PMCID: PMC7691430 DOI: 10.3389/fmicb.2020.583242] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/28/2020] [Indexed: 12/21/2022] Open
Abstract
Peas are an important legume for human and animal consumption and are also being used as green manure or intermediate crops to sustain and improve soil condition. Pea production faces constraints from fungal, bacterial, and viral diseases. We investigated the virome of German pea crops over the course of three successive seasons in different regions of pea production to gain an overview of the existing viruses. Pools from 540 plants, randomly selected from symptomatic and asymptomatic peas, and non-crop plants surrounding the pea fields were used for ribosomal RNA-depleted total RNA extraction followed by high-throughput sequencing (HTS) and RT-PCR confirmation. Thirty-five different viruses were detected in addition to nine associated nucleic acids. From these viruses, 25 are classified as either new viruses, novel strains or viruses that have not been reported previously from Germany. Pea enation mosaic virus 1 and 2 were the most prevalent viruses detected in the pea crops, followed by pea necrotic yellow dwarf virus (PNYDV) and turnip yellows virus which was also found also in the surrounding non-legume weeds. Moreover, a new emaravirus was detected in symptomatic peas in one region for two successive seasons. Most of the identified viruses are known to be aphid transmissible. The results revealed a high virodiversity in the German pea fields that poses new challenges to diagnosticians, researchers, risk assessors and policy makers, as the impact of the new findings are currently unknown.
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Affiliation(s)
- Yahya Z A Gaafar
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Kerstin Herz
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Jonas Hartrick
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - John Fletcher
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Arnaud G Blouin
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand.,School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Robin MacDiarmid
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand.,School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Heiko Ziebell
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
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31
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Ekrami E, Pouresmaieli M, Barati F, Asghari S, Ziarani FR, Shariati P, Mamoudifard M. Potential Diagnostic Systems for Coronavirus Detection: a Critical Review. Biol Proced Online 2020; 22:21. [PMID: 32884452 PMCID: PMC7462115 DOI: 10.1186/s12575-020-00134-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/23/2020] [Indexed: 02/06/2023] Open
Abstract
Abstract Currently there are no effective anti-viral drugs for SARS-CoV-2, so the primary line of defense is to detect infected cases as soon as possible. The high rate of contagion for this virus and the highly nonspecific symptoms of the disease (Coronovirus disease 2019, (Covid-19)) that it causes, such as respiratory symptoms, cough, dyspnea, fever, and viral pneumonia, require the urgent establishment of precise and fast diagnostic tests to verify suspected cases, screen patients, and conduct virus surveillance. Nowadays, several virus detection methods are available for viral diseases, which act on specific properties of each virus or virus family, therefore, further investigations and trials are needed to find a highly efficient and accurate detection method to detect and prevent the outcomes of the disease. Hence, there is an urgent need for more and precise studies in this field. In this review, we discussed the properties of a new generation of coronaviruses (SARS-CoV-2) following routine virus detection methods and proposed new strategies and the use of potential samples for SARS-CoV-2 detection. Graphical Abstract ![]()
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Affiliation(s)
- Elena Ekrami
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Mahdi Pouresmaieli
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Fatemeh Barati
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Sahar Asghari
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Farzad Ramezani Ziarani
- Department of Microbiology, School of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Parvin Shariati
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Matin Mamoudifard
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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32
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Sidharthan VK, Sevanthi AM, Jaiswal S, Baranwal VK. Robust Virome Profiling and Whole Genome Reconstruction of Viruses and Viroids Enabled by Use of Available mRNA and sRNA-Seq Datasets in Grapevine ( Vitis vinifera L.). Front Microbiol 2020; 11:1232. [PMID: 32582126 PMCID: PMC7289960 DOI: 10.3389/fmicb.2020.01232] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/14/2020] [Indexed: 12/19/2022] Open
Abstract
Next-generation sequencing (NGS) based virome analyses of mRNA and sRNA have recently become a routine approach for reliable detection of plant viruses and viroids. In the present study we identified the viral/viroidal spectrum of several Indian grapevine cultivars and reconstructed their whole genomes using the publically available mRNAome and sRNAome datasets. Twenty three viruses and viroids (including two variants of grapevine leafroll associated virus 4) were identified from two tissues (fruit peels and young leaves) of three cultivars among which nine unique grapevine viruses and viroids were identified for the first time in India. Irrespective of the assemblers and tissues used, the mRNA based approach identified more acellular pathogens than the sRNA based approach across cultivars. Further, the mRNAome was on par with the whole transcriptome in viral identification. Through de novo assembly of transcriptomes followed by mapping against reference genome, we reconstructed 19 complete/near complete genomes of identified viruses and viroids. The reconstructed viral genomes included four larger RNA genomes (>13 kb), a DNA genome (RG grapevine geminivirus A), a divergent genome (RG grapevine virus B) and a genome for which no reference is available (RG grapevine virus L). A large number of SNPs detected in this study ascertained the quasispecies nature of viruses. Detection of three recombination events and phylogenetic analyses using reconstructed genomes suggested the possible introduction of viruses and viroids into India from several continents through the planting material. The whole genome sequences generated in this study can serve as a resource for reliable indexing of grapevine viruses and viroids in quarantine stations and certification programs.
