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Marais A, Gentit P, Brans Y, Renvoisé JP, Faure C, Saison A, Cousseau P, Castaing J, Chambon F, Pion A, Calado G, Lefebvre M, Garnier S, Latour F, Bresson K, Grasseau N, Candresse T. Comparative Performance Evaluation of Double-Stranded RNA High-Throughput Sequencing for the Detection of Viral Infection in Temperate Fruit Crops. PHYTOPATHOLOGY 2024:PHYTO12230480R. [PMID: 38376958 DOI: 10.1094/phyto-12-23-0480-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
There is limited information on the compared performances of biological, serological. and molecular assays with high-throughput sequencing (HTS) for viral indexing in temperate fruit crops. Here, using a range of samples of predetermined virological status, we compared two performance criteria (inclusivity and analytical sensitivity) of enzyme-linked immunosorbent assay (ELISA), molecular hybridization, reverse transcription (RT)-PCR, and double-stranded RNA (dsRNA) HTS for the detection of a total of 14 viruses (10 genera) and four viroids (three genera). When undiluted samples from individual plants were used, ELISA had the lowest performance, with an overall detection rate of 68.7%, followed by RT-PCR (82.5%) and HTS (90.7%; 100% if considering only viruses). The lower performance of RT-PCR reflected the inability to amplify some isolates as a consequence of point mutations affecting primer-binding sites. In addition, HTS identified viruses that had not been identified by other assays in nearly two-thirds of the samples. Analysis of serial dilutions of fruit tree samples allowed comparison of analytical sensitivities for various viruses. ELISA showed the lowest analytical sensitivity, but RT-PCR showed higher analytical sensitivity than HTS for most of the samples. Overall, these results confirm the superiority of HTS over biological indexing in terms of speed and inclusivity and show that while the absolute analytical sensitivity of RT-PCR tends to be higher than that of HTS, PCR inclusivity is affected by viral genetic diversity. Taken together, these results make a strong case for the implementation of HTS-based approaches in fruit tree viral testing protocols supporting quarantine and certification programs.
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Affiliation(s)
- Armelle Marais
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Pascal Gentit
- ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM, 7 rue Jean Dixméras, 49044 Angers Cedex 01, France
| | - Yoann Brans
- CTIFL, Laboratoire de virologie fruitière, Centre de Lanxade, 24130 Prigonrieux, France
| | | | - Chantal Faure
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Anne Saison
- ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM, 7 rue Jean Dixméras, 49044 Angers Cedex 01, France
| | - Pascaline Cousseau
- ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM, 7 rue Jean Dixméras, 49044 Angers Cedex 01, France
| | - Julie Castaing
- CTIFL, Laboratoire de virologie fruitière, Centre de Lanxade, 24130 Prigonrieux, France
| | - Fabien Chambon
- ANSES, Plant Health Laboratory, Unité de Quarantaine, 63370 Lempdes, France
| | - Angélique Pion
- ANSES, Plant Health Laboratory, Unité de Quarantaine, 63370 Lempdes, France
| | - Grégory Calado
- ANSES, Plant Health Laboratory, Unité de Quarantaine, 63370 Lempdes, France
| | - Marie Lefebvre
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Soraya Garnier
- ANSES, Plant Health Laboratory, Unité de Quarantaine, 63370 Lempdes, France
| | - François Latour
- CTIFL, Laboratoire de virologie fruitière, Centre de Lanxade, 24130 Prigonrieux, France
| | - Kévin Bresson
- CTIFL, Laboratoire de virologie fruitière, Centre de Lanxade, 24130 Prigonrieux, France
| | - Nathalie Grasseau
- CTIFL, Laboratoire de virologie fruitière, Centre de Lanxade, 24130 Prigonrieux, France
| | - Thierry Candresse
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
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Alvarez-Quinto R, Grinstead S, Kinard G, Martin R, Mollov D. Complete genome sequence of vaccinium-associated virus C, a new member of the family Totiviridae from Vaccinium floribundum. Arch Virol 2024; 169:86. [PMID: 38558201 DOI: 10.1007/s00705-024-06008-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 02/15/2024] [Indexed: 04/04/2024]
Abstract
Blueberries (Vaccinium sp.) are a major crop grown in the Pacific Northwest region. Currently, there are at least 17 known viruses that infect blueberry plants, and some of them cause a wide range of symptoms and economic losses. A new virus, vaccinium-associated virus C (VaVC) (family Totiviridae, genus Totivirus) was identified in an imported blueberry accession from the USDA-ARS National Clonal Germplasm Repository in Corvallis, Oregon. The complete genomic sequence of VaVC was determined, but the biological significance of VaVC is unknown and requires further study. Additional Vaccinium sp. accessions should be screened to investigate the incidence of this new virus.
