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Jaybhaye SG, Chavhan RL, Hinge VR, Deshmukh AS, Kadam US. CRISPR-Cas assisted diagnostics of plant viruses and challenges. Virology 2024; 597:110160. [PMID: 38955083 DOI: 10.1016/j.virol.2024.110160] [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: 02/16/2024] [Revised: 06/04/2024] [Accepted: 06/21/2024] [Indexed: 07/04/2024]
Abstract
Plant viruses threaten global food security by infecting commercial crops, highlighting the critical need for efficient virus detection to enable timely preventive measures. Current techniques rely on polymerase chain reaction (PCR) for viral genome amplification and require laboratory conditions. This review explores the applications of CRISPR-Cas assisted diagnostic tools, specifically CRISPR-Cas12a and CRISPR-Cas13a/d systems for plant virus detection and analysis. The CRISPR-Cas12a system can detect viral DNA/RNA amplicons and can be coupled with PCR or isothermal amplification, allowing multiplexed detection in plants with mixed infections. Recent studies have eliminated the need for expensive RNA purification, streamlining the process by providing a visible readout through lateral flow strips. The CRISPR-Cas13a/d system can directly detect viral RNA with minimal preamplification, offering a proportional readout to the viral load. These approaches enable rapid viral diagnostics within 30 min of leaf harvest, making them valuable for onsite field applications. Timely identification of diseases associated with pathogens is crucial for effective treatment; yet developing rapid, specific, sensitive, and cost-effective diagnostic technologies remains challenging. The current gold standard, PCR technology, has drawbacks such as lengthy operational cycles, high costs, and demanding requirements. Here we update the technical advancements of CRISPR-Cas in viral detection, providing insights into future developments, versatile applications, and potential clinical translation. There is a need for approaches enabling field plant viral nucleic acid detection with high sensitivity, specificity, affordability, and portability. Despite challenges, CRISPR-Cas-mediated pathogen diagnostic solutions hold robust capabilities, paving the way for ideal diagnostic tools. Alternative applications in virus research are also explored, acknowledging the technology's limitations and challenges.
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Affiliation(s)
- Siddhant G Jaybhaye
- Vilasrao Deshmukh College of Agricultural Biotechnology, Nanded Road, Latur, Vasantrao Naik Marathwada Krishi Vidyapeeth, Maharashtra, India
| | - Rahul L Chavhan
- Vilasrao Deshmukh College of Agricultural Biotechnology, Nanded Road, Latur, Vasantrao Naik Marathwada Krishi Vidyapeeth, Maharashtra, India
| | - Vidya R Hinge
- Vilasrao Deshmukh College of Agricultural Biotechnology, Nanded Road, Latur, Vasantrao Naik Marathwada Krishi Vidyapeeth, Maharashtra, India
| | - Abhijit S Deshmukh
- Vilasrao Deshmukh College of Agricultural Biotechnology, Nanded Road, Latur, Vasantrao Naik Marathwada Krishi Vidyapeeth, Maharashtra, India
| | - Ulhas S Kadam
- Plant Molecular Biology and Biotechnology Research Centre (PMBBRC), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Gyeongsangnam-do, South Korea.
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Rott ME, Ghoshal K, Lerat S, Brosseau C, Clément G, Phelan J, Poojari S, Gaafar Y, Vemulapati BM, Scheer H, Ritzenthaler C, Fall ML, Moffett P. Improving grapevine virus diagnostics: Comparative analysis of three dsRNA enrichment methods for high-throughput sequencing. J Virol Methods 2024; 329:114997. [PMID: 39059502 DOI: 10.1016/j.jviromet.2024.114997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024]
Abstract
The extraction of double stranded (ds) RNA is a common enrichment method for the study, characterization, and detection of RNA viruses. In addition to RNA viruses, viroids, and some DNA viruses, can also be detected from dsRNA enriched extracts which makes it an attractive method for detecting a wide range of viruses when coupled with HTS. Several dsRNA enrichment strategies have been developed. The oldest utilizes the selective binding properties of dsRNA to cellulose. More recent methods are based on the application of anti-dsRNA antibodies and viral proteins with a specific affinity for dsRNA. All three methods have been used together with HTS for plant virus detection and study. To our knowledge, this is the first comparative study of three alternative dsRNA enrichment methods for virus and viroid detection through HTS using virus-infected, and healthy grapevine test plants. Extracts were performed in triplicate using methods based on, the anti-dsRNA antibody mAb rJ2 (Millipore Sigma Canada Ltd, Oakville, ON, Canada), the B2 dsRNA binding protein, and ReliaPrep™ Resin (Promega Corporation, Madison, WI, USA). The results show that the workflows for all three methods are effectively comparable, apart from purification steps related to antibody and binding protein construct. Both the cellulose resin and dsRNA binding protein construct methods provide highly enriched dsRNA extracts suitable for HTS with the B2 method providing a 36× and the ReliaPrep™ Resin a 163× increase in dsRNA enrichment compared to the mAb rJ2 antibody. The overall consistency and cost effectiveness of the ReliaPrep™ cellulose resin-based method and the potentially simpler adaptation to robotics made it the method of choice for future transfer to a semi-automated workflow.
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Affiliation(s)
- Michael E Rott
- Canadian Food Inspection Agency, Centre for Plant Health, Sidney Laboratory, 8801 East Saanich Rd, North Saanich, British Columbia V8L 1H3, Canada.
| | - Kankana Ghoshal
- Canadian Food Inspection Agency, Centre for Plant Health, Sidney Laboratory, 8801 East Saanich Rd, North Saanich, British Columbia V8L 1H3, Canada
| | - Sylvain Lerat
- Département de Biologie, Université de Sherbrooke, 2500 Bd de l'Université, Sherbrooke, Québec J1K 2R1, Canada
| | - Chantal Brosseau
- Département de Biologie, Université de Sherbrooke, 2500 Bd de l'Université, Sherbrooke, Québec J1K 2R1, Canada
| | - Geneviève Clément
- Département de Biologie, Université de Sherbrooke, 2500 Bd de l'Université, Sherbrooke, Québec J1K 2R1, Canada
| | - James Phelan
- Canadian Food Inspection Agency, Centre for Plant Health, Sidney Laboratory, 8801 East Saanich Rd, North Saanich, British Columbia V8L 1H3, Canada
| | - Sudarsana Poojari
- Cool Climate Oenology and Viticulture Institute, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Yahya Gaafar
- Canadian Food Inspection Agency, Centre for Plant Health, Sidney Laboratory, 8801 East Saanich Rd, North Saanich, British Columbia V8L 1H3, Canada
| | - Bhadra M Vemulapati
- Cool Climate Oenology and Viticulture Institute, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Hélène Scheer
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg 67000, France
| | - Christophe Ritzenthaler
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg 67000, France
| | - Mamadou L Fall
- Agriculture and Agri-Food Canada, 430 Gouin Boulevard, Saint-Jean-sur-Richelieu, Québec J3B 3EB, Canada
| | - Peter Moffett
- Département de Biologie, Université de Sherbrooke, 2500 Bd de l'Université, Sherbrooke, Québec J1K 2R1, Canada
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Smadi M, Lee E, Phelan J, Wang A, Bilodeau GJ, Pernal SF, Guarna MM, Rott M, Griffiths JS. Plant virus diversity in bee and pollen samples from apple ( Malus domestica) and sweet cherry ( Prunus avium) agroecosystems. FRONTIERS IN PLANT SCIENCE 2024; 15:1335281. [PMID: 38444533 PMCID: PMC10913894 DOI: 10.3389/fpls.2024.1335281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/05/2024] [Indexed: 03/07/2024]
Abstract
Introduction Honey bee (Apis mellifera) pollination is widely used in tree fruit production systems to improve fruit set and yield. Many plant viruses can be associated with pollen or transmitted through pollination, and can be detected through bee pollination activities. Honey bees visit multiple plants and flowers in one foraging trip, essentially sampling small amounts of pollen from a wide area. Here we report metagenomics-based area-wide monitoring of plant viruses in cherry (Prunus avium) and apple (Malus domestica) orchards in Creston Valley, British Columbia, Canada, through bee-mediated pollen sampling. Methods Plant viruses were identified in total RNA extracted from bee and pollen samples, and compared with profiles from double stranded RNA extracted from leaf and flower tissues. CVA, PDV, PNRSV, and PVF coat protein nucleotide sequences were aligned and compared for phylogenetic analysis. Results A wide array of plant viruses were identified in both systems, with cherry virus A (CVA), prune dwarf virus (PDV), prunus necrotic ringspot virus (PNRSV), and prunus virus F (PVF) most commonly detected. Citrus concave gum associated virus and apple stem grooving virus were only identified in samples collected during apple bloom, demonstrating changing viral profiles from the same site over time. Different profiles of viruses were identified in bee and pollen samples compared to leaf and flower samples reflective of pollen transmission affinity of individual viruses. Phylogenetic and pairwise analysis of the coat protein regions of the four most commonly detected viruses showed unique patterns of nucleotide sequence diversity, which could have implications in their evolution and management approaches. Coat protein sequences of CVA and PVF were broadly diverse with multiple distinct phylogroups identified, while PNRSV and PDV were more conserved. Conclusion The pollen virome in fruit production systems is incredibly diverse, with CVA, PDV, PNRSV, and PVF widely prevalent in this region. Bee-mediated monitoring in agricultural systems is a powerful approach to study viral diversity and can be used to guide more targeted management approaches.
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Affiliation(s)
- Malek Smadi
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Eunseo Lee
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - James Phelan
- Canadian Food Inspection Agency, Centre for Plant Health, Sidney Laboratory, North Saanich, BC, Canada
| | - Aiming Wang
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | | | - Stephen F. Pernal
- Beaverlodge Research Farm, Agriculture and Agri-Food Canada, Beaverlodge, AB, Canada
| | - M. Marta Guarna
- Beaverlodge Research Farm, Agriculture and Agri-Food Canada, Beaverlodge, AB, Canada
- Department of Computer Science, University of Victoria, Victoria, BC, Canada
| | - Mike Rott
- Canadian Food Inspection Agency, Centre for Plant Health, Sidney Laboratory, North Saanich, BC, Canada
| | - Jonathan S. Griffiths
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
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Keremane M, Singh K, Ramadugu C, Krueger RR, Skaggs TH. Next Generation Sequencing, and Development of a Pipeline as a Tool for the Detection and Discovery of Citrus Pathogens to Facilitate Safer Germplasm Exchange. PLANTS (BASEL, SWITZERLAND) 2024; 13:411. [PMID: 38337944 PMCID: PMC10856814 DOI: 10.3390/plants13030411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024]
Abstract
Citrus is affected by many diseases, and hence, the movement of citrus propagative materials is highly regulated in the USA. Currently used regulatory pathogen detection methods include biological and laboratory-based technologies, which are time-consuming, expensive, and have many limitations. There is an urgent need to develop alternate, rapid, economical, and reliable testing methods for safe germplasm exchange. Citrus huanglongbing (HLB) has devastated citrus industries leading to an increased need for germplasm exchanges between citrus growing regions for evaluating many potentially valuable hybrids for both HLB resistance and multilocational performance. In the present study, Next-Generation Sequencing (NGS) methods were used to sequence the transcriptomes of 21 test samples, including 15 well-characterized pathogen-positive plants. A workflow was designed in the CLC Genomics Workbench software, v 21.0.5 for bioinformatics analysis of the sequence data for the detection of pathogens. NGS was rapid and found to be a valuable technique for the detection of viral and bacterial pathogens, and for the discovery of new citrus viruses, complementary to the existing array of biological and laboratory assays. Using NGS methods, we detected beet western yellows virus, a newly reported citrus virus, and a variant of the citrus yellow vein-associated virus associated with the "fatal yellows" disease.
