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Marais A, Gentit P, Brans Y, Renvoisé JP, Faure C, Saison A, Cousseau P, Castaing J, Chambon F, Pion A, Calado G, Lefebvre M, Garnier S, Latour F, Bresson K, Grasseau N, Candresse T. Comparative Performance Evaluation of Double-Stranded RNA High-Throughput Sequencing for the Detection of Viral Infection in Temperate Fruit Crops. PHYTOPATHOLOGY 2024; 114:1701-1709. [PMID: 38376958 DOI: 10.1094/phyto-12-23-0480-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
There is limited information on the compared performances of biological, serological. and molecular assays with high-throughput sequencing (HTS) for viral indexing in temperate fruit crops. Here, using a range of samples of predetermined virological status, we compared two performance criteria (inclusivity and analytical sensitivity) of enzyme-linked immunosorbent assay (ELISA), molecular hybridization, reverse transcription (RT)-PCR, and double-stranded RNA (dsRNA) HTS for the detection of a total of 14 viruses (10 genera) and four viroids (three genera). When undiluted samples from individual plants were used, ELISA had the lowest performance, with an overall detection rate of 68.7%, followed by RT-PCR (82.5%) and HTS (90.7%; 100% if considering only viruses). The lower performance of RT-PCR reflected the inability to amplify some isolates as a consequence of point mutations affecting primer-binding sites. In addition, HTS identified viruses that had not been identified by other assays in nearly two-thirds of the samples. Analysis of serial dilutions of fruit tree samples allowed comparison of analytical sensitivities for various viruses. ELISA showed the lowest analytical sensitivity, but RT-PCR showed higher analytical sensitivity than HTS for most of the samples. Overall, these results confirm the superiority of HTS over biological indexing in terms of speed and inclusivity and show that while the absolute analytical sensitivity of RT-PCR tends to be higher than that of HTS, PCR inclusivity is affected by viral genetic diversity. Taken together, these results make a strong case for the implementation of HTS-based approaches in fruit tree viral testing protocols supporting quarantine and certification programs.
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Affiliation(s)
- Armelle Marais
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Pascal Gentit
- ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM, 7 rue Jean Dixméras, 49044 Angers Cedex 01, France
| | - Yoann Brans
- CTIFL, Laboratoire de virologie fruitière, Centre de Lanxade, 24130 Prigonrieux, France
| | | | - Chantal Faure
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Anne Saison
- ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM, 7 rue Jean Dixméras, 49044 Angers Cedex 01, France
| | - Pascaline Cousseau
- ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM, 7 rue Jean Dixméras, 49044 Angers Cedex 01, France
| | - Julie Castaing
- CTIFL, Laboratoire de virologie fruitière, Centre de Lanxade, 24130 Prigonrieux, France
| | - Fabien Chambon
- ANSES, Plant Health Laboratory, Unité de Quarantaine, 63370 Lempdes, France
| | - Angélique Pion
- ANSES, Plant Health Laboratory, Unité de Quarantaine, 63370 Lempdes, France
| | - Grégory Calado
- ANSES, Plant Health Laboratory, Unité de Quarantaine, 63370 Lempdes, France
| | - Marie Lefebvre
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Soraya Garnier
- ANSES, Plant Health Laboratory, Unité de Quarantaine, 63370 Lempdes, France
| | - François Latour
- CTIFL, Laboratoire de virologie fruitière, Centre de Lanxade, 24130 Prigonrieux, France
| | - Kévin Bresson
- CTIFL, Laboratoire de virologie fruitière, Centre de Lanxade, 24130 Prigonrieux, France
| | - Nathalie Grasseau
- CTIFL, Laboratoire de virologie fruitière, Centre de Lanxade, 24130 Prigonrieux, France
| | - Thierry Candresse
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
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Bester R, Steyn C, Breytenbach JHJ, de Bruyn R, Cook G, Maree HJ. Reproducibility and Sensitivity of High-Throughput Sequencing (HTS)-Based Detection of Citrus Tristeza Virus and Three Citrus Viroids. PLANTS 2022; 11:plants11151939. [PMID: 35893644 PMCID: PMC9330035 DOI: 10.3390/plants11151939] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/01/2022] [Accepted: 07/19/2022] [Indexed: 11/16/2022]
Abstract
The credibility of a pathogen detection assay is measured using specific parameters including repeatability, specificity, sensitivity, and reproducibility. The use of high-throughput sequencing (HTS) as a routine detection assay for viruses and viroids in citrus was previously evaluated and, in this study, the reproducibility and sensitivity of the HTS assay were assessed. To evaluate the reproducibility of HTS, the same plants assayed in a previous study were sampled again, one year later, and assessed in triplicate using the same analyses to construct the virome profile. The sensitivity of the HTS assay was compared to routinely used RT-PCR assays in a time course experiment, to compensate for natural pathogen accumulation in plants over time. The HTS pipeline applied in this study produced reproducible and comparable results to standard RT-PCR assays for the detection of CTV and three viroid species in citrus. Even though the limit of detection of HTS can be influenced by pathogen concentration, sample processing method and sequencing depth, detection with HTS was found to be either equivalent or more sensitive than RT-PCR in this study.