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Affiliation(s)
- Robert Alvarez-Quinto
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97333, USA
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Samuel Grinstead
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD, 20705, USA
| | - Gary Kinard
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD, 20705, USA
| | - Robert Martin
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97333, USA
| | - Dimitre Mollov
- USDA-ARS, Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR, 97330, USA.
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Ho T, Broome JC, Buhler JP, O'Donovan W, Tian T, Diaz-Lara A, Martin RR, Tzanetakis IE. Integration of Rubus yellow net virus in the raspberry genome: A story centuries in the making. Virology 2024; 591:109991. [PMID: 38242059 DOI: 10.1016/j.virol.2024.109991] [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: 10/29/2023] [Revised: 12/16/2023] [Accepted: 01/08/2024] [Indexed: 01/21/2024]
Abstract
Rubus yellow net virus (RYNV) belongs to genus Badnavirus. Badnaviruses are found in plants as endogenous, inactive or activatable sequences, and/or in episomal (infectious and active) forms. To assess the state of RYNV in Rubus germplasm, we sequenced the genomes of various cultivars and mined eight raspberry whole genome datasets. Bioinformatics analysis revealed the presence of a diverse array of endogenous RYNV (endoRYNV) sequences that differ significantly in their structure; some lineages have nearly complete, yet non-functional genomes whereas others have rudimentary, short sequence fragments. We developed assays to genotype the main lineages as well as the only known episomal lineage present in the United States. This study discloses the widespread presence of endoRYNVs in commercial raspberries, likely because breeding efforts have focused on a limited pool of germplasm that harbored endoRYNVs.
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Affiliation(s)
- Thien Ho
- Driscoll's Inc., Watsonville, CA, 95076, USA.
| | | | | | | | - Tongyan Tian
- California Department of Food and Agriculture, Sacramento, CA 95832, USA
| | - Alfredo Diaz-Lara
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico
| | - Robert R Martin
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97330, USA; USDA-ARS Horticultural Crops Research Unit, Corvallis, OR 97330, USA
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA.
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Druciarek T, Sierra-Mejia A, Zagrodzki SK, Singh S, Ho T, Lewandowski M, Tzanetakis IE. Phyllocoptes parviflori is a distinct species and a vector of the pervasive blackberry leaf mottle associated virus. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 117:105538. [PMID: 38072369 DOI: 10.1016/j.meegid.2023.105538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/02/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023]
Abstract
Several viruses are transmitted by eriophyid mites (Acariformes: Eriophyoidea) including blackberry leaf mottle-associated emaravirus (BLMaV) (Emaravirus rubi). BLMaV is transmitted by an unidentified eriophyid species and is involved in blackberry yellow vein, a devastating disease in the southeastern United States. In this study, we assessed the eriophyid mite Phylocoptes parviflori as a vector of BLMaV and clarified its taxonomic status as it was previously synonymized with Phyllocoptes gracilis. P. parviflori can efficiently transmit BLMaV. The virus was found to cause yellow vein disease symptoms on 'Ouachita' blackberry marking a paradigm shift as disease symptoms have always been associated with multiple virus infections. Therefore, we propose renaming the virus to blackberry leaf mottle virus. The occurrence of P. parviflori on wild and cultivated blackberries, as well as its ability to colonize other Rubus species, enhances its importance as a major contributor to the spread of yellow vein disease.