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Affiliation(s)
- Manjunath Keremane
- USDA ARS, National Clonal Germplasm Repository for Citrus and Dates, Riverside, CA 92507, USA;
| | - Khushwant Singh
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA;
| | - Chandrika Ramadugu
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA;
| | - Robert R. Krueger
- USDA ARS, National Clonal Germplasm Repository for Citrus and Dates, Riverside, CA 92507, USA;
| | - Todd H. Skaggs
- USDA ARS, U.S. Salinity Laboratory, Riverside, CA 92507, USA;
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Bester R, Maree HJ. Validation of High-Throughput Sequencing (HTS) for Routine Detection of Citrus Viruses and Viroids. Methods Mol Biol 2024; 2732:199-219. [PMID: 38060127 DOI: 10.1007/978-1-0716-3515-5_14] [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 management of plant diseases relies on the accurate identification of pathogens that requires a robust and validated tool in terms of specificity, sensitivity, repeatability, and reproducibility. High-throughput sequencing (HTS) has become the method of choice for virus detection when either a complete viral status of a plant is required in a single assay or if an unknown viral agent is expected. To ensure that the most accurate diagnosis is made from an HTS data analysis, a standardized protocol per pathosystem is required. This chapter presents a detailed protocol for the detection of viruses and viroids infecting citrus using HTS. The protocol describes all the steps from sample processing, nucleic acid extraction, and bioinformatic analyses validated to be an efficient method for detection in this pathosystem. The protocol also includes a section on citrus tristeza virus (CTV) genotype differentiation using HTS data.
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Affiliation(s)
- Rachelle Bester
- Citrus Research International, Stellenbosch, South Africa
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Hans J Maree
- Citrus Research International, Stellenbosch, South Africa.
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa.
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Khalili M, Candresse T, Koloniuk I, Safarova D, Brans Y, Faure C, Delmas M, Massart S, Aranda MA, Caglayan K, Decroocq V, Drogoudi P, Glasa M, Pantelidis G, Navratil M, Latour F, Spak J, Pribylova J, Mihalik D, Palmisano F, Saponari A, Necas T, Sedlak J, Marais A. The Expanding Menagerie of Prunus-Infecting Luteoviruses. PHYTOPATHOLOGY 2023; 113:345-354. [PMID: 35972890 DOI: 10.1094/phyto-06-22-0203-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
Members of the genus Luteovirus are responsible for economically destructive plant diseases worldwide. Over the past few years, three luteoviruses infecting Prunus trees have been characterized. However, the biological properties, prevalence, and genetic diversity of those viruses have not yet been studied. High-throughput sequencing of samples of various wild, cultivated, and ornamental Prunus species enabled the identification of four novel species in the genus Luteovirus for which we obtained complete or nearly complete genomes. Additionally, we identified another new putative species recovered from Sequence Read Archive data. Furthermore, we conducted a survey on peach-infecting luteoviruses in eight European countries. Analyses of 350 leaf samples collected from germplasm, production orchards, and private gardens showed that peach-associated luteovirus (PaLV), nectarine stem pitting-associated virus (NSPaV), and a novel luteovirus, peach-associated luteovirus 2 (PaLV2), are present in all countries; the most prevalent virus was NSPaV, followed by PaLV. The genetic diversity of these viruses was also analyzed. Moreover, the biological indexing on GF305 peach indicator plants demonstrated that PaLV and PaLV2, like NSPaV, are transmitted by graft at relatively low rates. No clear viral symptoms have been observed in either graft-inoculated GF305 indicators or different peach tree varieties observed in an orchard. The data generated during this study provide a broader overview of the genetic diversity, geographical distribution, and prevalence of peach-infecting luteoviruses and suggest that these viruses are likely asymptomatic in peach under most circumstances.
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Affiliation(s)
- Maryam Khalili
- Université de Bordeaux, INRAE, UMR BFP, Villenave d'Ornon, France
| | | | - Igor Koloniuk
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Dana Safarova
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Yoann Brans
- Laboratoire de Virologie et de Biologie Moléculaire, CTIFL, Prigonrieux, France
| | - Chantal Faure
- Université de Bordeaux, INRAE, UMR BFP, Villenave d'Ornon, France
| | - Marine Delmas
- INRAE, Unité Expérimentale Arboricole, Toulenne, France
| | - Sébastien Massart
- Laboratory of Plant Pathology, TERRA, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Miguel A Aranda
- Department of Stress Biology and Plant Pathology, Centro de Edafología y Biología Aplicada del Segura, CSIC, Murcia, Spain
| | - Kadriye Caglayan
- Department of Plant Protection, Hatay Mustafa Kemal University, Antakya, Hatay, Turkey
| | | | - Pavlina Drogoudi
- Department of Deciduous Fruit Trees, Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Naoussa, Greece
| | - Miroslav Glasa
- Biomedical Research Center of the Slovak Academy of Sciences, Institute of Virology, Bratislava, Slovakia
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Trnava, Slovakia
| | - George Pantelidis
- Department of Deciduous Fruit Trees, Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Naoussa, Greece
| | - Milan Navratil
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - François Latour
- Laboratoire de Virologie et de Biologie Moléculaire, CTIFL, Prigonrieux, France
| | - Josef Spak
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Jaroslava Pribylova
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Daniel Mihalik
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Trnava, Slovakia
| | - Francesco Palmisano
- Centro di Ricerca, Sperimentazione e Formazione in Agricoltura "Basile Caramia", Locorotondo, Italy
| | - Antonella Saponari
- Centro di Ricerca, Sperimentazione e Formazione in Agricoltura "Basile Caramia", Locorotondo, Italy
| | - Tomas Necas
- Department of Fruit Science, Faculty of Horticulture, Mendel University, Lednice, Czech Republic
| | - Jiri Sedlak
- Vyzkumny A Slechtitelsky Ustav Ovocnarsky, Holovousy, Czech Republic
| | - Armelle Marais
- Université de Bordeaux, INRAE, UMR BFP, Villenave d'Ornon, France
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Costa LC, Atha B, Hu X, Lamour K, Yang Y, O’Connell M, McFarland C, Foster JA, Hurtado-Gonzales OP. High-throughput detection of a large set of viruses and viroids of pome and stone fruit trees by multiplex PCR-based amplicon sequencing. FRONTIERS IN PLANT SCIENCE 2022; 13:1072768. [PMID: 36578329 PMCID: PMC9791224 DOI: 10.3389/fpls.2022.1072768] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
A comprehensive diagnostic method of known plant viruses and viroids is necessary to provide an accurate phytosanitary status of fruit trees. However, most widely used detection methods have a small limit on either the number of targeted viruses/viroids or the number of samples to be evaluated at a time, hampering the ability to rapidly scale up the test capacity. Here we report that by combining the power of high multiplexing PCR (499 primer pairs) of small amplicons (120-135bp), targeting 27 viruses and 7 viroids of fruit trees, followed by a single high-throughput sequencing (HTS) run, we accurately diagnosed the viruses and viroids on as many as 123 pome and stone fruit tree samples. We compared the accuracy, sensitivity, and reproducibility of this approach and contrast it with other detection methods including HTS of total RNA (RNA-Seq) and individual RT-qPCR for every fruit tree virus or viroid under the study. We argue that this robust and high-throughput cost-effective diagnostic tool will enhance the viral/viroid knowledge of fruit trees while increasing the capacity for large scale diagnostics. This approach can also be adopted for the detection of multiple viruses and viroids in other crops.
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Affiliation(s)
- Larissa Carvalho Costa
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Benjamin Atha
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Xiaojun Hu
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, United States
| | - Yu Yang
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Mary O’Connell
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Clint McFarland
- Plant Protection and Quarantine - Field Operations, Animal and Plant Health Inspection Service, United States Department of Agriculture, Raleigh, NC, United States
| | - Joseph A. Foster
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Oscar P. Hurtado-Gonzales
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
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8
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Viromes of Hungarian Peach Trees Identified by High-Throughput Sequencing of Small RNAs. PLANTS 2022; 11:plants11121591. [PMID: 35736743 PMCID: PMC9230589 DOI: 10.3390/plants11121591] [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: 04/13/2022] [Revised: 06/06/2022] [Accepted: 06/13/2022] [Indexed: 11/17/2022]
Abstract
Peach trees can be infected with viruses and viroids. As we do not have efficient plant protection methods against these pathogens, the prevention of infection is crucial. Fruit trees are maintained by vegetative propagation. Planting material such as certified mother trees and rootstocks should be free from viruses and viroids, and this status has to be regularly checked to prevent infections. We surveyed certified peach trees for the presence of viruses and viroids using small RNA high-throughput sequencing (HTS), an unbiased virus diagnostic method. The results of the bioinformatic analysis of HTS were validated by other molecular methods including RT-PCR, Northern blot hybridization and loop-mediated isothermal amplification (LAMP). We found the presence of plum pox virus and peach latent mosaic viroid (PLMVd) in the vector-free isolator houses, whose presence should be regularly tested. Moreover, we detected frequent infection with recently described viruses such as nectarine stem pitting-associated virus and peach-associated luteovirus (PaLV). During the survey, PLMVd and PaLV were detected for the first time in Hungary. The analysis of the presenting virus variants and possible sources of infection suggests that the source of the viral infection could be the infected propagating material. Our study emphasizes the importance of using sensitive and trustworthy diagnostic techniques to be able to detect viral infections and successfully prevent their spread by propagation material.