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Affiliation(s)
- V Kavi Sidharthan
- Division of Plant Pathology, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi, India
| | - Amitha Mithra Sevanthi
- Indian Council of Agricultural Research-National Institute for Plant Biotechnology, New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - V K Baranwal
- Division of Plant Pathology, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi, India
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33
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Rubio L, Galipienso L, Ferriol I. Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution. FRONTIERS IN PLANT SCIENCE 2020; 11:1092. [PMID: 32765569 PMCID: PMC7380168 DOI: 10.3389/fpls.2020.01092] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/02/2020] [Indexed: 05/04/2023]
Abstract
Plant viruses cause considerable economic losses and are a threat for sustainable agriculture. The frequent emergence of new viral diseases is mainly due to international trade, climate change, and the ability of viruses for rapid evolution. Disease control is based on two strategies: i) immunization (genetic resistance obtained by plant breeding, plant transformation, cross-protection, or others), and ii) prophylaxis to restrain virus dispersion (using quarantine, certification, removal of infected plants, control of natural vectors, or other procedures). Disease management relies strongly on a fast and accurate identification of the causal agent. For known viruses, diagnosis consists in assigning a virus infecting a plant sample to a group of viruses sharing common characteristics, which is usually referred to as species. However, the specificity of diagnosis can also reach higher taxonomic levels, as genus or family, or lower levels, as strain or variant. Diagnostic procedures must be optimized for accuracy by detecting the maximum number of members within the group (sensitivity as the true positive rate) and distinguishing them from outgroup viruses (specificity as the true negative rate). This requires information on the genetic relationships within-group and with members of other groups. The influence of the genetic diversity of virus populations in diagnosis and disease management is well documented, but information on how to integrate the genetic diversity in the detection methods is still scarce. Here we review the techniques used for plant virus diagnosis and disease control, including characteristics such as accuracy, detection level, multiplexing, quantification, portability, and designability. The effect of genetic diversity and evolution of plant viruses in the design and performance of some detection and disease control techniques are also discussed. High-throughput or next-generation sequencing provides broad-spectrum and accurate identification of viruses enabling multiplex detection, quantification, and the discovery of new viruses. Likely, this technique will be the future standard in diagnostics as its cost will be dropping and becoming more affordable.
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Affiliation(s)
- Luis Rubio
- Centro de Protección Vegetal y Biotecnology, Instituto Valenciano de Investigaciones Agrarias, Moncada, Spain
- *Correspondence: Luis Rubio,
| | - Luis Galipienso
- Centro de Protección Vegetal y Biotecnology, Instituto Valenciano de Investigaciones Agrarias, Moncada, Spain
| | - Inmaculada Ferriol
- Plant Responses to Stress Programme, Centre for Research in Agricultural Genomics (CRAG-CSIC_UAB-UB) Cerdanyola del Vallès, Barcelona, Spain
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34
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Garcia S, Hily JM, Komar V, Gertz C, Demangeat G, Lemaire O, Vigne E. Detection of Multiple Variants of Grapevine Fanleaf Virus in Single Xiphinema index Nematodes. Viruses 2019; 11:v11121139. [PMID: 31835488 PMCID: PMC6950412 DOI: 10.3390/v11121139] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/08/2019] [Accepted: 12/05/2019] [Indexed: 11/16/2022] Open
Abstract
Grapevine fanleaf virus (GFLV) is responsible for a widespread disease in vineyards worldwide. Its genome is composed of two single-stranded positive-sense RNAs, which both show a high genetic diversity. The virus is transmitted from grapevine to grapevine by the ectoparasitic nematode Xiphinema index. Grapevines in diseased vineyards are often infected by multiple genetic variants of GFLV but no information is available on the molecular composition of virus variants retained in X. index following nematodes feeding on roots. In this work, aviruliferous X. index were fed on three naturally GFLV-infected grapevines for which the virome was characterized by RNAseq. Six RNA-1 and four RNA-2 molecules were assembled segregating into four and three distinct phylogenetic clades of RNA-1 and RNA-2, respectively. After 19 months of rearing, single and pools of 30 X. index tested positive for GFLV. Additionally, either pooled or single X. index carried multiple variants of the two GFLV genomic RNAs. However, the full viral genetic diversity found in the leaves of infected grapevines was not detected in viruliferous nematodes, indicating a genetic bottleneck. Our results provide new insights into the complexity of GFLV populations and the putative role of X. index as reservoirs of virus diversity.
