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Schönegger D, Moubset O, Margaria P, Menzel W, Winter S, Roumagnac P, Marais A, Candresse T. Benchmarking of virome metagenomic analysis approaches using a large, 60+ members, viral synthetic community. J Virol 2023; 97:e0130023. [PMID: 37888981 PMCID: PMC10688312 DOI: 10.1128/jvi.01300-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE We report here efforts to benchmark performance of two widespread approaches for virome analysis, which target either virion-associated nucleic acids (VANA) or highly purified double-stranded RNAs (dsRNAs). This was achieved using synthetic communities of varying complexity levels, up to a highly complex community of 72 viral agents (115 viral molecules) comprising isolates from 21 families and 61 genera of plant viruses. The results obtained confirm that the dsRNA-based approach provides a more complete representation of the RNA virome, in particular, for high complexity ones. However, for viromes of low to medium complexity, VANA appears a reasonable alternative and would be the preferred choice if analysis of DNA viruses is of importance. Several parameters impacting performance were identified as well as a direct relationship between the completeness of virome description and sample sequencing depth. The strategy, results, and tools used here should prove useful in a range of virome analysis efforts.
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Affiliation(s)
| | - Oumaima Moubset
- CIRAD, UMR PHIM, Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Paolo Margaria
- Plant Virus Department, Leibniz-Institute DSMZ, Braunschweig, Germany
| | - Wulf Menzel
- Plant Virus Department, Leibniz-Institute DSMZ, Braunschweig, Germany
| | - Stephan Winter
- Plant Virus Department, Leibniz-Institute DSMZ, Braunschweig, Germany
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR BFP, Villenave d’Ornon, France
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Lowder SR, Neill TM, Peetz AB, Miles TD, Moyer MM, Oliver C, Stergiopoulos I, Ding S, Mahaffee WF. A Rapid Glove-Based Inoculum Sampling Technique to Monitor Erysiphe necator in Commercial Vineyards. PLANT DISEASE 2023; 107:3096-3105. [PMID: 37079020 DOI: 10.1094/pdis-02-23-0216-re] [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: 05/03/2023]
Abstract
Information on the presence and severity of grape powdery mildew (GPM), caused by Erysiphe necator, has long been used to guide management decisions. While recent advances in the available molecular diagnostic assays and particle samplers have made monitoring easier, there is still a need for more efficient field collection of E. necator. The use of vineyard worker gloves worn during canopy manipulation as a sampler (glove swab) of E. necator was compared with samples identified by visual assessment with subsequent molecular confirmation (leaf swabs) and airborne spore samples collected by rotating-arm impaction traps (impaction traps). Samples from United States commercial vineyards in Oregon, Washington, and California were analyzed using two TaqMan qPCR assays targeting the internal transcribed spacer regions or cytochrome b gene of E. necator. Based on qPCR assays, visual disease assessments misidentified GPM up to 59% of the time with a higher frequency of misidentification occurring earlier in the growing season. Comparison of the aggregated leaf swab results for a row (n = 915) to the row's corresponding glove swab had 60% agreement. The latent class analysis (LCA) indicated that glove swabs were more sensitive than leaf swabs in detecting E. necator presence. The impaction trap results had 77% agreement to glove swabs (n = 206) taken from the same blocks. The LCAs estimated that the glove swabs and impaction trap samplers varied each year in which was more sensitive for detection. This likely indicates that these methods have similar levels of uncertainty and provide equivalent information. Additionally, all samplers, once E. necator was detected, were similarly sensitive and specific for detection of the A-143 resistance allele. Together, these results suggest that glove swabs are an effective sampling method for monitoring the presence of E. necator and, subsequently, the G143A amino acid substitution associated with resistance to quinone outside inhibitor fungicides in vineyards. Glove swabs could reduce sampling costs due to the lack of need for specialized equipment and time required for swab collection and processing.