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9
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Tahzima R, Foucart Y, Peusens G, Reynard JS, Massart S, Beliën T, De Jonghe K. An Advanced One-Step RT-LAMP for Rapid Detection of Little cherry virus 2 Combined with High-Throughput Sequence-Based Phylogenomics Reveal Divergent Flowering Cherry Isolates. PLANT DISEASE 2022; 106:835-845. [PMID: 34546772 DOI: 10.1094/pdis-03-21-0677-re] [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: 06/13/2023]
Abstract
Little cherry virus 2 (LChV-2, genus Ampelovirus) is considered to be the main causal agent of the economically damaging little cherry disease, which can only be controlled by removal of infected trees. The widespread viral disease of sweet cherry (Prunus avium L.) is affecting the survival of long-standing orchards in North America and Europe, hence the dire need for an early and accurate diagnosis to establish a sound disease control strategy. The endemic presence of LChV-2 is mainly confirmed using laborious time-consuming reverse-transcription (RT-PCR). A rapid reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay targeting a conserved region of the coat protein was developed and compared with conventional RT-PCR for the specific detection of LChV-2. This affordable assay, combined with a simple RNA extraction, deploys desirable characteristics such as higher ability for faster (<15 min), more analytically sensitive (100-fold), and robust broad-range diagnosis of LChV-2 isolates from sweet cherry, ornamental flowering cherry displaying heterogenous viral etiology and, for the first time, newly identified potential insect vectors. Moreover, use of Sanger and total RNA high-throughput sequencing as complementary metaviromics approaches confirmed the LChV-2 RT-LAMP detection of divergent LChV-2 isolates in new hosts and the relationship of their whole-genome was exhaustively inferred using maximum-likelihood phylogenomics. This entails unprecedented critical understanding of a novel evolutionary clade further expanding LChV-2 viral diversity. In conclusion, this highly effective diagnostic platform facilitates strategical support for early in-field testing to reliably prevent dissemination of new LChV-2 outbreaks from propagative plant stocks or newly postulated insect vectors. Validated results and major advantages are herein thoroughly discussed, in light of the knowledge required to increase the potential accuracy of future diagnostics and the essential epidemiological considerations to proactively safeguard cherries and Prunus horticultural crop systems from little cherry disease.
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Affiliation(s)
- Rachid Tahzima
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
- Department of Integrated and Urban Phytopathology, Gembloux Agro-BioTech, University of Liège, 5030 Gembloux, Belgium
| | - Yoika Foucart
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | - Gertie Peusens
- Department of Zoology, Proefcentrum Fruitteelt vzw, 3800 Sint-Truiden, Belgium
| | | | - Sébastien Massart
- Department of Integrated and Urban Phytopathology, Gembloux Agro-BioTech, University of Liège, 5030 Gembloux, Belgium
| | - Tim Beliën
- Department of Zoology, Proefcentrum Fruitteelt vzw, 3800 Sint-Truiden, Belgium
| | - Kris De Jonghe
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
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10
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Villamor DEV, Keller KE, Martin RR, Tzanetakis IE. Comparison of High Throughput Sequencing to Standard Protocols for Virus Detection in Berry Crops. PLANT DISEASE 2022; 106:518-525. [PMID: 34282931 DOI: 10.1094/pdis-05-21-0949-re] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We completed a comprehensive study comparing virus detection between high throughput sequencing (HTS) and standard protocols in 30 berry selections (12 Fragaria, 10 Vaccinium, and eight Rubus) with known virus profiles. The study examined temporal detection of viruses at four sampling times encompassing two growing seasons. Within the standard protocols, reverse transcription (RT) PCR proved better than biological indexing. Detection of known viruses by HTS and RT-PCR nearly mirrored each other. HTS provided superior detection compared with RT-PCR on a wide spectrum of variants and discovery of novel viruses. More importantly, in most cases in which the two protocols showed parallel virus detection, 11 viruses in 16 selections were not consistently detected by both methods at all sampling points. Based on these data, we propose a testing requirement of four sampling times over two growing seasons for berry and potentially other crops, to ensure that no virus remains undetected independent of titer, distribution, or other virus-virus or virus-host interactions.
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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
| | - K E Keller
- U.S. Department of Agriculture Agricultural Research Service, Corvallis, OR 97330
| | - R R Martin
- 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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11
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Bester R, Cook G, Breytenbach JHJ, Steyn C, De Bruyn R, Maree HJ. Towards the validation of high-throughput sequencing (HTS) for routine plant virus diagnostics: measurement of variation linked to HTS detection of citrus viruses and viroids. Virol J 2021; 18:61. [PMID: 33752714 PMCID: PMC7986492 DOI: 10.1186/s12985-021-01523-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/02/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND High-throughput sequencing (HTS) has been applied successfully for virus and viroid discovery in many agricultural crops leading to the current drive to apply this technology in routine pathogen detection. The validation of HTS-based pathogen detection is therefore paramount. METHODS Plant infections were established by graft inoculating a suite of viruses and viroids from established sources for further study. Four plants (one healthy plant and three infected) were sampled in triplicate and total RNA was extracted using two different methods (CTAB extraction protocol and the Zymo Research Quick-RNA Plant Miniprep Kit) and sent for Illumina HTS. One replicate sample of each plant for each RNA extraction method was also sent for HTS on an Ion Torrent platform. The data were evaluated for biological and technical variation focussing on RNA extraction method, platform used and bioinformatic analysis. RESULTS The study evaluated the influence of different HTS protocols on the sensitivity, specificity and repeatability of HTS as a detection tool. Both extraction methods and sequencing platforms resulted in significant differences between the data sets. Using a de novo assembly approach, complemented with read mapping, the Illumina data allowed a greater proportion of the expected pathogen scaffolds to be inferred, and an accurate virome profile was constructed. The complete virome profile was also constructed using the Ion Torrent data but analyses showed that more sequencing depth is required to be comparative to the Illumina protocol and produce consistent results. The CTAB extraction protocol lowered the proportion of viroid sequences recovered with HTS, and the Zymo Research kit resulted in more variation in the read counts obtained per pathogen sequence. The expression profiles of reference genes were also investigated to assess the suitability of these genes as internal controls to allow for the comparison between samples across different protocols. CONCLUSIONS This study highlights the need to measure the level of variation that can arise from the different variables of an HTS protocol, from sample preparation to data analysis. HTS is more comprehensive than any assay previously used, but with the necessary validations and standard operating procedures, the implementation of HTS as part of routine pathogen screening practices is possible.
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Affiliation(s)
- Rachelle Bester
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Glynnis Cook
- Citrus Research International, P.O. Box 28, Nelspruit, 1200, South Africa
| | | | - Chanel Steyn
- Citrus Research International, P.O. Box 28, Nelspruit, 1200, South Africa
- Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Rochelle De Bruyn
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
- Citrus Research International, P.O. Box 28, Nelspruit, 1200, South Africa
| | - Hans J Maree
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
- Citrus Research International, P.O. Box 2201, Matieland, 7602, South Africa.
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12
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Current Developments and Challenges in Plant Viral Diagnostics: A Systematic Review. Viruses 2021; 13:v13030412. [PMID: 33807625 PMCID: PMC7999175 DOI: 10.3390/v13030412] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/10/2021] [Accepted: 02/18/2021] [Indexed: 12/24/2022] Open
Abstract
Plant viral diseases are the foremost threat to sustainable agriculture, leading to several billion dollars in losses every year. Many viruses infecting several crops have been described in the literature; however, new infectious viruses are emerging frequently through outbreaks. For the effective treatment and prevention of viral diseases, there is great demand for new techniques that can provide accurate identification on the causative agents. With the advancements in biochemical and molecular biology techniques, several diagnostic methods with improved sensitivity and specificity for the detection of prevalent and/or unknown plant viruses are being continuously developed. Currently, serological and nucleic acid methods are the most widely used for plant viral diagnosis. Nucleic acid-based techniques that amplify target DNA/RNA have been evolved with many variants. However, there is growing interest in developing techniques that can be based in real-time and thus facilitate in-field diagnosis. Next-generation sequencing (NGS)-based innovative methods have shown great potential to detect multiple viruses simultaneously; however, such techniques are in the preliminary stages in plant viral disease diagnostics. This review discusses the recent progress in the use of NGS-based techniques for the detection, diagnosis, and identification of plant viral diseases. New portable devices and technologies that could provide real-time analyses in a relatively short period of time are prime important for in-field diagnostics. Current development and application of such tools and techniques along with their potential limitations in plant virology are likewise discussed in detail.
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13
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Bester R, Cook G, Maree HJ. Citrus Tristeza Virus Genotype Detection Using High-Throughput Sequencing. Viruses 2021; 13:168. [PMID: 33498597 PMCID: PMC7910887 DOI: 10.3390/v13020168] [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: 12/18/2020] [Revised: 01/05/2021] [Accepted: 01/11/2021] [Indexed: 12/14/2022] Open
Abstract
The application of high-throughput sequencing (HTS) has successfully been used for virus discovery to resolve disease etiology in many agricultural crops. The greatest advantage of HTS is that it can provide a complete viral status of a plant, including information on mixed infections of viral species or virus variants. This provides insight into the virus population structure, ecology, or evolution and can be used to differentiate among virus variants that may contribute differently toward disease etiology. In this study, the use of HTS for citrus tristeza virus (CTV) genotype detection was evaluated. A bioinformatic pipeline for CTV genotype detection was constructed and evaluated using simulated and real data sets to determine the parameters to discriminate between false positive read mappings and true genotype-specific genome coverage. A 50% genome coverage cut-off was identified for non-target read mappings. HTS with the associated bioinformatic pipeline was validated and proposed as a CTV genotyping assay.
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Affiliation(s)
- Rachelle Bester
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa;
| | - Glynnis Cook
- Citrus Research International, P.O. Box 28, Nelspruit 1200, South Africa;
| | - Hans J. Maree
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa;
- Citrus Research International, Stellenbosch, P.O. Box 2201, Matieland 7602, South Africa
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14
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Shahid MS, Sattar MN, Iqbal Z, Raza A, Al-Sadi AM. Next-Generation Sequencing and the CRISPR-Cas Nexus: A Molecular Plant Virology Perspective. Front Microbiol 2021; 11:609376. [PMID: 33584572 PMCID: PMC7874184 DOI: 10.3389/fmicb.2020.609376] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022] Open
Abstract
In recent years, next-generation sequencing (NGS) and contemporary Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) technologies have revolutionized the life sciences and the field of plant virology. Both these technologies offer an unparalleled platform for sequencing and deciphering viral metagenomes promptly. Over the past two decades, NGS technologies have improved enormously and have impacted plant virology. NGS has enabled the detection of plant viruses that were previously undetectable by conventional approaches, such as quarantine and archeological plant samples, and has helped to track the evolutionary footprints of viral pathogens. The CRISPR-Cas-based genome editing (GE) and detection techniques have enabled the development of effective approaches to virus resistance. Different versions of CRISPR-Cas have been employed to successfully confer resistance against diverse plant viruses by directly targeting the virus genome or indirectly editing certain host susceptibility factors. Applications of CRISPR-Cas systems include targeted insertion and/or deletion, site-directed mutagenesis, induction/expression/repression of the gene(s), epigenome re-modeling, and SNPs detection. The CRISPR-Cas toolbox has been equipped with precision GE tools to engineer the target genome with and without double-stranded (ds) breaks or donor templates. This technique has also enabled the generation of transgene-free genetically engineered plants, DNA repair, base substitution, prime editing, detection of small molecules, and biosensing in plant virology. This review discusses the utilities, advantages, applications, bottlenecks of NGS, and CRISPR-Cas in plant virology.