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Affiliation(s)
- Shahinez Garcia
- Unité Mixte de Recherche (UMR) Santé de la Vigne et Qualité du Vin, Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg, BP 20507, 68021 Colmar Cedex, France; (S.G.); (V.K.); (C.G.); (G.D.); (O.L.)
| | - Jean-Michel Hily
- Unité Mixte de Recherche (UMR) Santé de la Vigne et Qualité du Vin, Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg, BP 20507, 68021 Colmar Cedex, France; (S.G.); (V.K.); (C.G.); (G.D.); (O.L.)
- Institut Français de la Vigne et du Vin (IFV), 30240 Le Grau-Du-Roi, France
| | - Véronique Komar
- Unité Mixte de Recherche (UMR) Santé de la Vigne et Qualité du Vin, Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg, BP 20507, 68021 Colmar Cedex, France; (S.G.); (V.K.); (C.G.); (G.D.); (O.L.)
| | - Claude Gertz
- Unité Mixte de Recherche (UMR) Santé de la Vigne et Qualité du Vin, Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg, BP 20507, 68021 Colmar Cedex, France; (S.G.); (V.K.); (C.G.); (G.D.); (O.L.)
| | - Gérard Demangeat
- Unité Mixte de Recherche (UMR) Santé de la Vigne et Qualité du Vin, Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg, BP 20507, 68021 Colmar Cedex, France; (S.G.); (V.K.); (C.G.); (G.D.); (O.L.)
| | - Olivier Lemaire
- Unité Mixte de Recherche (UMR) Santé de la Vigne et Qualité du Vin, Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg, BP 20507, 68021 Colmar Cedex, France; (S.G.); (V.K.); (C.G.); (G.D.); (O.L.)
| | - Emmanuelle Vigne
- Unité Mixte de Recherche (UMR) Santé de la Vigne et Qualité du Vin, Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg, BP 20507, 68021 Colmar Cedex, France; (S.G.); (V.K.); (C.G.); (G.D.); (O.L.)
- Correspondence: ; Tel.: +33-389-224-955
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Bragard C, Dehnen-Schmutz K, Gonthier P, Jacques MA, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Milonas P, Navas-Cortes JA, Parnell S, Potting R, Reignault PL, Thulke HH, Van der Werf W, Vicent Civera A, Yuen J, Zappalà L, Candresse T, Chatzivassiliou E, Finelli F, Martelli GP, Winter S, Bosco D, Chiumenti M, Di Serio F, Kaluski T, Minafra A, Rubino L. Pest categorisation of non-EU viruses and viroids of Vitis L. EFSA J 2019; 17:e05669. [PMID: 32626420 PMCID: PMC7009087 DOI: 10.2903/j.efsa.2019.5669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Following a request from the EU Commission, the Panel on Plant Health addressed the pest categorisation of the viruses and viroids of Vitis L. determined as being either non-EU or of undetermined standing in a previous EFSA opinion. These infectious agents belong to different genera and are heterogeneous in their biology. With the exclusion of grapevine virus 101-14.N.23.9.1/South Africa/2009 for which very limited information exists, the pest categorisation was completed for 30 viruses or viroids having acknowledged identities and available detection methods. All these viruses are efficiently transmitted by vegetative propagation techniques, with plants for planting representing the major pathway for long-distance dispersal and thus considered as the major pathway for potential entry. Depending on the virus, additional pathway(s) can also be seeds, pollen and/or vector(s). Most of the viruses categorised here are known to infect only one or few plant genera, but some of them have a wide host range, thus extending the possible entry pathways. Grapevine yellow speckle viroid 2, blueberry leaf mottle virus, grapevine Ajinashika virus, grapevine Anatolian ringspot virus, grapevine berry inner necrosis virus, grapevine deformation virus, grapevine fabavirus, grapevine red blotch virus, grapevine stunt virus, grapevine Tunisian ringspot virus, grapevine vein-clearing virus, temperate fruit decay-associated virus, peach rosette mosaic virus, tobacco ringspot virus, tomato ringspot virus meet all the criteria evaluated by EFSA to qualify as potential Union quarantine pests (QPs). With the exception of impact for the EU territory, on which the Panel was unable to conclude, blackberry virus S, grapevine geminivirus A, grapevine leafroll-associated virus 7, grapevine leafroll-associated virus 13, grapevine satellite virus, grapevine virus E, grapevine virus I, grapevine virus J, grapevine virus S, summer grape enamovirus, summer grape latent virus satisfy all the other criteria to be considered as potential Union QPs. Australian grapevine viroid, grapevine cryptic virus 1, grapevine endophyte endornavirus and wild vitis virus 1 do not meet all the criteria evaluated by EFSA to be regarded as potential Union QPs because they are not known to cause an impact on Vitis. For several viruses, especially those recently discovered, the categorisation is associated with high uncertainties mainly because of the absence of data on their biology, distribution and impact. Since this opinion addresses specifically non-EU viruses, in general these viruses do not meet the criteria assessed by EFSA to qualify as a potential Union regulated non-quarantine pests.