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Affiliation(s)
- Rachelle Bester
- Citrus Research International, P.O. Box 2201, Matieland 7602, South Africa;
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa;
| | - Chanel Steyn
- Citrus Research International, P.O. Box 28, Nelspruit 1200, South Africa; (C.S.); (J.H.J.B.); (G.C.)
- 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; (C.S.); (J.H.J.B.); (G.C.)
| | - Glynnis Cook
- Citrus Research International, P.O. Box 28, Nelspruit 1200, South Africa; (C.S.); (J.H.J.B.); (G.C.)
| | - Hans J. Maree
- Citrus Research International, P.O. Box 2201, Matieland 7602, South Africa;
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa;
- Correspondence: ; Tel.: +27-21-808-9579
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Reconstruction and Characterization of Full-Length Begomovirus and Alphasatellite Genomes Infecting Pepper through Metagenomics. Viruses 2020; 12:v12020202. [PMID: 32054104 PMCID: PMC7077291 DOI: 10.3390/v12020202] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 01/10/2020] [Accepted: 01/16/2020] [Indexed: 01/18/2023] Open
Abstract
In northwestern Argentina (NWA), pepper crops are threatened by the emergence of begomoviruses due to the spread of its vector, Bemisia tabaci (Gennadius). The genus Begomovirus includes pathogens that can have a monopartite or bipartite genome and are occasionally associated with sub-viral particles called satellites. This study characterized the diversity of begomovirus and alphasatellite species infecting pepper in NWA using a metagenomic approach. Using RCA-NGS (rolling circle amplification-next generation sequencing), 19 full-length begomovirus genomes (DNA-A and DNA-B) and one alphasatellite were assembled. This ecogenomic approach revealed six begomoviruses in single infections: soybean blistering mosaic virus (SbBMV), tomato yellow spot virus (ToYSV), tomato yellow vein streak virus (ToYVSV), tomato dwarf leaf virus (ToDfLV), sida golden mosaic Brazil virus (SiGMBRV), and a new proposed species, named pepper blistering leaf virus (PepBLV). SbBMV was the most frequently detected species, followed by ToYSV. Moreover, a new alphasatellite associated with ToYSV, named tomato yellow spot alphasatellite 2 (ToYSA-2), was reported for the first time in Argentina. For the Americas, this was the first report of an alphasatellite found in a crop (pepper) and in a weed (Leonurus japonicus). We also detected intra-species and inter-species recombination.
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Torre C, Donaire L, Gómez-Aix C, Juárez M, Peterschmitt M, Urbino C, Hernando Y, Agüero J, Aranda MA. Characterization of Begomoviruses Sampled during Severe Epidemics in Tomato Cultivars Carrying the Ty-1 Gene. Int J Mol Sci 2018; 19:E2614. [PMID: 30177671 PMCID: PMC6164481 DOI: 10.3390/ijms19092614] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 08/25/2018] [Accepted: 08/28/2018] [Indexed: 12/27/2022] Open
Abstract
Tomato yellow leaf curl virus (TYLCV, genus Begomovirus, family Geminiviridae) is a major species that causes a tomato disease for which resistant tomato hybrids (mainly carriers of the Ty-1/Ty-3 gene) are being used widely. We have characterized begomoviruses severely affecting resistant tomato crops in Southeast Spain. Circular DNA was prepared from samples by rolling circle amplification, and sequenced by massive sequencing (2015) or cloning and Sanger sequencing (2016). Thus, 23 complete sequences were determined, all belonging to the TYLCV Israel strain (TYLCV-IL). Massive sequencing also revealed the absence of other geminiviral and beta-satellite sequences. A phylogenetic analysis showed that the Spanish isolates belonged to two groups, one related to early TYLCV-IL isolates in the area (Group 1), and another (Group 2) closely related to El Jadida (Morocco) isolates, suggesting a recent introduction. The most parsimonious evolutionary scenario suggested that the TYLCV isolates of Group 2 are back recombinant isolates derived from TYLCV-IS76, a recombinant virus currently predominating in Moroccan epidemics. Thus, an infectious Group 2 clone (TYLCV-Mu15) was constructed and used in in planta competition assays against TYLCV-IS76. TYLCV-Mu15 predominated in single infections, whereas TYLCV-IS76 did so in mixed infections, providing credibility to a scenario of co-occurrence of both types of isolates.