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Affiliation(s)
- Muhammad Shafiq Shahid
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | | | - Zafar Iqbal
- Central Laboratories, King Faisal University, Hofuf, Saudi Arabia
| | - Amir Raza
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - Abdullah M. Al-Sadi
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
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15
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Hanafi M, Tahzima R, Ben Kaab S, Tamisier L, Roux N, Massart S. Identification of Divergent Isolates of Banana Mild Mosaic Virus and Development of a New Diagnostic Primer to Improve Detection. Pathogens 2020; 9:pathogens9121045. [PMID: 33322809 PMCID: PMC7764570 DOI: 10.3390/pathogens9121045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 02/05/2023] Open
Abstract
Banana mild mosaic virus (BanMMV) (Betaflexiviridae, Quinvirinae, unassigned species) is a filamentous virus belonging to the Betaflexiviridae family. It infects Musa spp. with a very wide geographic distribution. The genome variability of plant viruses, including the members of the Betaflexiviridae family, makes their molecular detection by specific primers particularly challenging. During routine indexing of the Musa germplasm accessions, a discrepancy was observed between electron microscopy and immunocapture (IC) reverse transcription (RT) polymerase chain reaction (PCR) test results for one asymptomatic accession. Filamentous viral particles were observed while molecular tests failed to amplify any fragment. The accession underwent high-throughput sequencing and two complete genomes of BanMMV with 75.3% of identity were assembled. Based on these sequences and on the 54 coat protein sequences available from GenBank, a new forward primer, named BanMMV CP9, compatible with Poty1, an oligodT reverse primer already used in diagnostics, was designed. A retrospective analysis of 110 different germplasm accessions from diverse origins was conducted, comparing BanMMCP2 and BanMMV CP9 primers. Of these 110 accessions, 16 tested positive with both BanMMCP2 and BanMMV CP9, 3 were positive with only BanMMCP2 and 2 tested positive with only BanMMV CP9. Otherwise, 89 were negative with the two primers and free of flexuous virions. Sanger sequencing was performed from purified PCR products in order to confirm the amplification of the BanMMV sequence for the five accessions with contrasting results. It is highly recommended to use the two primers successively to improve the inclusiveness of the protocol.
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Affiliation(s)
- Marwa Hanafi
- Integrated and Urban Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, 2, Passage des Déportés, 5030 Gembloux, Belgium; (R.T.); (S.B.K.); (L.T.); (S.M.)
- Correspondence:
| | - Rachid Tahzima
- Integrated and Urban Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, 2, Passage des Déportés, 5030 Gembloux, Belgium; (R.T.); (S.B.K.); (L.T.); (S.M.)
| | - Sofiene Ben Kaab
- Integrated and Urban Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, 2, Passage des Déportés, 5030 Gembloux, Belgium; (R.T.); (S.B.K.); (L.T.); (S.M.)
| | - Lucie Tamisier
- Integrated and Urban Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, 2, Passage des Déportés, 5030 Gembloux, Belgium; (R.T.); (S.B.K.); (L.T.); (S.M.)
| | - Nicolas Roux
- Consultative Group on International Agricultural Research, 34090 Montpellier, France;
| | - Sébastien Massart
- Integrated and Urban Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, 2, Passage des Déportés, 5030 Gembloux, Belgium; (R.T.); (S.B.K.); (L.T.); (S.M.)
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16
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Hu Y, Wilson S, Schwessinger B, Rathjen JP. Blurred lines: integrating emerging technologies to advance plant biosecurity. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:127-134. [PMID: 32610220 DOI: 10.1016/j.pbi.2020.04.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/09/2020] [Accepted: 04/26/2020] [Indexed: 05/25/2023]
Abstract
Plant diseases threaten global food security and biodiversity. Rapid dispersal of pathogens particularly via human means has accelerated in recent years. Timely detection of plant pathogens is essential to limit their spread. At the same time, international regulations must keep abreast of advances in plant disease diagnostics. In this review we describe recent progress in developing modern plant disease diagnostics based on detection of pathogen components, high-throughput image analysis, remote sensing, and machine learning. We discuss how different diagnostic approaches can be integrated in detection frameworks that can work at different scales and account for sampling biases. Lastly, we briefly discuss the requirements to apply these advances under regulatory settings to improve biosecurity measures globally.
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Affiliation(s)
- Yiheng Hu
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Salome Wilson
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Benjamin Schwessinger
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - John P Rathjen
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia.
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17
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Bester R, Malan SS, Maree HJ. A Plum Marbling Conundrum: Identification of a New Viroid Associated with Marbling and Corky Flesh in Japanese Plums. PHYTOPATHOLOGY 2020; 110:1476-1482. [PMID: 32264738 DOI: 10.1094/phyto-12-19-0474-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Over the past 2 decades, fruit symptoms resembling a marbling pattern on the fruit skin or corking of the fruit flesh were observed on Japanese plums in South Africa, resulting in unmarketable fruit. The ability of high-throughput sequencing (HTS) to detect known and unknown pathogens was exploited by assaying affected and unaffected fruit tree accessions to identify the potential aetiological agent of marbling and/or corky flesh disease. In this study, it is shown that the disease is associated with a previously undescribed small RNA with typical viroid structural features. The potential viroid was the only pathological agent consistently detected in all symptomatic trees by HTS, and the association with the symptoms was confirmed in field surveys over two seasons. To date, this RNA was not detectable by RT-PCR in seedlings raised from seeds collected from infected trees. Although the autonomous replication of this viroid-like RNA was not proven, it was shown to be transmissible by grafting and associated with a range of symptoms that include marbling on the fruit skin, corky flesh, reduced fruit size, irregular shape, and uneven fruit surface depending on the cultivar. Moreover, the circular RNA genome, consisting of 317 nucleotides, strongly supports that this viroid-like RNA is most likely a viroid for which the name plum viroid I (PVd-I) is proposed. The primary structure of this viroid showed a less than 90% nucleotide sequence identity to viroids of the genus Apscaviroid, with which it has close phylogenetic relationships and shares conserved structural motifs.
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Affiliation(s)
- Rachelle Bester
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
- Citrus Research International, P.O. Box 2201, Matieland, 7602, South Africa
| | - Sophia S Malan
- SAPO Trust, Private Bag X5023, Stellenbosch, 7599, South Africa
| | - Hans J Maree
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
- Citrus Research International, P.O. Box 2201, Matieland, 7602, South Africa
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18
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Zhang S, Yang L, Ma L, Tian X, Li R, Zhou C, Cao M. Virome of Camellia japonica: Discovery of and Molecular Characterization of New Viruses of Different Taxa in Camellias. Front Microbiol 2020; 11:945. [PMID: 32499772 PMCID: PMC7243478 DOI: 10.3389/fmicb.2020.00945] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 04/20/2020] [Indexed: 01/09/2023] Open
Abstract
Many species of the genus Camellia are native to China, and several species such as C. japonica have been cultivated as garden plants for over 1,000 years. Virus-like symptoms have been recorded for years. In this study, C. japonica plants with various leaf symptoms were observed in Jiangxi and Chongqing provinces. The species composition of potential viruses in the symptomatic plants was analyzed by next-generation sequencing of six libraries prepared from total RNAs of specimens from 10 trees. Five new viruses were discovered, and their genome sequences were determined. These viruses were tentatively named Camellia chlorotic ringspot viruses (CaCRSVs), Camellia yellow ringspot virus (CaYRSV), Camellia-associated badnavirus (CaBaV), and Camellia-associated marafivirus (CaMaV) based on comprehensive analyses. Among these viruses, CaYRSV, CaBaV, and CaMaV share similar genome organizations and clear sequence homology with known viruses in databases and could potentially be classified as new species of the genera Badnavirus, Idaeovirus, and Marafivirus, respectively. CaCRSVs comprise two distinct viruses, and each likely contains five genomic RNA segments that were found to be distantly related to viral RNAs of members in the genus Emaravirus (family Fimoviridae). The RNAs of CaCRSVs show conserved terminal sequences that differ markedly from those of emaraviral RNAs. These data, together with the phylogenetic analysis, suggest that the evolutionary status of CaCRSVs may represent a novel genus in the family Fimoviridae. In addition, two known viruses (geminivirus and blunervirus) and a mass of betaflexiviruses existing as heterogeneous mixtures were detected, and their roles in symptom formation were studied. Collectively, the information of the viral species and detection protocols that were developed can serve as a basis for better management of these viruses. Distinguishing the virus-related symptoms from genetic characteristics of C. japonica is also significant for breeding efforts.
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Affiliation(s)
- Song Zhang
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Chongqing, China.,State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Liu Yang
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Chongqing, China.,State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Lisha Ma
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Chongqing, China.,State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Xin Tian
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Chongqing, China.,State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Ruhui Li
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD, United States
| | - Changyong Zhou
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Chongqing, China.,State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Chongqing, China.,State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
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19
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Identification and characterization of a novel rhabdovirus infecting peach in China. Virus Res 2020; 280:197905. [PMID: 32105763 DOI: 10.1016/j.virusres.2020.197905] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 02/23/2020] [Indexed: 02/08/2023]
Abstract
A novel negative-sense, single-stranded (ss) RNA virus was identified in peach trees by high-throughput sequencing, and named peach virus 1 (PeV1). The genome of PeV1 consists of 13,949 nucleotides (nt), and its organization is typical of rhabdoviruses with six open reading frames (ORFs) encoding deduced proteins N-P-P3-M-G-L on the antisense strand. These ORFs are separated by highly conserved intergenic sequences and flanked by complementary 3'-leader and 5'-trailer sequences. PeV1 shared highest complete genome (41.9%), N amino acid (43.6%), G amino acid (41.0%), and L amino acid (42.7%) identities with viruses which belong to the genus Alphanucleorhabdovirus, suggesting it may belong to a new species. This was further supported by phylogenetic analyses using amino acid sequences of N, G, and L proteins, in which this virus is always clustered with alphanucleorhabdoviruses. Collectively, results suggest that PeV1 is a member of a new alphanucleorhabdovirus species. Moreover, bioassays revealed that it could be transmitted through grafting. The findings expand our knowledge of peach-infecting viruses and alphanucleorhabdoviruses.