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Bragard C, Dehnen-Schmutz K, Gonthier P, Jacques MA, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Milonas P, Navas-Cortes JA, Parnell S, Potting R, Reignault PL, Thulke HH, der Werf WV, Vicent Civera A, Yuen J, Zappalà L, Candresse T, Chatzivassiliou E, Winter S, Chiumenti M, Di Serio F, Kaluski T, Minafra A, Rubino L. List of non-EU viruses and viroids of Cydonia Mill., Fragaria L., Malus Mill., Prunus L., Pyrus L., Ribes L., Rubus L. and Vitis L. EFSA J 2019; 17:e05501. [PMID: 32626418 PMCID: PMC7009187 DOI: 10.2903/j.efsa.2019.5501] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The Panel on Plant Health performed a listing of non-EU viruses and viroids (reported hereinafter as viruses) of Cydonia Mill., Fragaria L., Malus Mill., Prunus L., Pyrus L., Ribes L., Rubus L. and Vitis L. A systematic literature review identified 197 viruses infecting one or more of the host genera under consideration. Viruses were allocated into three categories (i) 86 non-EU viruses, known to occur only outside the EU or having only limited presence in the EU (i.e. reported in only one or few Member States (MSs), known to have restricted distribution, outbreaks), (ii) 97 viruses excluded at this stage from further categorisation efforts because they have significant presence in the EU (i.e. only reported so far from the EU or known to occur or be widespread in some MSs or frequently reported in the EU), (iii) 14 viruses with undetermined standing for which available information did not readily allow to allocate to one or the other of the two above groups. Comments provided by MSs during consultation phases were integrated in the opinion. The main knowledge gaps and uncertainties of this listing concern (i) the geographic distribution and prevalence of the viruses analysed, in particular when they were recently described; (ii) the taxonomy and biological status of a number of poorly characterised viruses; (iii) the host status of particular plant genera in relation to some viruses. The viruses considered as non-EU and those with undetermined standing will be categorised in the next steps to answer a specific mandate from the Commission to develop pest categorisations for non-EU viruses. This list does not imply a prejudice on future needs for a pest categorisation for other viruses which are excluded from the current categorisation efforts.
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Pooggin MM. Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization. Front Microbiol 2018; 9:2779. [PMID: 30524398 PMCID: PMC6256188 DOI: 10.3389/fmicb.2018.02779] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/30/2018] [Indexed: 11/13/2022] Open
Abstract
RNA interference (RNAi)-based antiviral defense generates small interfering RNAs that represent the entire genome sequences of both RNA and DNA viruses as well as viroids and viral satellites. Therefore, deep sequencing and bioinformatics analysis of small RNA population (small RNA-ome) allows not only for universal virus detection and genome reconstruction but also for complete virome reconstruction in mixed infections. Viral infections (like other stress factors) can also perturb the RNAi and gene silencing pathways regulating endogenous gene expression and repressing transposons and host genome-integrated endogenous viral elements which can potentially be released from the genome and contribute to disease. This review describes the application of small RNA-omics for virus detection, virome reconstruction and antiviral defense characterization in cultivated and non-cultivated plants. Reviewing available evidence from a large and ever growing number of studies of naturally or experimentally infected hosts revealed that all families of land plant viruses, their satellites and viroids spawn characteristic small RNAs which can be assembled into contigs of sufficient length for virus, satellite or viroid identification and for exhaustive reconstruction of complex viromes. Moreover, the small RNA size, polarity and hotspot profiles reflect virome interactions with the plant RNAi machinery and allow to distinguish between silent endogenous viral elements and their replicating episomal counterparts. Models for the biogenesis and functions of small interfering RNAs derived from all types of RNA and DNA viruses, satellites and viroids as well as endogenous viral elements are presented and discussed.