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Affiliation(s)
- Covadonga Torre
- Abiopep S.L., Departamento de I + D + i, Parque Científico de Murcia, Ctra. de Madrid, Km 388, Complejo de Espinardo, Edf. R, 2°, 30100 Murcia, Spain.
| | - Livia Donaire
- Centro de Edafología y Biología Aplicada del Segura (CEBAS)-CSIC, Departamento de Biología del Estrés y Patología Vegetal, P.O. Box 164, 30100 Murcia, Spain.
| | - Cristina Gómez-Aix
- Abiopep S.L., Departamento de I + D + i, Parque Científico de Murcia, Ctra. de Madrid, Km 388, Complejo de Espinardo, Edf. R, 2°, 30100 Murcia, Spain.
| | - Miguel Juárez
- Escuela Politécnica Superior de Orihuela, Universidad Miguel Hernández de Elche, Ctra. de Beniel, Km 3.2, 03312 Alicante, Spain.
| | - Michel Peterschmitt
- Centre de Coopération Internationale en Recherche Agronomique Pour le Développement (CIRAD), UMR-BGPI, Equipe Interactions Virus-Insecte-Plante, TA A-54/K, Campus International de Baillarguet, CEDEX 5, 34398 Monptellier, France.
| | - Cica Urbino
- Centre de Coopération Internationale en Recherche Agronomique Pour le Développement (CIRAD), UMR-BGPI, Equipe Interactions Virus-Insecte-Plante, TA A-54/K, Campus International de Baillarguet, CEDEX 5, 34398 Monptellier, France.
| | - Yolanda Hernando
- Abiopep S.L., Departamento de I + D + i, Parque Científico de Murcia, Ctra. de Madrid, Km 388, Complejo de Espinardo, Edf. R, 2°, 30100 Murcia, Spain.
| | - Jesús Agüero
- Abiopep S.L., Departamento de I + D + i, Parque Científico de Murcia, Ctra. de Madrid, Km 388, Complejo de Espinardo, Edf. R, 2°, 30100 Murcia, Spain.
| | - Miguel A Aranda
- Centro de Edafología y Biología Aplicada del Segura (CEBAS)-CSIC, Departamento de Biología del Estrés y Patología Vegetal, P.O. Box 164, 30100 Murcia, Spain.
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Maree HJ, Fox A, Al Rwahnih M, Boonham N, Candresse T. Application of HTS for Routine Plant Virus Diagnostics: State of the Art and Challenges. FRONTIERS IN PLANT SCIENCE 2018; 9:1082. [PMID: 30210506 PMCID: PMC6119710 DOI: 10.3389/fpls.2018.01082] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 07/04/2018] [Indexed: 05/04/2023]
Affiliation(s)
- Hans J. Maree
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
- Agricultural Research Council, Infruitec-Nietvoorbij, The Fruit, Vine and Wine Institute, Stellenbosch, South Africa
| | - Adrian Fox
- Department of Plant Protection, Fera Science Ltd., York, United Kingdom
| | - Maher Al Rwahnih
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Neil Boonham
- School of Natural and Environmental Sciences, University of Newcastle, Newcastle Upon Tyne, United Kingdom
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, Bordeaux, France
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Jo Y, Choi H, Kim SM, Kim SL, Lee BC, Cho WK. The pepper virome: natural co-infection of diverse viruses and their quasispecies. BMC Genomics 2017; 18:453. [PMID: 28595635 PMCID: PMC5465472 DOI: 10.1186/s12864-017-3838-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 06/01/2017] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The co-infection of diverse viruses in a host plant is common; however, little is known about viral populations and their quasispecies in the host. RESULTS Here, we report the first pepper viromes that were co-infected by different types of viral genomes. The pepper viromes are dominated by geminivirus DNA-A followed by a novel carlavirus referred to as Pepper virus A. The two pepper cultivars share similar viral populations and replications. However, the quasispecies for double-stranded RNA virus and two satellite DNAs were heterogeneous and homogenous in susceptible and resistant cultivars, respectively, indicating the quasispecies of an individual virus depends on the host. CONCLUSIONS Taken together, we provide the first evidence that the host plant resistant to viruses has an unrevealed antiviral system, affecting viral quasispecies, not replication.