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20
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Kinoti WM, Nancarrow N, Dann A, Rodoni BC, Constable FE. Updating the Quarantine Status of Prunus Infecting Viruses in Australia. Viruses 2020; 12:v12020246. [PMID: 32102210 PMCID: PMC7077234 DOI: 10.3390/v12020246] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/14/2020] [Accepted: 02/20/2020] [Indexed: 12/30/2022] Open
Abstract
One hundred Prunus trees, including almond (P. dulcis), apricot (P. armeniaca), nectarine (P. persica var. nucipersica), peach (P. persica), plum (P. domestica), purple leaf plum (P. cerasifera) and sweet cherry (P. avium), were selected from growing regions Australia-wide and tested for the presence of 34 viruses and three viroids using species-specific reverse transcription-polymerase chain reaction (RT-PCR) or polymerase chain reaction (PCR) tests. In addition, the samples were tested using some virus family or genus-based RT-PCR tests. The following viruses were detected: Apple chlorotic leaf spot virus (ACLSV) (13/100), Apple mosaic virus (ApMV) (1/100), Cherry green ring mottle virus (CGRMV) (4/100), Cherry necrotic rusty mottle virus (CNRMV) (2/100), Cherry virus A (CVA) (14/100), Little cherry virus 2 (LChV2) (3/100), Plum bark necrosis stem pitting associated virus (PBNSPaV) (4/100), Prune dwarf virus (PDV) (3/100), Prunus necrotic ringspot virus (PNRSV) (52/100), Hop stunt viroid (HSVd) (9/100) and Peach latent mosaic viroid (PLMVd) (6/100). The results showed that PNRSV is widespread in Prunus trees in Australia. Metagenomic high-throughput sequencing (HTS) and bioinformatics analysis were used to characterise the genomes of some viruses that were detected by RT-PCR tests and Apricot latent virus (ApLV), Apricot vein clearing associated virus (AVCaV), Asian Prunus Virus 2 (APV2) and Nectarine stem pitting-associated virus (NSPaV) were also detected. This is the first report of ApLV, APV2, CGRMV, CNRNV, LChV1, LChV2, NSPaV and PBNSPaV occurring in Australia. It is also the first report of ASGV infecting Prunus species in Australia, although it is known to infect other plant species including pome fruit and citrus.
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Affiliation(s)
- Wycliff M. Kinoti
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
- Correspondence:
| | | | - Alison Dann
- Plant Biosecurity and Diagnostic Branch, Bioisecurity Tasmania, Hobart, TAS 7001, Australia
| | - Brendan C. Rodoni
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
| | - Fiona E. Constable
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
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21
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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, Winter S, Bosco D, Chiumenti M, Di Serio F, Kaluski T, Minafra A, Rubino L. Pest categorisation of non-EU viruses and viroids of Prunus L. EFSA J 2019; 17:e05735. [PMID: 32626421 PMCID: PMC7009144 DOI: 10.2903/j.efsa.2019.5735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Following a request from the EU Commission, the Panel on Plant Health addressed the pest categorisation of the viruses and viroids of Prunus 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 Ilarvirus S1 and Ilarvirus S2, for which very limited information exists, the pest categorisation was completed for 26 viruses and 1 viroid having acknowledged identities and available detection methods. All these viruses are efficiently transmitted by vegetative plant propagation techniques, with plants for planting representing the major pathway for long-distance dispersal and thus considered as the major pathway for entry. Depending on the virus, additional pathway(s) can also be Prunus 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. Apple scar skin viroid, American plum line pattern virus, cherry mottle leaf virus, cherry rasp leaf virus, cherry rosette virus, cherry rusty mottle-associated virus, cherry twisted leaf-associated virus, peach enation virus, peach mosaic virus, peach rosette mosaic virus, tobacco ringspot virus and tomato ringspot virus meet all the criteria evaluated by EFSA to qualify as potential Union quarantine pests (QPs). With the exception of impact in the EU territory, on which the Panel was unable to conclude, apricot vein clearing virus, Asian prunus virus 1, Asian prunus virus 2, Asian prunus virus 3, Caucasus prunus virus, cherry virus B, Mume virus A, nectarine stem pitting-associated virus, nectarine virus M, peach chlorotic mottle virus, peach leaf pitting-associated virus, peach virus D, prunus virus F and prunus virus T satisfy all the other criteria to be considered as potential Union QPs. Prunus geminivirus A does not meet the criterion of having negative impact in the EU. 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 the non-EU viruses, in general these viruses do not meet the criteria assessed by EFSA to qualify as 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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Analyses of virus/viroid communities in nectarine trees by next-generation sequencing and insight into viral synergisms implication in host disease symptoms. Sci Rep 2019; 9:12261. [PMID: 31439919 PMCID: PMC6706421 DOI: 10.1038/s41598-019-48714-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 08/09/2019] [Indexed: 01/02/2023] Open
Abstract
We analyzed virus and viroid communities in five individual trees of two nectarine cultivars with different disease phenotypes using next-generation sequencing technology. Different viral communities were found in different cultivars and individual trees. A total of eight viruses and one viroid in five families were identified in a single tree. To our knowledge, this is the first report showing that the most-frequently identified viral and viroid species co-infect a single individual peach tree, and is also the first report of peach virus D infecting Prunus in China. Combining analyses of genetic variation and sRNA data for co-infecting viruses/viroid in individual trees revealed for the first time that viral synergisms involving a few virus genera in the Betaflexiviridae, Closteroviridae, and Luteoviridae families play a role in determining disease symptoms. Evolutionary analysis of one of the most dominant peach pathogens, peach latent mosaic viroid (PLMVd), shows that the PLMVd sequences recovered from symptomatic and asymptomatic nectarine leaves did not all cluster together, and intra-isolate divergent sequence variants co-infected individual trees. Our study provides insight into the role that mixed viral/viroid communities infecting nectarine play in host symptom development, and will be important in further studies of epidemiological features of host-pathogen interactions.
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Villamor DEV, Ho T, Al Rwahnih M, Martin RR, Tzanetakis IE. High Throughput Sequencing For Plant Virus Detection and Discovery. PHYTOPATHOLOGY 2019; 109:716-725. [PMID: 30801236 DOI: 10.1094/phyto-07-18-0257-rvw] [Citation(s) in RCA: 162] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Over the last decade, virologists have discovered an unprecedented number of viruses using high throughput sequencing (HTS), which led to the advancement of our knowledge on the diversity of viruses in nature, particularly unraveling the virome of many agricultural crops. However, these new virus discoveries have often widened the gaps in our understanding of virus biology; the forefront of which is the actual role of a new virus in disease, if any. Yet, when used critically in etiological studies, HTS is a powerful tool to establish disease causality between the virus and its host. Conversely, with globalization, movement of plant material is increasingly more common and often a point of dispute between countries. HTS could potentially resolve these issues given its capacity to detect and discover. Although many pipelines are available for plant virus discovery, all share a common backbone. A description of the process of plant virus detection and discovery from HTS data are presented, providing a summary of the different pipelines available for scientists' utility in their research.
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Affiliation(s)
- D E V Villamor
- 1 Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - T Ho
- 1 Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - M Al Rwahnih
- 2 Department of Plant Pathology, University of California, Davis 95616; and
| | - R R Martin
- 3 Horticulture Crops Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330
| | - I E Tzanetakis
- 1 Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
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Pallás V, Sánchez-Navarro JA, James D. Recent Advances on the Multiplex Molecular Detection of Plant Viruses and Viroids. Front Microbiol 2018; 9:2087. [PMID: 30250456 PMCID: PMC6139301 DOI: 10.3389/fmicb.2018.02087] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/15/2018] [Indexed: 12/14/2022] Open
Abstract
Plant viruses are still one of the main contributors to economic losses in agriculture. It has been estimated that plant viruses can cause as much as 50 billion euros loss worldwide, per year. This situation may be worsened by recent climate change events and the associated changes in disease epidemiology. Reliable and early detection methods are still one of the main and most effective actions to develop control strategies for plant viral diseases. During the last years, considerable progress has been made to develop tools with high specificity and low detection limits for use in the detection of these plant pathogens. Time and cost reductions have been some of the main objectives pursued during the last few years as these increase their feasibility for routine use. Among other strategies, these objectives can be achieved by the simultaneous detection and (or) identification of several viruses in a single assay. Nucleic acid-based detection techniques are especially suitable for this purpose. Polyvalent detection has allowed the detection of multiple plant viruses at the genus level. Multiplexing RT polymerase chain reaction (PCR) has been optimized for the simultaneous detection of more than 10 plant viruses/viroids. In this short review, we provide an update on the progress made during the last decade on techniques such as multiplex PCR, polyvalent PCR, non-isotopic molecular hybridization techniques, real-time PCR, and array technologies to allow simultaneous detection of multiple plant viruses. Also, the potential and benefits of the powerful new technique of deep sequencing/next-generation sequencing are described.
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Affiliation(s)
- Vicente Pallás
- Instituto de Biología Molecular y Celular de Plantas, IBMCP, Universitat Politècnica de València – Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Jesus A. Sánchez-Navarro
- Instituto de Biología Molecular y Celular de Plantas, IBMCP, Universitat Politècnica de València – Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Delano James
- Sidney Laboratory, Canadian Food Inspection Agency, Sidney, BC, Canada
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Maliogka VI, Minafra A, Saldarelli P, Ruiz-García AB, Glasa M, Katis N, Olmos A. Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies. Viruses 2018; 10:E436. [PMID: 30126105 PMCID: PMC6116224 DOI: 10.3390/v10080436] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/09/2018] [Accepted: 08/13/2018] [Indexed: 12/21/2022] Open
Abstract
Perennial crops, such as fruit trees, are infected by many viruses, which are transmitted through vegetative propagation and grafting of infected plant material. Some of these pathogens cause severe crop losses and often reduce the productive life of the orchards. Detection and characterization of these agents in fruit trees is challenging, however, during the last years, the wide application of high-throughput sequencing (HTS) technologies has significantly facilitated this task. In this review, we present recent advances in the discovery, detection, and characterization of fruit tree viruses and virus-like agents accomplished by HTS approaches. A high number of new viruses have been described in the last 5 years, some of them exhibiting novel genomic features that have led to the proposal of the creation of new genera, and the revision of the current virus taxonomy status. Interestingly, several of the newly identified viruses belong to virus genera previously unknown to infect fruit tree species (e.g., Fabavirus, Luteovirus) a fact that challenges our perspective of plant viruses in general. Finally, applied methodologies, including the use of different molecules as templates, as well as advantages and disadvantages and future directions of HTS in fruit tree virology are discussed.