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Affiliation(s)
- Sarah R Lowder
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Tara M Neill
- USDA-ARS Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR 97330
| | - Amy B Peetz
- Revolution Crop Consultants, LLC, Albany, OR 97321
| | - Timothy D Miles
- Department of Plant, Soil, and Microbial Science, Michigan State University, East Lansing, MI 48824
| | - Michelle M Moyer
- Department of Viticulture and Enology, Washington State University, Prosser, WA 99350
| | | | | | - Shunping Ding
- Department of Wine and Viticulture, California Polytechnic State University, San Luis Obispo, CA 93407
| | - Walter F Mahaffee
- USDA-ARS Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR 97330
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Chirkov S, Sheveleva A, Tsygankova S, Slobodova N, Sharko F, Petrova K, Mitrofanova I. First Report and Complete Genome Characterization of Cherry Virus A and Little Cherry Virus 1 from Russia. PLANTS (BASEL, SWITZERLAND) 2023; 12:3295. [PMID: 37765462 PMCID: PMC10534684 DOI: 10.3390/plants12183295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023]
Abstract
Virus diseases affect the yield and fruit quality and shorten the productive life of stone fruits (Prunus spp. in the family Rosaceae). Of over fifty known viruses infecting these crops, cherry virus A (CVA) is among the most common, and little cherry virus 1 (LChV1) is one of the most economically important. Using high-throughput sequencing, full-length genomes of CVA and LChV1 isolates, found on interspecies hybrids in the Prunus collection of the Nikita Botanical Gardens, Russia, were sequenced, assembled, and characterized. CVA was found in the P. cerasifera × P. armeniaca hybrid and in phylogenetic analysis clustered with non-cherry virus isolates. The LChV1 isolate Stepnoe was detected in ((P. cerasifera Ehrh. × P. armeniaca L.) × P. brigantiaca Vill.) trihybrid suggesting that both P. cerasifera and P. brigantiaca potentially can be the LChV1 hosts. The isolate Stepnoe was most closely related to the Greece isolate G15_3 from sweet cherry, sharing 77.3% identity at the nucleotide level. Possibly, the highly divergent Russian isolate represents one more phylogroup of this virus. This is the first report of CVA and LChV1 from Russia, expanding the information on their geographical distribution and genetic diversity.
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Affiliation(s)
- Sergei Chirkov
- Department of Virology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia;
| | - Anna Sheveleva
- Department of Virology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia;
| | - Svetlana Tsygankova
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (S.T.); (N.S.); (F.S.); (K.P.)
| | - Natalia Slobodova
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (S.T.); (N.S.); (F.S.); (K.P.)
- Faculty of Biology and Biotechnology, HSE University, 101000 Moscow, Russia
| | - Fedor Sharko
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (S.T.); (N.S.); (F.S.); (K.P.)
- Federal Research Center “Fundamentals of Biotechnology”, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Kristina Petrova
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (S.T.); (N.S.); (F.S.); (K.P.)
- Research Center for Medical Genetics, 115552 Moscow, Russia
| | - Irina Mitrofanova
- Tsitsin Main Botanical Garden of Russian Academy of Sciences, 127276 Moscow, Russia;
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Sanogo S, Lamour K, Kousik CS, Lozada DN, Parada-Rojas CH, Quesada-Ocampo LM, Wyenandt CA, Babadoost M, Hausbeck MK, Hansen Z, Ali E, McGrath MT, Hu J, Crosby K, Miller SA. Phytophthora capsici, 100 Years Later: Research Mile Markers from 1922 to 2022. PHYTOPATHOLOGY 2023; 113:921-930. [PMID: 36401843 DOI: 10.1094/phyto-08-22-0297-rvw] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In 1922, Phytophthora capsici was described by Leon Hatching Leonian as a new pathogen infecting pepper (Capsicum annuum), with disease symptoms of root rot, stem and fruit blight, seed rot, and plant wilting and death. Extensive research has been conducted on P. capsici over the last 100 years. This review succinctly describes the salient mile markers of research on P. capsici with current perspectives on the pathogen's distribution, economic importance, epidemiology, genetics and genomics, fungicide resistance, host susceptibility, pathogenicity mechanisms, and management.