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Affiliation(s)
- Tobiasz Druciarek
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System Fayetteville, AR 72701, USA; Department of Plant Protection, Institute of Horticultural Sciences, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Andrea Sierra-Mejia
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System Fayetteville, AR 72701, USA
| | - Stanislaw K Zagrodzki
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System Fayetteville, AR 72701, USA; Department of Plant Protection, Institute of Horticultural Sciences, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Shivani Singh
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System Fayetteville, AR 72701, USA
| | - Thien Ho
- Driscoll's Inc., Watsonville, CA 95076, USA
| | - Mariusz Lewandowski
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System Fayetteville, AR 72701, USA; Department of Plant Protection, Institute of Horticultural Sciences, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System Fayetteville, AR 72701, USA.
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Singh S, Stainton D, Tzanetakis IE. Development of Rapid and Affordable Virus-Mimicking Artificial Positive Controls. PLANT DISEASE 2024; 108:30-34. [PMID: 37578360 DOI: 10.1094/pdis-06-23-1072-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
A major bottleneck in the development of detection assays is the availability of positive controls. Their acquisition can be problematic, their maintenance is expensive, and without them, assays cannot be validated. Herein, we present a novel strategy for the development of virus-mimicking artificial positive controls (ViMAPCs). The time between design and application is less than 5 days, unlike alternatives which normally take several weeks to obtain and implement. The ViMAPCs provide a realistic representation of natural infection unlike alternatives and allow for an effortless recognition of laboratory-based contamination. The feasibility and adaptability of the strategy was evaluated using several RNA and DNA plant viruses. ViMAPCs can be used in diagnostics laboratories but also in the monitoring of pathogen outbreaks where rapid response is of utmost importance.
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Affiliation(s)
- Shivani Singh
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - Daisy Stainton
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
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Koloniuk I, Fránová J, Přibylová J, Sarkisova T, Špak J, Tan JL, Zemek R, Čmejla R, Rejlová M, Valentová L, Sedlák J, Holub J, Skalík J, Blystad DR, Sapkota B, Hamborg Z. Molecular Characterization of a Novel Enamovirus Infecting Raspberry. Viruses 2023; 15:2281. [PMID: 38140523 PMCID: PMC10747458 DOI: 10.3390/v15122281] [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: 10/27/2023] [Revised: 11/10/2023] [Accepted: 11/16/2023] [Indexed: 12/24/2023] Open
Abstract
Raspberry plants, valued for their fruits, are vulnerable to a range of viruses that adversely affect their yield and quality. Utilizing high-throughput sequencing (HTS), we identified a novel virus, tentatively named raspberry enamovirus 1 (RaEV1), in three distinct raspberry plants. This study provides a comprehensive characterization of RaEV1, focusing on its genomic structure, phylogeny, and possible transmission routes. Analysis of nearly complete genomes from 14 RaEV1 isolates highlighted regions of variance, particularly marked by indel events. The evidence from phylogenetic and sequence analyses supports the classification of RaEV1 as a distinct species within the Enamovirus genus. Among the 289 plant and 168 invertebrate samples analyzed, RaEV1 was detected in 10.4% and 0.4%, respectively. Most detections occurred in plants that were also infected with other common raspberry viruses. The virus was present in both commercial and wild raspberries, indicating the potential of wild plants to act as viral reservoirs. Experiments involving aphids as potential vectors demonstrated their ability to acquire RaEV1 but not to successfully transmit it to plants.