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Affiliation(s)
- Varvara I Maliogka
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Angelantonio Minafra
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/D, 70126 Bari, Italy.
| | - Pasquale Saldarelli
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/D, 70126 Bari, Italy.
| | - Ana B Ruiz-García
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113 Moncada, Valencia, Spain.
| | - Miroslav Glasa
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84505 Bratislava, Slovak Republic.
| | - Nikolaos Katis
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Antonio Olmos
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113 Moncada, Valencia, Spain.
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27
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Katsiani A, Maliogka VI, Katis N, Svanella-Dumas L, Olmos A, Ruiz-García AB, Marais A, Faure C, Theil S, Lotos L, Candresse T. High-Throughput Sequencing Reveals Further Diversity of Little Cherry Virus 1 with Implications for Diagnostics. Viruses 2018; 10:E385. [PMID: 30037079 PMCID: PMC6070981 DOI: 10.3390/v10070385] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/11/2018] [Accepted: 07/19/2018] [Indexed: 12/21/2022] Open
Abstract
Little cherry virus 1 (LChV1, Velarivirus, Closteroviridae) is a widespread pathogen of sweet or sour cherry and other Prunus species, which exhibits high genetic diversity and lacks a putative efficient transmission vector. Thus far, four distinct phylogenetic clusters of LChV1 have been described, including isolates from different Prunus species. The recent application of high throughput sequencing (HTS) technologies in fruit tree virology has facilitated the acquisition of new viral genomes and the study of virus diversity. In the present work, several new LChV1 isolates from different countries were fully sequenced using different HTS approaches. Our results reveal the presence of further genetic diversity within the LChV1 species. Interestingly, mixed infections of the same sweet cherry tree with different LChV1 variants were identified for the first time. Taken together, the high intra-host and intra-species diversities of LChV1 might affect its pathogenicity and have clear implications for its accurate diagnostics.
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Affiliation(s)
- Asimina Katsiani
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Varvara I Maliogka
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Nikolaos Katis
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Laurence Svanella-Dumas
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, CS20032, Villenave d'Ornon CEDEX, F-33882 Bordeaux, France.
| | - Antonio Olmos
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Naquera km 4.5, Moncada, 46113 Valencia, Spain.
| | - Ana B Ruiz-García
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Naquera km 4.5, Moncada, 46113 Valencia, Spain.
| | - Armelle Marais
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, CS20032, Villenave d'Ornon CEDEX, F-33882 Bordeaux, France.
| | - Chantal Faure
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, CS20032, Villenave d'Ornon CEDEX, F-33882 Bordeaux, France.
| | - Sébastien Theil
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, CS20032, Villenave d'Ornon CEDEX, F-33882 Bordeaux, France.
| | - Leonidas Lotos
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, CS20032, Villenave d'Ornon CEDEX, F-33882 Bordeaux, France.
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28
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Liu H, Wu L, Nikolaeva E, Peter K, Liu Z, Mollov D, Cao M, Li R. Characterization of a new apple luteovirus identified by high-throughput sequencing. Virol J 2018; 15:85. [PMID: 29764461 PMCID: PMC5952423 DOI: 10.1186/s12985-018-0998-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 05/06/2018] [Indexed: 01/05/2023] Open
Abstract
Background ‘Rapid Apple Decline’ (RAD) is a newly emerging problem of young, dwarf apple trees in the Northeastern USA. The affected trees show trunk necrosis, cracking and canker before collapse in summer. In this study, we discovered and characterized a new luteovirus from apple trees in RAD-affected orchards using high-throughput sequencing (HTS) technology and subsequent Sanger sequencing. Methods Illumina NextSeq sequencing was applied to total RNAs prepared from three diseased apple trees. Sequence reads were de novo assembled, and contigs were annotated by BLASTx. RT-PCR and 5′/3’ RACE sequencing were used to obtain the complete genome of a new virus. RT-PCR was used to detect the virus. Results Three common apple viruses and a new luteovirus were identified from the diseased trees by HTS and RT-PCR. Sequence analyses of the complete genome of the new virus show that it is a new species of the genus Luteovirus in the family Luteoviridae. The virus is graft transmissible and detected by RT-PCR in apple trees in a couple of orchards. Conclusions A new luteovirus and/or three known viruses were found to be associated with RAD. Molecular characterization of the new luteovirus provides important information for further investigation of its distribution and etiological role. Electronic supplementary material The online version of this article (10.1186/s12985-018-0998-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Huawei Liu
- USDA-ARS, National Germplasm Resources Laboratory, Bldg. 004/Rm 015, Beltsville, Maryland, 20705, USA
| | - Liping Wu
- USDA-ARS, National Germplasm Resources Laboratory, Bldg. 004/Rm 015, Beltsville, Maryland, 20705, USA.,School of Life Science, Nanchang University, Nanchang, 330031, Jiangxi, China
| | - Ekaterina Nikolaeva
- Pennsylvania Department of Agriculture, Harrisburg, Pennsylvania, 17110, USA
| | - Kari Peter
- Pennsylvania State University, Biglerville, Pennsylvania, 17307, USA
| | - Zongrang Liu
- USDA-ARS, Appalachian Fruit Research Station, Kearneysville, West Virginia, 25430, USA
| | - Dimitre Mollov
- USDA-ARS, National Germplasm Resources Laboratory, Bldg. 004/Rm 015, Beltsville, Maryland, 20705, USA
| | - Mengji Cao
- Citrus Research Institute, Southwest University, Chongqing, 400712, China
| | - Ruhui Li
- USDA-ARS, National Germplasm Resources Laboratory, Bldg. 004/Rm 015, Beltsville, Maryland, 20705, USA.
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29
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Green KJ, Mollov D, Tran LT, Alvarez-Quinto RA, Ochoa JB, Quito-Avila DF, Karasev AV. Characterization of a New Tymovirus Causing Stunting and Chlorotic Mosaic in Naranjilla (Solanum quitoense). PLANT DISEASE 2018; 102:911-918. [PMID: 30673388 DOI: 10.1094/pdis-10-17-1534-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Naranjilla ("little orange"), also known as lulo (Solanum quitoense Lam.), is a perennial shrub species cultivated in the Andes for fresh fruit and juice production. In 2015, a naranjilla plant exhibiting stunting, mosaic, and chlorotic spots was sampled in the Pastaza province of Ecuador and maintained under greenhouse conditions. An infectious agent was mechanically transmitted to indicator plants and was subjected to biological and molecular characterization. Spherical particles approximately 30 nm in diameter, composed of a single 20-kDa capsid protein, were observed under an electron microscope in infected naranjilla plants. High-throughput sequencing conducted on inoculated Nicotiana benthamiana plants produced a single sequence contig sharing the closest relationship with several tymoviruses. The entire 6,245-nucleotide genome of a new tymovirus was amplified using reverse-transcription polymerase chain reaction and resequenced with the Sanger methodology. The genome had three open reading frames typical of tymoviruses, and displayed a whole-genome nucleotide identity level with the closest tymovirus, Eggplant mosaic virus, at 71% (90% coverage). This tymovirus from naranjilla was able to systemically infect eggplant, tamarillo, N. benthamiana, and naranjilla. In naranjilla, it produced mosaic, chlorotic spots, and stunting, similar to the symptoms observed in the original plant. The virus was unable to infect potato and tobacco and unable to systemically infect pepper plants, replicating only in inoculated leaves. We concluded that this virus represented a new tymovirus infecting naranjilla, and proposed the tentative name Naranjilla chlorotic mosaic virus (NarCMV).
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Affiliation(s)
- Kelsie J Green
- Department of Entomology, Plant Pathology and Nematology (EPPN), University of Idaho, Moscow
| | - Dimitre Mollov
- United States Department of Agriculture-Agricultural Research Service, National Germplasm Resources Laboratory, Beltsville, MD
| | | | - Robert A Alvarez-Quinto
- Centro de Investigaciones Biotecnológicas del Ecuador and Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Ecuador
| | - Jose B Ochoa
- Instituto Nacional Autónomo de Investigaciones Agropecuarias, Quito, Ecuador
| | - Diego F Quito-Avila
- Centro de Investigaciones Biotecnológicas del Ecuador and Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral
| | - Alexander V Karasev
- Department of EPPN and Bioinformatics and Computational Biology Program, University of Idaho
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Molecular Characterization of a Novel Species of Capillovirus from Japanese Apricot (Prunus mume). Viruses 2018; 10:v10040144. [PMID: 29570605 PMCID: PMC5923438 DOI: 10.3390/v10040144] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/17/2018] [Accepted: 03/21/2018] [Indexed: 11/17/2022] Open
Abstract
With the increased use of high-throughput sequencing methods, new viruses infecting Prunus spp. are being discovered and characterized, especially in the family Betaflexiviridae. Double-stranded RNAs from symptomatic leaves of a Japanese apricot (Prunusmume) tree from Japan were purified and analyzed by Illumina sequencing. Blast comparisons of reconstructed contigs showed that the P. mume sample was infected by a putative novel virus with homologies to Cherry virus A (CVA) and to the newly described Currant virus A (CuVA), both members of genus Capillovirus. Completion of the genome showed the new agent to have a genomic organization typical of capilloviruses, with two overlapping open reading frames encoding a large replication-associated protein fused to the coat protein (CP), and a putative movement protein (MP). This virus shares only, respectively, 63.2% and 62.7% CP amino acid identity with the most closely related viruses, CVA and CuVA. Considering the species demarcation criteria in the family and phylogenetic analyses, this virus should be considered as representing a new viral species in the genus Capillovirus, for which the name of Mume virus A is proposed.
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Abstract
Many recent studies have demonstrated that several known and unknown viruses infect many horticultural plants. However, the elucidation of a viral population and the understanding of the genetic complexity of viral genomes in a single plant are rarely reported. Here, we conducted metatranscriptome analyses using six different peach trees representing six individual peach cultivars. We identified six viruses including five viruses in the family Betaflexiviridae and a novel virus belonging to the family Tymoviridae as well as two viroids. The number of identified viruses and viroids in each transcriptome ranged from one to six. We obtained 18 complete or nearly complete genomes for six viruses and two viroids using transcriptome data. Furthermore, we analyzed single nucleotide variations for individual viral genomes. In addition, we analyzed the amount of viral RNA and copy number for identified viruses and viroids. Some viruses or viroids were commonly present in different cultivars; however, the list of infected viruses and viroids in each cultivar was different. Taken together, our study reveals the viral population in a single peach tree and a comprehensive overview for the diversities of viral communities in different peach cultivars.