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Affiliation(s)
- Yeonhwa Jo
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Hoseong Choi
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Sang-Min Kim
- Crop Foundation Division, National Institute of Crop Science, RDA, Wanju, 55365, South Korea
| | - Sun-Lim Kim
- Crop Foundation Division, National Institute of Crop Science, RDA, Wanju, 55365, South Korea
| | - Bong Choon Lee
- Crop Foundation Division, National Institute of Crop Science, RDA, Wanju, 55365, South Korea
| | - Won Kyong Cho
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. .,The Taejin Genome Institute, Gadam-gil 61, Hoeongseong, 25239, Republic of Korea.
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Wylie SJ, Li H, Saqib M, Jones MGK. The global trade in fresh produce and the vagility of plant viruses: a case study in garlic. PLoS One 2014; 9:e105044. [PMID: 25133543 PMCID: PMC4136854 DOI: 10.1371/journal.pone.0105044] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 07/20/2014] [Indexed: 11/28/2022] Open
Abstract
As cuisine becomes globalized, large volumes of fresh produce are traded internationally. The potential exists for pathogens infecting fresh produce to hitchhike to new locations and perhaps to establish there. It is difficult to identify them using traditional methods if pathogens are novel, scarce, and/or unexpected. In an attempt to overcome this limitation, we used high-throughput sequencing technology as a means of detecting all RNA viruses infecting garlic (Allium sativum L.) bulbs imported into Australia from China, the USA, Mexico, Argentina and Spain, and those growing in Australia. Bulbs tested were grown over multiple vegetative generations and all were stably infected with one or more viruses, including two species not previously recorded in Australia. Present in various combinations from 10 garlic bulbs were 41 virus isolates representing potyviruses (Onion yellow dwarf virus, Leek yellow stripe virus), carlaviruses (Shallot latent virus, Garlic common latent virus) and allexiviruses (Garlic virus A, B, C, D, and X), for which 19 complete and 22 partial genome sequences were obtained, including the first complete genome sequences of two isolates of GarVD. The most genetically distinct isolates of GarVA and GarVX described so far were identified from Mexico and Argentina, and possible scenarios explaining this are presented. The complete genome sequence of an isolate of the potexvirus Asparagus virus 3 (AV3) was obtained in Australia from wild garlic (A. vineale L.), a naturalized weed. This is first time AV3 has been identified from wild garlic and the first time it has been identified beyond China and Japan. The need for routine generic diagnosis and appropriate legislation to address the risks to primary production and wild plant communities from pathogens spread through the international trade in fresh produce is discussed.
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Affiliation(s)
- Stephen J. Wylie
- Plant Virology Group, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, W.A., Australia
- * E-mail:
| | - Hua Li
- Plant Virology Group, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, W.A., Australia
| | - Muhammad Saqib
- Plant Gene Regulation Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Michael G. K. Jones
- Plant Virology Group, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, W.A., Australia
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Jeske H, Kober S, Schäfer B, Strohmeier S. Circomics of Cuban geminiviruses reveals the first alpha-satellite DNA in the Caribbean. Virus Genes 2014; 49:312-24. [DOI: 10.1007/s11262-014-1090-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 05/26/2014] [Indexed: 11/24/2022]
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Boonham N, Kreuze J, Winter S, van der Vlugt R, Bergervoet J, Tomlinson J, Mumford R. Methods in virus diagnostics: From ELISA to next generation sequencing. Virus Res 2014; 186:20-31. [DOI: 10.1016/j.virusres.2013.12.007] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 12/08/2013] [Accepted: 12/09/2013] [Indexed: 01/02/2023]
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Massart S, Olmos A, Jijakli H, Candresse T. Current impact and future directions of high throughput sequencing in plant virus diagnostics. Virus Res 2014; 188:90-6. [PMID: 24717426 DOI: 10.1016/j.virusres.2014.03.029] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 03/27/2014] [Accepted: 03/28/2014] [Indexed: 12/17/2022]
Abstract
The ability to provide a fast, inexpensive and reliable diagnostic for any given viral infection is a key parameter in efforts to fight and control these ubiquitous pathogens. The recent developments of high-throughput sequencing (also called Next Generation Sequencing - NGS) technologies and bioinformatics have drastically changed the research on viral pathogens. It is now raising a growing interest for virus diagnostics. This review provides a snapshot vision on the current use and impact of high throughput sequencing approaches in plant virus characterization. More specifically, this review highlights the potential of these new technologies and their interplay with current protocols in the future of molecular diagnostic of plant viruses. The current limitations that will need to be addressed for a wider adoption of high-throughput sequencing in plant virus diagnostics are thoroughly discussed.