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Affiliation(s)
- Igor Koloniuk
- Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (J.F.); (J.P.); (T.S.); (J.Š.)
| | - Jana Fránová
- Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (J.F.); (J.P.); (T.S.); (J.Š.)
| | - Jaroslava Přibylová
- Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (J.F.); (J.P.); (T.S.); (J.Š.)
| | - Tatiana Sarkisova
- Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (J.F.); (J.P.); (T.S.); (J.Š.)
| | - Josef Špak
- Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (J.F.); (J.P.); (T.S.); (J.Š.)
| | - Jiunn Luh Tan
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (J.L.T.); (R.Z.)
- Faculty of Science, University of South Bohemia, 370 05 Ceske Budejovice, Czech Republic
| | - Rostislav Zemek
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (J.L.T.); (R.Z.)
| | - Radek Čmejla
- Research and Breeding Institute of Pomology Holovousy Ltd., 508 01 Horice, Czech Republic; (R.Č.); (M.R.); (L.V.); (J.S.)
| | - Martina Rejlová
- Research and Breeding Institute of Pomology Holovousy Ltd., 508 01 Horice, Czech Republic; (R.Č.); (M.R.); (L.V.); (J.S.)
| | - Lucie Valentová
- Research and Breeding Institute of Pomology Holovousy Ltd., 508 01 Horice, Czech Republic; (R.Č.); (M.R.); (L.V.); (J.S.)
| | - Jiří Sedlák
- Research and Breeding Institute of Pomology Holovousy Ltd., 508 01 Horice, Czech Republic; (R.Č.); (M.R.); (L.V.); (J.S.)
| | - Jan Holub
- Jan Holub Ltd., 783 25 Bouzov, Czech Republic; (J.H.); (J.S.)
| | - Jan Skalík
- Jan Holub Ltd., 783 25 Bouzov, Czech Republic; (J.H.); (J.S.)
| | - Dag-Ragnar Blystad
- Norwegian Institute of Bioeconomy Research, 1433 Aas, Norway; (D.-R.B.); (B.S.); (Z.H.)
| | - Bijaya Sapkota
- Norwegian Institute of Bioeconomy Research, 1433 Aas, Norway; (D.-R.B.); (B.S.); (Z.H.)
| | - Zhibo Hamborg
- Norwegian Institute of Bioeconomy Research, 1433 Aas, Norway; (D.-R.B.); (B.S.); (Z.H.)
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Nyirakanani C, Tamisier L, Bizimana JP, Rollin J, Nduwumuremyi A, Bigirimana VDP, Selmi I, Lasois L, Vanderschuren H, Massart S. Going beyond consensus genome sequences: An innovative SNP-based methodology reconstructs different Ugandan cassava brown streak virus haplotypes at a nationwide scale in Rwanda. Virus Evol 2023; 9:vead053. [PMID: 37692897 PMCID: PMC10491861 DOI: 10.1093/ve/vead053] [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: 03/06/2023] [Revised: 06/14/2023] [Accepted: 08/20/2023] [Indexed: 09/12/2023] Open
Abstract
Cassava Brown Streak Disease (CBSD), which is caused by cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), represents one of the most devastating threats to cassava production in Africa, including in Rwanda where a dramatic epidemic in 2014 dropped cassava yield from 3.3 million to 900,000 tonnes (1). Studying viral genetic diversity at the genome level is essential in disease management, as it can provide valuable information on the origin and dynamics of epidemic events. To fill the current lack of genome-based diversity studies of UCBSV, we performed a nationwide survey of cassava ipomovirus genomic sequences in Rwanda by high-throughput sequencing (HTS) of pools of plants sampled from 130 cassava fields in thirteen cassava-producing districts, spanning seven agro-ecological zones with contrasting climatic conditions and different cassava cultivars. HTS allowed the assembly of a nearly complete consensus genome of UCBSV in twelve districts. The phylogenetic analysis revealed high homology between UCBSV genome sequences, with a maximum of 0.8 per cent divergence between genomes at the nucleotide level. An in-depth investigation based on Single Nucleotide Polymorphisms (SNPs) was conducted to explore the genome diversity beyond the consensus sequences. First, to ensure the validity of the result, a panel of SNPs was confirmed by independent reverse transcription polymerase chain reaction (RT-PCR) and Sanger sequencing. Furthermore, the combination of fixation index (FST) calculation and Principal Component Analysis (PCA) based on SNP patterns identified three different UCBSV haplotypes geographically clustered. The haplotype 2 (H2) was restricted to the central regions, where the NAROCAS 1 cultivar is predominantly farmed. RT-PCR and Sanger sequencing of individual NAROCAS1 plants confirmed their association with H2. Haplotype 1 was widely