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Pandey B, Naidu RA, Grove GG. Detection and analysis of mycovirus-related RNA viruses from grape powdery mildew fungus Erysiphe necator. Arch Virol 2018; 163:1019-1030. [PMID: 29356991 DOI: 10.1007/s00705-018-3714-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 12/05/2017] [Indexed: 10/18/2022]
Abstract
The fungus, Erysiphe necator Schw., is an important plant pathogen causing powdery mildew disease in grapevines worldwide. In this study, high-throughput sequencing of double-stranded RNA extracted from the fungal tissue combined with bioinformatics was used to examine mycovirus-related sequences associated with E. necator. The results showed the presence of eight mycovirus-related sequences. Five of these sequences representing three new mycoviruses showed alignment with sequences of viruses classified in the genus Alphapartitivirus in the family Partitiviridae. Another three sequences representing three new mycoviruses showed similarity to classifiable members of the genus Mitovirus in the family Narnaviridae. These mycovirus isolates were named Erysiphe necator partitivirus 1, 2, and 3 (EnPV 1-3) and Erysiphe necator mitovirus 1, 2, and 3 (EnMV 1-3) reflecting their E. necator origin and their phylogenetic affiliation with other mycoviruses.
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Affiliation(s)
- B Pandey
- Department of Plant Pathology, Washington State University, Irrigated Agriculture Research and Extension Center, Prosser, WA, 99350, USA. .,Department of Plant Pathology, North Dakota State University, 306 Walster Hall, Fargo, ND, 58102, USA.
| | - R A Naidu
- Department of Plant Pathology, Washington State University, Irrigated Agriculture Research and Extension Center, Prosser, WA, 99350, USA
| | - G G Grove
- Department of Plant Pathology, Washington State University, Irrigated Agriculture Research and Extension Center, Prosser, WA, 99350, USA
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Mu F, Xie J, Cheng S, You MP, Barbetti MJ, Jia J, Wang Q, Cheng J, Fu Y, Chen T, Jiang D. Virome Characterization of a Collection of S. sclerotiorum from Australia. Front Microbiol 2018; 8:2540. [PMID: 29375495 PMCID: PMC5768646 DOI: 10.3389/fmicb.2017.02540] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 12/06/2017] [Indexed: 11/13/2022] Open
Abstract
Sclerotinia sclerotiorum is a devastating plant pathogen that attacks numerous economically important broad acre and vegetable crops worldwide. Mycoviruses are widespread viruses that infect fungi, including S. sclerotiorum. As there were no previous reports of the presence of mycoviruses in this pathogen in Australia, studies were undertaken using RNA_Seq analysis to determine the diversity of mycoviruses in 84 Australian S. sclerotiorum isolates collected from various hosts. After RNA sequences were subjected to BLASTp analysis using NCBI database, 285 contigs representing partial or complete genomes of 57 mycoviruses were obtained, and 34 of these (59.6%) were novel viruses. These 57 viruses were grouped into 10 distinct lineages, namely Endornaviridae (four novel mycoviruses), Genomoviridae (isolate of SsHADV-1), Hypoviridae (two novel mycoviruses), Mononegavirales (four novel mycovirusess), Narnaviridae (10 novel mycoviruses), Partitiviridae (two novel mycoviruses), Ourmiavirus (two novel mycovirus), Tombusviridae (two novel mycoviruses), Totiviridae (one novel mycovirus), Tymovirales (five novel mycoviruses), and two non-classified mycoviruses lineages (one Botrytis porri RNA virus 1, one distantly related to Aspergillus fumigatus tetramycovirus-1). Twenty-five mitoviruses were determined and mitoviruses were dominant in the isolates tested. This is not only the first study to show existence of mycoviruses in S. sclerotiorum in Australia, but highlights how they are widespread and that many novel mycoviruses occur there. Further characterization of these mycoviruses is warranted, both in terms of exploring these novel mycoviruses for innovative biocontrol of Sclerotinia diseases and in enhancing our overall knowledge on viral diversity, taxonomy, ecology, and evolution.
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Affiliation(s)
- Fan Mu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Shufen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Ming Pei You
- Faculty of Science, UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - Martin J. Barbetti
- Faculty of Science, UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - Jichun Jia
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Qianqian Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Yanping Fu
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Tao Chen
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
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Alexander MM, Mohr JP, DeBlasio SL, Chavez JD, Ziegler-Graff V, Brault V, Bruce JE, Heck MC. Insights in luteovirid structural biology guided by chemical cross-linking and high resolution mass spectrometry. Virus Res 2017; 241:42-52. [PMID: 28502641 DOI: 10.1016/j.virusres.2017.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 05/09/2017] [Accepted: 05/09/2017] [Indexed: 10/19/2022]
Abstract
Interactions among plant pathogenic viruses in the family Luteoviridae and their plant hosts and insect vectors are governed by the topology of the viral capsid, which is the sole vehicle for long distance movement of the viral genome. Previous application of a mass spectrometry-compatible cross-linker to preparations of the luteovirid Potato leafroll virus (PLRV; Luteoviridae: Polerovirus) revealed a detailed network of interactions between viral structural proteins and enabled generation of the first cross-linking guided coat protein models. In this study, we extended application of chemical cross-linking technology to the related Turnip yellows virus (TuYV; Luteoviridae: Polerovirus). Remarkably, all cross-links found between sites in the viral coat protein found for TuYV were also found in PLRV. Guided by these data, we present two models for the TuYV coat protein trimer, the basic structural unit of luteovirid virions. Additional cross-links found between the TuYV coat protein and a site in the viral protease domain suggest a possible role for the luteovirid protease in regulating the structural biology of these viruses.
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Affiliation(s)
- Mariko M Alexander
- School of Integrative Plant Science, Plant Pathology and Plant Microbe Biology Section, Cornell University, Ithaca, NY, USA; Boyce Thompson Institute, Ithaca, NY, USA
| | - Jared P Mohr
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Stacy L DeBlasio
- USDA-Agricultural Research Service, Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA
| | - Juan D Chavez
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | | | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Michelle Cilia Heck
- School of Integrative Plant Science, Plant Pathology and Plant Microbe Biology Section, Cornell University, Ithaca, NY, USA; Boyce Thompson Institute, Ithaca, NY, USA; USDA-Agricultural Research Service, Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA.
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35
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Complete Genome Sequence of Nectarine stem pitting-associated virus, Isolated from Prunus persica in Cheongdo County, South Korea. GENOME ANNOUNCEMENTS 2017; 5:5/35/e00908-17. [PMID: 28860259 PMCID: PMC5578857 DOI: 10.1128/genomea.00908-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the first complete genome sequence of a South Korean isolate of Nectarine stem pitting-associated virus (NSPaV) from peach and compare it with previously described complete NSPaV genome sequences. The highest whole-genome nucleotide sequence identity was 95.3% with GenBank accession no. KT273409 (NSPaV) from the United States.
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36
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Rott M, Xiang Y, Boyes I, Belton M, Saeed H, Kesanakurti P, Hayes S, Lawrence T, Birch C, Bhagwat B, Rast H. Application of Next Generation Sequencing for Diagnostic Testing of Tree Fruit Viruses and Viroids. PLANT DISEASE 2017; 101:1489-1499. [PMID: 30678581 DOI: 10.1094/pdis-03-17-0306-re] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Conventional detection of viruses and virus-like diseases of plants is accomplished using a combination of molecular, serological, and biological indexing. These are the primary tools used by plant virologists to monitor and ensure trees are free of known viral pathogens. The biological indexing assay, or bioassay, is considered to be the "gold standard" as it is the only method of the three that can detect new, uncharacterized, or poorly characterized viral disease agents. Unfortunately, this method is also the most labor intensive and can take up to three years to complete. Next generation sequencing (NGS) is a technology with rapidly expanding possibilities including potential applications for the detection of plant viruses. In this study, comparisons are made between tree fruit testing by conventional and NGS methods, to demonstrate the efficacy of NGS. A comparison of 178 infected trees, many infected with several viral pathogens, demonstrated that conventional and NGS were equally capable of detecting known viruses and viroids. Comparable results were obtained for 170 of 178 of the specimens. Of the remaining eight specimens, some discrepancies were observed between viruses detected by the two methods, representing less than 5% of the specimens. NGS was further demonstrated to be equal or superior for the detection of new or poorly characterized viruses when compared with a conventional bioassay. These results validated both the effectiveness of conventional virus testing methods and the use of NGS as an additional or alternative method for plant virus detection.
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Affiliation(s)
- M Rott
- Centre for Plant Health, Sidney Laboratory, Canadian Food Inspection Agency, North Saanich, BC, V8L 1H3, Canada
| | - Y Xiang
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, BC, V0H1Z0, Canada
| | - I Boyes
- Centre for Plant Health, Sidney Laboratory, Canadian Food Inspection Agency, North Saanich, BC, V8L 1H3, Canada
| | - M Belton
- Centre for Plant Health, Sidney Laboratory, Canadian Food Inspection Agency, North Saanich, BC, V8L 1H3, Canada
| | - H Saeed
- Centre for Plant Health, Sidney Laboratory, Canadian Food Inspection Agency, North Saanich, BC, V8L 1H3, Canada
| | - P Kesanakurti
- Centre for Plant Health, Sidney Laboratory, Canadian Food Inspection Agency, North Saanich, BC, V8L 1H3, Canada
| | - S Hayes
- Centre for Plant Health, Sidney Laboratory, Canadian Food Inspection Agency, North Saanich, BC, V8L 1H3, Canada
| | - T Lawrence
- Centre for Plant Health, Sidney Laboratory, Canadian Food Inspection Agency, North Saanich, BC, V8L 1H3, Canada
| | - C Birch
- Centre for Plant Health, Sidney Laboratory, Canadian Food Inspection Agency, North Saanich, BC, V8L 1H3, Canada
| | - B Bhagwat
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, BC, V0H1Z0, Canada
| | - H Rast
- Centre for Plant Health, Sidney Laboratory, Canadian Food Inspection Agency, North Saanich, BC, V8L 1H3, Canada
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37
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Wu LP, Liu HW, Bateman M, Liu Z, Li R. Molecular characterization of a novel luteovirus from peach identified by high-throughput sequencing. Arch Virol 2017; 162:2903-2905. [PMID: 28550432 DOI: 10.1007/s00705-017-3388-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 04/12/2017] [Indexed: 11/30/2022]
Abstract
Contigs with sequence homologies to cherry-associated luteovirus were identified by high-throughput sequencing analysis in two peach accessions. Complete genomic sequences of the two isolates of this virus were determined to be 5,819 and 5,814 nucleotides long, respectively. The genome of the new virus is typical of luteoviruses, containing eight open reading frames in a very similar arrangement. Its genomic sequence is 58-74% identical to those of other members of the genus Luteovirus. These sequences thus belong to a new virus, which we have named "peach-associated luteovirus".
