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Gholampour Z, Zakiaghl M, Asquini E, Moser M, Gualandri V, Mehrvar M, Si-Ammour A. Application of High-Throughput Sequencing for Comprehensive Virome Profiling in Grapevines Shows Yellows in Iran. Viruses 2024; 16:204. [PMID: 38399980 PMCID: PMC10891595 DOI: 10.3390/v16020204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/25/2024] Open
Abstract
A comprehensive study on the whole spectrum of viruses and viroids in five Iranian grapevine cultivars was carried out using sRNA libraries prepared from phloem tissue. A comparison of two approaches to virus detection from sRNAome data indicated a significant difference in the results and performance of the aligners in viral genome reconstruction. The results showed a complex virome in terms of viral composition, abundance, and richness. Thirteen viruses and viroids were identified in five Iranian grapevine cultivars, among which the grapevine red blotch virus and grapevine satellite virus were detected for the first time in Iranian vineyards. Grapevine leafroll-associated virus 1 (GLRaV1) and grapevine fanleaf virus (GFLV) were highly dominant in the virome. However, their frequency and abundance were somewhat different among grapevine cultivars. The results revealed a mixed infection of GLRaV1/grapevine yellow speckle viroid 1 (GYSVd1) and GFLV/GYSVd1 in grapevines that exhibited yellows and vein banding. We also propose a threshold of 14% of complete reconstruction as an appropriate threshold for detection of grapevine viruses that can be used as indicators for reliable grapevine virome profiling or in quarantine stations and certification programs.
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Affiliation(s)
- Zahra Gholampour
- Department of Plant Pathology, College of Agriculture, Ferdowsi University of Mashhad, Mashhad 9177948978, Iran; (Z.G.); (M.M.)
| | - Mohammad Zakiaghl
- Department of Plant Pathology, College of Agriculture, Ferdowsi University of Mashhad, Mashhad 9177948978, Iran; (Z.G.); (M.M.)
| | - Elisa Asquini
- Research and Innovation Center, Fondazione Edmund Mach, 38098 San Michele All’Adige, Italy; (E.A.); (M.M.); (V.G.)
| | - Mirko Moser
- Research and Innovation Center, Fondazione Edmund Mach, 38098 San Michele All’Adige, Italy; (E.A.); (M.M.); (V.G.)
| | - Valeria Gualandri
- Research and Innovation Center, Fondazione Edmund Mach, 38098 San Michele All’Adige, Italy; (E.A.); (M.M.); (V.G.)
| | - Mohsen Mehrvar
- Department of Plant Pathology, College of Agriculture, Ferdowsi University of Mashhad, Mashhad 9177948978, Iran; (Z.G.); (M.M.)
| | - Azeddine Si-Ammour
- Research and Innovation Center, Fondazione Edmund Mach, 38098 San Michele All’Adige, Italy; (E.A.); (M.M.); (V.G.)
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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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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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Lelwala RV, LeBlanc Z, Gauthier MEA, Elliott CE, Constable FE, Murphy G, Tyle C, Dinsdale A, Whattam M, Pattemore J, Barrero RA. Implementation of GA-VirReport, a Web-Based Bioinformatics Toolkit for Post-Entry Quarantine Screening of Virus and Viroids in Plants. Viruses 2022; 14:v14071480. [PMID: 35891459 PMCID: PMC9317486 DOI: 10.3390/v14071480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/29/2022] [Accepted: 06/29/2022] [Indexed: 02/01/2023] Open
Abstract
High-throughput sequencing (HTS) of host plant small RNA (sRNA) is a popular approach for plant virus and viroid detection. The major bottlenecks for implementing this approach in routine virus screening of plants in quarantine include lack of computational resources and/or expertise in command-line environments and limited availability of curated plant virus and viroid databases. We developed: (1) virus and viroid report web-based bioinformatics workflows on Galaxy Australia called GA-VirReport and GA-VirReport-Stats for detecting viruses and viroids from host plant sRNA extracts and (2) a curated higher plant virus and viroid database (PVirDB). We implemented sRNA sequencing with unique dual indexing on a set of plants with known viruses. Sequencing data were analyzed using GA-VirReport and PVirDB to validate these resources. We detected all known viruses in this pilot study with no cross-sample contamination. We then conducted a large-scale diagnosis of 105 imported plants processed at the post-entry quarantine facility (PEQ), Australia. We detected various pathogens in 14 imported plants and discovered that de novo assembly using 21–22 nt sRNA fraction and the megablast algorithm yielded better sensitivity and specificity. This study reports the successful, large-scale implementation of HTS and a user-friendly bioinformatics workflow for virus and viroid screening of imported plants at the PEQ.
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Affiliation(s)
- Ruvini V. Lelwala
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD 4001, Australia; (R.V.L.); (Z.L.); (M.-E.A.G.)
- Science and Surveillance Group, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia; (C.E.E.); (J.P.)
| | - Zacharie LeBlanc
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD 4001, Australia; (R.V.L.); (Z.L.); (M.-E.A.G.)
| | - Marie-Emilie A. Gauthier
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD 4001, Australia; (R.V.L.); (Z.L.); (M.-E.A.G.)
| | - Candace E. Elliott
- Science and Surveillance Group, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia; (C.E.E.); (J.P.)
| | - Fiona E. Constable
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia;
| | - Greg Murphy
- Technology Infrastructure Branch, Information Services Division, Department of Agriculture, Fisheries and Forestry, Canberra, ACT 2601, Australia; (G.M.); (C.T.)
| | - Callum Tyle
- Technology Infrastructure Branch, Information Services Division, Department of Agriculture, Fisheries and Forestry, Canberra, ACT 2601, Australia; (G.M.); (C.T.)
| | - Adrian Dinsdale
- Plant Innovation Centre, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia; (A.D.); (M.W.)
| | - Mark Whattam
- Plant Innovation Centre, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia; (A.D.); (M.W.)
| | - Julie Pattemore
- Science and Surveillance Group, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia; (C.E.E.); (J.P.)
| | - Roberto A. Barrero
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD 4001, Australia; (R.V.L.); (Z.L.); (M.-E.A.G.)
- Correspondence:
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