spread, with a 100 per cent occurrence in the Eastern region, while Haplotype 3 was only found in the Western region. These haplotypes' associations with specific cultivars or regions would need further confirmation. Our results prove that a much more complex picture of genetic diversity can be deciphered beyond the consensus sequences, with practical implications on virus epidemiology, evolution, and disease management. Our methodology proposes a high-resolution analysis of genome diversity beyond the consensus between and within samples. It can be used at various scales, from individual plants to pooled samples of virus-infected plants. Our findings also showed how subtle genetic differences could be informative on the potential impact of agricultural practices, as the presence and frequency of a virus haplotype could be correlated with the dissemination and adoption of improved cultivars.
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Affiliation(s)
- Chantal Nyirakanani
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
- Department of Crop Sciences, School of Agriculture and Food Sciences, College of Agriculture, Animal Sciences and Veterinary Medicine, University of Rwanda, Musanze 210, Rwanda
| | - Lucie Tamisier
- Integrated and Urban Plant Pathology Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
| | - Jean Pierre Bizimana
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
- Department of Research, Rwanda Agriculture and Animal Resources Development Board, Huye 5016, Rwanda
| | - Johan Rollin
- Integrated and Urban Plant Pathology Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
- Department of Research, DNAVision, Gosselies, Charleroi 6041, Belgium
| | - Athanase Nduwumuremyi
- Department of Research, Rwanda Agriculture and Animal Resources Development Board, Huye 5016, Rwanda
| | - Vincent de Paul Bigirimana
- Department of Crop Sciences, School of Agriculture and Food Sciences, College of Agriculture, Animal Sciences and Veterinary Medicine, University of Rwanda, Musanze 210, Rwanda
| | - Ilhem Selmi
- Integrated and Urban Plant Pathology Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
| | - Ludivine Lasois
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
| | - Hervé Vanderschuren
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
- Tropical Crop Improvement Laboratory, Department of Biosystems, Katholieke Universiteit Leuven, Heverlee, Leuven 3001, Belgium
| | - Sébastien Massart
- Integrated and Urban Plant Pathology Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
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Koloniuk I, Matyášová A, Brázdová S, Veselá J, Přibylová J, Várallyay E, Fránová J. Analysis of Virus-Derived siRNAs in Strawberry Plants Co-Infected with Multiple Viruses and Their Genotypes. PLANTS (BASEL, SWITZERLAND) 2023; 12:2564. [PMID: 37447124 DOI: 10.3390/plants12132564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023]
Abstract
Plants can be infected with multiple viruses. High-throughput sequencing tools have enabled numerous discoveries of multi-strain infections, when more than one viral strain or divergent genomic variant infects a single plant. Here, we investigated small interfering RNAs (siRNAs) in a single strawberry plant co-infected with several strains of strawberry mottle virus (SMoV), strawberry crinkle virus (SCV) and strawberry virus 1 (StrV-1). A range of plants infected with subsets of the initial viral species and strains that were obtained by aphid-mediated transmission were also evaluated. Using high-throughput sequencing, we characterized the small RNA fractions associated with different genotypes of these three viruses and determined small RNA hotspot regions in viral genomes. A comparison of virus-specific siRNA (vsiRNA) abundance with relative viral concentrations did not reveal any consistent agreement. Strawberry mottle virus strains exhibiting considerable variations in concentrations were found to be associated with comparable quantities of vsiRNAs. Additionally, by estimating the specificity of siRNAs to different viral strains, we observed that a substantial pool of vsiRNAs could target all SMoV strains, while strain-specific vsiRNAs predominantly targeted rhabdoviruses, SCV and StrV-1. This highlights the intricate nature and potential interference of the antiviral response within a single infected plant when multiple viruses are present.