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Affiliation(s)
- L-P Wu
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD, 20705, USA.,School of Life Science, Key Laboratory of Poyang Lake Environment and Resource, Ministry of Education, Nanchang University, Nanchang, 330031, Jiangxi, China
| | - H-W Liu
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD, 20705, USA
| | - M Bateman
- USDA-APHIS, Plant Protection and Quarantine, Riverdale, MD, 20737, USA
| | - Z Liu
- USDA-ARS, Appalachian Fruit Research Station, Kearneysville, WV, 25430, USA
| | - R Li
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD, 20705, USA.
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38
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Krizbai L, Kriston E, Kreuze J, Melika G. Identification of
Nectarine stem pitting‐associated virus
infecting
Prunus persica
in Hungary. ACTA ACUST UNITED AC 2017. [DOI: 10.5197/j.2044-0588.2017.035.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- L. Krizbai
- Plant Health and Molecular Biology LaboratoryNational Food Chain Safety OfficeBudaörsi Str. 141‐145.1118BudapestHungary
| | - E. Kriston
- Plant Health and Molecular Biology LaboratoryNational Food Chain Safety OfficeBudaörsi Str. 141‐145.1118BudapestHungary
| | - J. Kreuze
- Virology LaboratoryInternational Potato CenterAv. La Molina 1895La MolinaLima12Peru
| | - G. Melika
- Plant Health and Molecular Biology LaboratoryNational Food Chain Safety OfficeBudaörsi Str. 141‐145.1118BudapestHungary
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39
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Complete nucleotide sequence and genome organization of peach virus D, a putative new member of the genus Marafivirus. Arch Virol 2017; 162:1769-1772. [PMID: 28188372 DOI: 10.1007/s00705-017-3255-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 01/17/2017] [Indexed: 10/20/2022]
Abstract
The complete nucleotide sequence of peach virus D (PeVD) from Prunus persica was determined. The PeVD genome consists of 6,612 nucleotides excluding the 3' poly(A) tail and contains a single open reading frame coding for a polyprotein of 227 kDa. Sequence comparisons and phylogenetic analysis revealed that PeVD is most closely related to viruses in the genus Marafivirus, family Tymoviridae. The complete nucleotide and CP amino acid sequences of PeVD were most similar (51.1-57.8% and 32.2-48.0%, respectively) to members of the genus Marafivirus, suggesting that PeVD is a new member of this genus.
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40
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Massart S, Candresse T, Gil J, Lacomme C, Predajna L, Ravnikar M, Reynard JS, Rumbou A, Saldarelli P, Škorić D, Vainio EJ, Valkonen JPT, Vanderschuren H, Varveri C, Wetzel T. A Framework for the Evaluation of Biosecurity, Commercial, Regulatory, and Scientific Impacts of Plant Viruses and Viroids Identified by NGS Technologies. Front Microbiol 2017; 8:45. [PMID: 28174561 PMCID: PMC5258733 DOI: 10.3389/fmicb.2017.00045] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 01/06/2017] [Indexed: 01/14/2023] Open
Abstract
Recent advances in high-throughput sequencing technologies and bioinformatics have generated huge new opportunities for discovering and diagnosing plant viruses and viroids. Plant virology has undoubtedly benefited from these new methodologies, but at the same time, faces now substantial bottlenecks, namely the biological characterization of the newly discovered viruses and the analysis of their impact at the biosecurity, commercial, regulatory, and scientific levels. This paper proposes a scaled and progressive scientific framework for efficient biological characterization and risk assessment when a previously known or a new plant virus is detected by next generation sequencing (NGS) technologies. Four case studies are also presented to illustrate the need for such a framework, and to discuss the scenarios.
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Affiliation(s)
- Sebastien Massart
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège Gembloux, Belgium
| | - Thierry Candresse
- Institut National de la Recherche Agronomique (INRA), University of Bordeaux, CS20032 UMR 1332 BFP Villenave d'Ornon, France
| | - José Gil
- Plant Biology, Linnean Centre for Plant Biology, Uppsala BioCentre, Swedish University of Agricultural Sciences Uppsala, Sweden
| | - Christophe Lacomme
- Virology and Zoology, Science and Advice for Scottish Agriculture Edinbourgh, UK
| | - Lukas Predajna
- Department of Plant Virology, Institute of Virology, Biomedical Research Center, Slovak Academy of Science (SAS) Bratislava, Slovakia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology Ljubljana, Slovenia
| | | | - Artemis Rumbou
- Division Phytomedicine Lentzeallee, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-University of Berlin Berlin, Germany
| | - Pasquale Saldarelli
- National Research Council Institute for Sustainable Plant Protection Bari, Italy
| | - Dijana Škorić
- Department of Biology, Faculty of Science, University of Zagreb Zagreb, Croatia
| | - Eeva J Vainio
- Management and Production of Renewable Resources, Natural Resources Institute Finland (Luke) Helsinki, Finland
| | - Jari P T Valkonen
- Department of Agricultural Sciences, University of Helsinki Helsinki, Finland
| | - Hervé Vanderschuren
- Plant Genetics, Gembloux Agro-Bio Tech, University of Liège Gembloux, Belgium
| | - Christina Varveri
- Department of Phytopathology, Benaki Phytopathological Institute Athens, Greece
| | - Thierry Wetzel
- DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse Germany
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41
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Matsumura EE, Coletta Filho HD, de Oliveira Dorta S, Nouri S, Machado MA. Genetic Structure and Molecular Variability Analysis of Citrus sudden death-associated virus Isolates from Infected Plants Grown in Brazil. Viruses 2016; 8:E330. [PMID: 27999249 PMCID: PMC5192391 DOI: 10.3390/v8120330] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/09/2016] [Accepted: 12/10/2016] [Indexed: 01/15/2023] Open
Abstract
Citrus sudden death-associated virus (CSDaV) is a monopartite positive-sense single-stranded RNA virus that was suggested to be associated with citrus sudden death (CSD) disease in Brazil. Here, we report the first study of the genetic structure and molecular variability among 31 CSDaV isolates collected from both symptomatic and asymptomatic trees in CSD-affected areas. Analyses of partial nucleotide sequences of five domains of the CSDaV genomic RNA, including those encoding for the methyltransferase, the multi-domain region (MDR), the helicase, the RNA-dependent RNA polymerase and the coat protein, showed that the MDR coding region was the most diverse region assessed here, and a possible association between this region and virus adaption to different host or plant tissues is considered. Overall, the nucleotide diversity (π) was low for CSDaV isolates, but the phylogenetic analyses revealed the predominance of two main groups, one of which showed a higher association with CSD-symptomatic plants. Isolates obtained from CSD-symptomatic plants, compared to those obtained from asymptomatic plants, showed higher nucleotide diversity, nonsynonymous and synonymous substitution rates and number of amino acid changes on the coding regions located closer to the 5' end region of the genomic RNA. This work provides new insights into the genetic diversity of the CSDaV, giving support for further epidemiological studies.
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Affiliation(s)
- Emilyn Emy Matsumura
- Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Botucatu, São Paulo 03178-200, Brazil.
- Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agronômico, Cordeiropolis, SP 13490-970, Brazil.
| | - Helvécio Della Coletta Filho
- Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agronômico, Cordeiropolis, SP 13490-970, Brazil.
| | - Silvia de Oliveira Dorta
- Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agronômico, Cordeiropolis, SP 13490-970, Brazil.
| | - Shahideh Nouri
- Department of Plant Pathology, University of California Davis, Davis, CA 95616, USA.
| | - Marcos Antonio Machado
- Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agronômico, Cordeiropolis, SP 13490-970, Brazil.
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42
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Villamor DEV, Pillai SS, Eastwell KC. High throughput sequencing reveals a novel fabavirus infecting sweet cherry. Arch Virol 2016; 162:811-816. [PMID: 27815695 DOI: 10.1007/s00705-016-3141-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 10/30/2016] [Indexed: 11/30/2022]
Abstract
The genus Fabavirus currently consists of five species represented by viruses that infect a wide range of hosts but none reported from temperate climate fruit trees. A virus with genomic features resembling fabaviruses (tentatively named Prunus virus F, PrVF) was revealed by high throughput sequencing of extracts from a sweet cherry tree (Prunus avium). PrVF was subsequently shown to be graft transmissible and further identified in three other non-symptomatic Prunus spp. from different geographical locations. Two genetic variants of RNA1 and RNA2 coexisted in the same samples. RNA1 consisted of 6,165 and 6,163 nucleotides, and RNA2 consisted of 3,622 and 3,468 nucleotides.
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Affiliation(s)
- D E V Villamor
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, 99350, USA.
| | - S S Pillai
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, 99350, USA
| | - K C Eastwell
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, 99350, USA
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43
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Hadidi A, Flores R, Candresse T, Barba M. Next-Generation Sequencing and Genome Editing in Plant Virology. Front Microbiol 2016; 7:1325. [PMID: 27617007 PMCID: PMC4999435 DOI: 10.3389/fmicb.2016.01325] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 08/11/2016] [Indexed: 01/18/2023] Open
Abstract
Next-generation sequencing (NGS) has been applied to plant virology since 2009. NGS provides highly efficient, rapid, low cost DNA, or RNA high-throughput sequencing of the genomes of plant viruses and viroids and of the specific small RNAs generated during the infection process. These small RNAs, which cover frequently the whole genome of the infectious agent, are 21-24 nt long and are known as vsRNAs for viruses and vd-sRNAs for viroids. NGS has been used in a number of studies in plant virology including, but not limited to, discovery of novel viruses and viroids as well as detection and identification of those pathogens already known, analysis of genome diversity and evolution, and study of pathogen epidemiology. The genome engineering editing method, clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system has been successfully used recently to engineer resistance to DNA geminiviruses (family, Geminiviridae) by targeting different viral genome sequences in infected Nicotiana benthamiana or Arabidopsis plants. The DNA viruses targeted include tomato yellow leaf curl virus and merremia mosaic virus (begomovirus); beet curly top virus and beet severe curly top virus (curtovirus); and bean yellow dwarf virus (mastrevirus). The technique has also been used against the RNA viruses zucchini yellow mosaic virus, papaya ringspot virus and turnip mosaic virus (potyvirus) and cucumber vein yellowing virus (ipomovirus, family, Potyviridae) by targeting the translation initiation genes eIF4E in cucumber or Arabidopsis plants. From these recent advances of major importance, it is expected that NGS and CRISPR-Cas technologies will play a significant role in the very near future in advancing the field of plant virology and connecting it with other related fields of biology.
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Affiliation(s)
- Ahmed Hadidi
- United States Department of Agriculture – Agricultural Research ServiceBeltsville, MD, USA
| | - Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia–Consejo Superior de Investigaciones CientíficasValencia, Spain
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Université de BordeauxBordeaux, France
| | - Marina Barba
- Consiglio per la Ricerca in Agricoltura e l’analisi dell’Economia Agraria, Centro di Ricerca per la Patologia VegetaleRome, Italy
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