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Affiliation(s)
- Sebastien Massart
- Laboratory of Phytopathology, University of Liège, Gembloux Agro-BioTech, Passage des déportés, 2, 5030 Gembloux, Belgium.
| | - Antonio Olmos
- Centro de Protección Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Apartado Oficial, 46113 Moncada, Valencia, Spain
| | - Haissam Jijakli
- Laboratory of Phytopathology, University of Liège, Gembloux Agro-BioTech, Passage des déportés, 2, 5030 Gembloux, Belgium
| | - Thierry Candresse
- UMR 1332 de Biologie du fruit et Pathologie, INRA, CS20032, 33882 Villenave d'Ornon cedex, France; UMR 1332 de Biologie du fruit et Pathologie, Université de Bordeaux, CS20032, 33882 Villenave d'Ornon cedex, France
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De novo reconstruction of consensus master genomes of plant RNA and DNA viruses from siRNAs. PLoS One 2014; 9:e88513. [PMID: 24523907 PMCID: PMC3921208 DOI: 10.1371/journal.pone.0088513] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 01/06/2014] [Indexed: 11/19/2022] Open
Abstract
Virus-infected plants accumulate abundant, 21-24 nucleotide viral siRNAs which are generated by the evolutionary conserved RNA interference (RNAi) machinery that regulates gene expression and defends against invasive nucleic acids. Here we show that, similar to RNA viruses, the entire genome sequences of DNA viruses are densely covered with siRNAs in both sense and antisense orientations. This implies pervasive transcription of both coding and non-coding viral DNA in the nucleus, which generates double-stranded RNA precursors of viral siRNAs. Consistent with our finding and hypothesis, we demonstrate that the complete genomes of DNA viruses from Caulimoviridae and Geminiviridae families can be reconstructed by deep sequencing and de novo assembly of viral siRNAs using bioinformatics tools. Furthermore, we prove that this 'siRNA omics' approach can be used for reliable identification of the consensus master genome and its microvariants in viral quasispecies. Finally, we utilized this approach to reconstruct an emerging DNA virus and two viroids associated with economically-important red blotch disease of grapevine, and to rapidly generate a biologically-active clone representing the wild type master genome of Oilseed rape mosaic virus. Our findings show that deep siRNA sequencing allows for de novo reconstruction of any DNA or RNA virus genome and its microvariants, making it suitable for universal characterization of evolving viral quasispecies as well as for studying the mechanisms of siRNA biogenesis and RNAi-based antiviral defense.
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12
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Lipkin WI, Firth C. Viral surveillance and discovery. Curr Opin Virol 2013; 3:199-204. [PMID: 23602435 DOI: 10.1016/j.coviro.2013.03.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 03/20/2013] [Indexed: 01/27/2023]
Abstract
The field of virus discovery has burgeoned with the advent of high throughput sequencing platforms and bioinformatics programs that enable rapid identification and molecular characterization of known and novel agents, investments in global microbial surveillance that include wildlife and domestic animals as well as humans, and recognition that viruses may be implicated in chronic as well as acute diseases. Here we review methods for viral surveillance and discovery, strategies and pitfalls in linking discoveries to disease, and identify opportunities for improvements in sequencing instrumentation and analysis, the use of social media and medical informatics that will further advance clinical medicine and public health.
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Affiliation(s)
- Walter Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health of Columbia University, 722 West 168th Street, New York, NY 10025, USA.
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