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Affiliation(s)
- Igor Koloniuk
- Institute of Plant Molecular Biology, Department of Plant Virology, Biology Centre CAS, 370 05 Ceske Budejovice, Czech Republic
| | - Alena Matyášová
- Institute of Plant Molecular Biology, Department of Plant Virology, Biology Centre CAS, 370 05 Ceske Budejovice, Czech Republic
| | - Sára Brázdová
- Institute of Plant Molecular Biology, Department of Plant Virology, Biology Centre CAS, 370 05 Ceske Budejovice, Czech Republic
- Faculty of Agriculture, University of South Bohemia, 370 05 Ceske Budejovice, Czech Republic
| | - Jana Veselá
- Institute of Plant Molecular Biology, Department of Plant Virology, Biology Centre CAS, 370 05 Ceske Budejovice, Czech Republic
| | - Jaroslava Přibylová
- Institute of Plant Molecular Biology, Department of Plant Virology, Biology Centre CAS, 370 05 Ceske Budejovice, Czech Republic
| | - Eva Várallyay
- Genomics Research Group, Institute of Plant Protection, Department of Plant Pathology, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, 2100 Gödöllő, Hungary
| | - Jana Fránová
- Institute of Plant Molecular Biology, Department of Plant Virology, Biology Centre CAS, 370 05 Ceske Budejovice, Czech Republic
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Lee E, Vansia R, Phelan J, Lofano A, Smith A, Wang A, Bilodeau GJ, Pernal SF, Guarna MM, Rott M, Griffiths JS. Area Wide Monitoring of Plant and Honey Bee ( Apis mellifera) Viruses in Blueberry ( Vaccinium corymbosum) Agroecosystems Facilitated by Honey Bee Pollination. Viruses 2023; 15:v15051209. [PMID: 37243295 DOI: 10.3390/v15051209] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/11/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Healthy agroecosystems are dependent on a complex web of factors and inter-species interactions. Flowers are hubs for pathogen transmission, including the horizontal or vertical transmission of plant-viruses and the horizontal transmission of bee-viruses. Pollination by the European honey bee (Apis mellifera) is critical for industrial fruit production, but bees can also vector viruses and other pathogens between individuals. Here, we utilized commercial honey bee pollination services in blueberry (Vaccinium corymbosum) farms for a metagenomics-based bee and plant virus monitoring system. Following RNA sequencing, viruses were identified by mapping reads to a reference sequence database through the bioinformatics portal Virtool. In total, 29 unique plant viral species were found at two blueberry farms in British Columbia (BC). Nine viruses were identified at one site in Ontario (ON), five of which were not identified in BC. Ilarviruses blueberry shock virus (BlShV) and prune dwarf virus (PDV) were the most frequently detected viruses in BC but absent in ON, while nepoviruses tomato ringspot virus and tobacco ringspot virus were common in ON but absent in BC. BlShV coat protein (CP) nucleotide sequences were nearly identical in all samples, while PDV CP sequences were more diverse, suggesting multiple strains of PDV circulating at this site. Ten bee-infecting viruses were identified, with black queen cell virus frequently detected in ON and BC. Area-wide bee-mediated pathogen monitoring can provide new insights into the diversity of viruses present in, and the health of, bee-pollination ecosystems. This approach can be limited by a short sampling season, biased towards pollen-transmitted viruses, and the plant material collected by bees can be very diverse. This can obscure the origin of some viruses, but bee-mediated virus monitoring can be an effective preliminary monitoring approach.