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Affiliation(s)
- Mikhail M. Pooggin
- Institut National de la Recherche Agronomique, UMR BGPI, Montpellier, France
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38
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Beuve M, Hily JM, Alliaume A, Reinbold C, Le Maguet J, Candresse T, Herrbach E, Lemaire O. A complex virome unveiled by deep sequencing analysis of RNAs from a French Pinot Noir grapevine exhibiting strong leafroll symptoms. Arch Virol 2018; 163:2937-2946. [PMID: 30033497 DOI: 10.1007/s00705-018-3949-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 05/11/2018] [Indexed: 11/25/2022]
Abstract
We have characterized the virome of a grapevine Pinot Noir accession (P70) that displayed, over the year, very stable and strong leafroll symptoms. For this, we have used two extraction methods (dsRNA and total RNA) coupled with the high throughput sequencing (HTS) Illumina technique. While a great disparity in viral sequences were observed, both approaches gave similar results, revealing a very complex infection status. Five virus and viroid isolates [Grapevine leafroll-associated viruse-1 (GLRaV-1), Grapevine virus A (GVA), Grapevine rupestris stem pitting-associated virus (GRSPaV), Hop stunt viroid (HSVd) and Grapevine yellow speckle viroid 1 (GYSVd1)] were detected in P70 with a grand total of eleven variants being identified and de novo assembled. A comparison between both extraction methods regarding their power to detect viruses and the ease of genome assembly is also provided.
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Affiliation(s)
- Monique Beuve
- SVQV, Université de Strasbourg, 68000, Colmar, France
| | | | | | | | - Jean Le Maguet
- SVQV, Université de Strasbourg, 68000, Colmar, France
- Institut Français des Productions Cidricoles (IFPC), 61500, Sées, France
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Villenave d'Ornon Cedex, France
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Baráth D, Jaksa-Czotter N, Molnár J, Varga T, Balássy J, Szabó LK, Kirilla Z, Tusnády GE, Preininger É, Várallyay É. Small RNA NGS Revealed the Presence of Cherry Virus A and Little Cherry Virus 1 on Apricots in Hungary. Viruses 2018; 10:E318. [PMID: 29891760 PMCID: PMC6024520 DOI: 10.3390/v10060318] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/08/2018] [Accepted: 06/09/2018] [Indexed: 12/14/2022] Open
Abstract
Fruit trees, such as apricot trees, are constantly exposed to the attack of viruses. As they are propagated in a vegetative way, this risk is present not only in the field, where they remain for decades, but also during their propagation. Metagenomic diagnostic methods, based on next generation sequencing (NGS), offer unique possibilities to reveal all the present pathogens in the investigated sample. Using NGS of small RNAs, a special field of these techniques, we tested leaf samples of different varieties of apricot originating from an isolator house or open field stock nursery. As a result, we identified Cherry virus A (CVA) and little cherry virus 1 (LChV-1) for the first time in Hungary. The NGS results were validated by RT-PCR and also by Northern blot in the case of CVA. Cloned and Sanger sequenced viral-specific PCR products enabled us to investigate their phylogenetic relationships. However, since these pathogens have not been described in our country before, their role in symptom development and modification during co-infection with other viruses requires further investigation.
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Affiliation(s)
- Dániel Baráth
- Agricultural Biotechnology Institute, NARIC, 2100 Gödöllő, Hungary.
| | | | - János Molnár
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, 7632 Pécs, Hungary.
| | - Tünde Varga
- Agricultural Biotechnology Institute, NARIC, 2100 Gödöllő, Hungary.
| | - Júlia Balássy
- Agricultural Biotechnology Institute, NARIC, 2100 Gödöllő, Hungary.
| | | | - Zoltán Kirilla
- Fruitculture Research Institute, NARIC, 1223 Budapest, Hungary.
| | - Gábor E Tusnády
- Institute of Enzymology, Research Center of Natural Sciences, HAS, 1117 Budapest, Hungary.
| | - Éva Preininger
- Fruitculture Research Institute, NARIC, 1223 Budapest, Hungary.
| | - Éva Várallyay
- Agricultural Biotechnology Institute, NARIC, 2100 Gödöllő, Hungary.
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