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Affiliation(s)
- Eunseo Lee
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
- London Research and Development Centre, Agriculture and Agri-Food Canada, 4902 Victoria Ave N, Vineland Station, ON L0R 2E0, Canada
| | - Raj Vansia
- London Research and Development Centre, Agriculture and Agri-Food Canada, 4902 Victoria Ave N, Vineland Station, ON L0R 2E0, Canada
- Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1, Canada
| | - James Phelan
- Sidney Laboratory, Centre for Plant Health, Canadian Food Inspection Agency, 8801 East Saanich Rd., North Saanich, BC V8L 1H3, Canada
| | - Andrea Lofano
- London Research and Development Centre, Agriculture and Agri-Food Canada, 4902 Victoria Ave N, Vineland Station, ON L0R 2E0, Canada
| | - Adam Smith
- Sidney Laboratory, Centre for Plant Health, Canadian Food Inspection Agency, 8801 East Saanich Rd., North Saanich, BC V8L 1H3, Canada
| | - Aiming Wang
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
| | - Guillaume J Bilodeau
- Ottawa Plant Laboratory, Canadian Food Inspection Agency, 3851 Fallowfield Rd., Ottawa, ON K2J 4S1, Canada
| | - Stephen F Pernal
- Beaverlodge Research Farm, Agriculture and Agri-Food Canada, P.O. Box 29, Beaverlodge, AB T0H 0C0, Canada
| | - M Marta Guarna
- Beaverlodge Research Farm, Agriculture and Agri-Food Canada, P.O. Box 29, Beaverlodge, AB T0H 0C0, Canada
| | - Michael Rott
- Sidney Laboratory, Centre for Plant Health, Canadian Food Inspection Agency, 8801 East Saanich Rd., North Saanich, BC V8L 1H3, Canada
| | - Jonathan S Griffiths
- London Research and Development Centre, Agriculture and Agri-Food Canada, 4902 Victoria Ave N, Vineland Station, ON L0R 2E0, Canada
- Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1, Canada
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10
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Medberry AN, Srivastava A, Diaz-Lara A, Rwahnih MA, Villamor DEV, Tzanetakis IE. A Novel, Divergent Member of the Rhabdoviridae Family Infects Strawberry. PLANT DISEASE 2023; 107:620-623. [PMID: 35857372 DOI: 10.1094/pdis-05-22-1078-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Strawberry (Fragaria × ananassa) is the most important berry crop worldwide and viruses pose a constant threat to the industry. In this communication, we describe a novel virus in the family Rhabdoviridae referred to as strawberry virus 3 (StrV-3). The virus does not show significant homology when compared with recognized rhabdoviruses and, therefore, the establishment of a new genus should be considered. A triplex reverse-transcription PCR test was developed and successfully employed in a survey of the National Clonal Germplasm Repository Fragaria collection. A CRISPR-Cas-based protocol was also developed and shown to detect the virus in as little as 1 fg of total RNA, a protocol to be used in the detection of the virus in candidate G1 plants. The strawberry aphid (Chaetosiphon fragaefolii) was evaluated-alas, unsuccessfully-as a potential vector of the virus. This work broadens our understanding of the family Rhabdoviridae and assists in the quest of releasing plant material free of viruses.
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Affiliation(s)
- Ava N Medberry
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, U.S.A
| | - Ashish Srivastava
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, U.S.A
- Amity Institute of Virology & Immunology, Amity University Uttar Pradesh, Sector 125, Noida, UP 284403, India
| | - Alfredo Diaz-Lara
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico
- Department of Plant Pathology, University of California-Davis, Davis, CA 95616, U.S.A
| | - Maher Al Rwahnih
- Department of Plant Pathology, University of California-Davis, Davis, CA 95616, U.S.A
| | - Dan E V Villamor
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, U.S.A
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, U.S.A
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11
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Villamor DEV, Mejia AS, Martin RR, Tzanetakis IE. Genomic Analysis and Development of Infectious Clone of a Novel Carlavirus Infecting Blueberry. PHYTOPATHOLOGY 2023; 113:98-103. [PMID: 35852469 DOI: 10.1094/phyto-05-22-0186-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A new blueberry virus was discovered using high-throughput sequencing. Using sequence identity values, phylogenetics, and serological and biological properties, we propose the virus, putatively named blueberry virus S (BluVS), to be a distinct species within the genus Carlavirus (family Betaflexiviridae). The genome was analyzed in depth, and an infectious clone was developed to initiate studies on virus pathogenicity. Agroinfiltration of the binary vector construct produced severe systemic symptoms in Nicotiana occidentalis. Back-inoculation using sap from agroinfiltrated N. occidentalis produced identical symptoms to the recipient plants (N. occidentalis), and virus purification yielded flexuous carlavirus-like particles. However, unlike blueberry scorch virus (BlScV), BluVS caused symptomless infection in Chenopodium quinoa and reacted weakly to BlScV antibodies in an enzyme-linked immunosorbent assay. Collectively, the results provide evidence for the distinct speciation of BluVS. The availability of an infectious clone provides tools for future studies on the biology of the virus.
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Affiliation(s)
- D E V Villamor
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - A Sierra Mejia
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - R R Martin
- Oregon State University and U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330
| | - I E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
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12
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Valenzuela SL, Norambuena T, Morgante V, García F, Jiménez JC, Núñez C, Fuentes I, Pollak B. Viroscope: Plant viral diagnosis from high-throughput sequencing data using biologically-informed genome assembly coverage. Front Microbiol 2022; 13:967021. [PMID: 36338106 PMCID: PMC9634423 DOI: 10.3389/fmicb.2022.967021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/29/2022] [Indexed: 11/25/2022] Open
Abstract
High-throughput sequencing (HTS) methods are transforming our capacity to detect pathogens and perform disease diagnosis. Although sequencing advances have enabled accessible and point-of-care HTS, data analysis pipelines have yet to provide robust tools for precise and certain diagnosis, particularly in cases of low sequencing coverage. Lack of standardized metrics and harmonized detection thresholds confound the problem further, impeding the adoption and implementation of these solutions in real-world applications. In this work, we tackle these issues and propose biologically-informed viral genome assembly coverage as a method to improve diagnostic certainty. We use the identification of viral replicases, an essential function of viral life cycles, to define genome coverage thresholds in which biological functions can be described. We validate the analysis pipeline, Viroscope, using field samples, synthetic and published datasets, and demonstrate that it provides sensitive and specific viral detection. Furthermore, we developed Viroscope.io a web-service to provide on-demand HTS data viral diagnosis to facilitate adoption and implementation by phytosanitary agencies to enable precise viral diagnosis.
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Affiliation(s)
| | | | | | | | | | | | | | - Bernardo Pollak
- Meristem SpA, Santiago, Chile
- Multiplex SpA, Santiago, Chile
- *Correspondence: Bernardo Pollak,
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13
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Shaffer CM, Michener DC, Vlasava NB, Chotkowski H, Botermans M, Starre J, Tzanetakis IE. First Report of Gentian Kobu-sho-Associated Virus Infecting Peony in the United States and the Netherlands. PLANT DISEASE 2022; 106:1311. [PMID: 34645308 DOI: 10.1094/pdis-06-21-1316-pdn] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- C M Shaffer
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - D C Michener
- University of Michigan Matthaei Botanical Gardens & Nichols Arboretum, Ann Arbor, MI 48105
| | - N B Vlasava
- Central Botanic Garden, National Academy of Sciences, Minsk, Belarus
| | | | - M Botermans
- National Reference Centre of Plant Health, Dutch National Plant Protection Organization, Wageningen, The Netherlands
| | - J Starre
- Naktuinbouw, Roelofarendsveen, The Netherlands
| | - I E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
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