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Affiliation(s)
- Soum Sanogo
- Department of Entomology, Plant Pathology, and Weed Science, New Mexico State University, Las Cruces, NM 88003
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, The University of Tennessee Institute of Agriculture, Knoxville, TN 37996
| | - Chandrasekar S Kousik
- U.S. Vegetable Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Charleston, SC 29414
| | - Dennis N Lozada
- Department of Plant and Environmental Sciences and Chile Pepper Institute, New Mexico State University, Las Cruces, NM 88003
| | - Camilo H Parada-Rojas
- Department of Entomology and Plant Pathology, NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC 27695
| | - Lina M Quesada-Ocampo
- Department of Entomology and Plant Pathology, NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC 27695
| | - Christian A Wyenandt
- Department of Plant Biology, Rutgers University, Rutgers Agricultural Research and Extension Center, Bridgeton, NJ 08302
| | | | - Mary K Hausbeck
- Department of Soil, Plant, and Microbial Sciences, Michigan State University, East Lansing, MI 48824
| | - Zachariah Hansen
- Department of Entomology and Plant Pathology, The University of Tennessee Institute of Agriculture, Knoxville, TN 37996
| | - Emran Ali
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH 03824
| | - Margaret T McGrath
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Long Island Horticultural Research and Extension Center, Riverhead, NY 11901
| | - Jiahuai Hu
- School of Plant Sciences, The University of Arizona, Tucson, AZ 85721
| | - Kevin Crosby
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843
| | - Sally A Miller
- Department of Plant Pathology, The Ohio State University, Wooster, OH 44691
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Candresse T, Faure C, Marais A. First report of grapevine red globe virus (GRGV) and grapevine rupestris vein feathering virus (GRVFV) infecting grapevine (Vitis vinifera L.) in Portugal. PLANT DISEASE 2022; 107:974. [PMID: 35939753 DOI: 10.1094/pdis-06-22-1326-pdn] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Grapevine Red globe virus (GRGV) and grapevine rupestris vein feathering virus (GRVFV) are relatively recently described grape viruses that respectively belong to the genera Maculavirus and Marafivirus in the family Tymoviridae [1]. Owing to their rather recent description, still limited information on their biology, on their molecular variability and on their geographic distribution is available. Both viruses are apparently completely or largely asymptomatic in European grapevine and have likely been overlooked in a wide range of situations (Martelli, 2014). According to sequences in GenBank, GRGV has been identified in Asia (Iran, Japan, China), the Americas (USA, Brazil) and Europe (Spain, France, Slovenia, Hungary, Czech Republic and Germany). GRVFV has been reported from the same countries but also in Oceania (New Zealand, Australia) and from a range of other countries including India, Pakistan and South Korea for Asia, Canada for North America and Switzerland, Slovakia, Italy and Russia for Europe. Evidence for the presence of GRGV and GRVFV in grapevine plants from northern Portugal (variety(ies) unknown) was obtained through the bioinformatic analysis [2] of RNASeq Illumina data obtained from phloem scrapings from five grapevine samples collected in different plots in 2016 [3]. Following grapevine genome substraction, contigs assembly and Blast-based contigs annotation using CLC Genomics Workbench, two plants, #4 and #5b, yielded contigs representing near complete GRGV genomes. The plant #4 contig integrated 474 reads (0.15% of reads for an average coverage of 10.1x) while the corresponding values for the contig for plant #5b are 2185 reads (2.4% of total reads) for a coverage of 47.2x. The two GRGV contigs show 91.4% nucleotide (nt) identity and the closest GRGV full genome sequence in GenBank, MZ451067 from Canada, shares respectively 98.9% and 91.6% nt identity with them. The near complete genome contigs have been deposited in GenBank (ON603917 and ON603918). Simultaneously, two near full length genomic contigs for GRVFV were identified from plant #5b and have also been deposited in GenBank (ON603919 and ON603920). These contigs show 84.4% nt identity to each other and were respectively assembled from 4643 (5.2% of total reads) and 5326 reads (6.0% of total reads) for respective average coverages of 102.3x and 117.3x. The closest full GRVFV genome in GenBank is MZ027155 from the USA, with 84.3-85.3% nt identity. Confirmation of the presence of GRVG and GRVFV in the doubly infected plant #5b was achieved by specific RT-PCR assays. A published assay [4] was used for GRGV and primers GRVFV-Cp-F 5'AAYCCTGTCACHCTCCACTG3' and GRVFV-Cp-R 5'TTCATGGTGGTGCCDGTGAG3' (Tm 55°C) were used for GRVFV. The obtained 447nt GRGV amplicon showed a single difference with the HTS contig while the 218 nt GRVFV amplicon showed 3 mutations as compared to one of the HTS contigs. The different grapevines had initially been sampled because they showed relatively poor and stunted growth but besides GRVFV and/or GRGV the HTS analysis indicated that they were also infected by hop stunt viroid, grapevine yellow speckle viroid 1, grapevine rupestris stem pitting virus, plus respectively a novel nepovirus (plant #4) and grapevine leafroll-associated virus 2 and grapevine Pinot gris virus (plant #5b) so that the results reported here do not shed novel light on the potential pathogenicity of GRGV or GRVFV. To the best of our knowledge, this is the first report of GRGV and GRVFV in Portugal.
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Affiliation(s)
- Thierry Candresse
- INRA Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, INRA - Université de Bordeaux, CS20032, Villenave d'Ornon , France, 33882 cedex;
| | | | - Armelle Marais
- INRA Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, INRA - Université de Bordeaux, 71 avenue E. Bourlaux CS20032, Villenave d'Ornon , France, 33882;
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Zhang H, Zhao X, Cao X, Khan LU, Zhao R, Wang H, Huang X. Transmission of Areca Palm Velarivirus 1 by Mealybugs Causes Yellow Leaf Disease in Betel Palm ( Areca catechu). PHYTOPATHOLOGY 2022; 112:700-707. [PMID: 34491795 DOI: 10.1094/phyto-06-21-0261-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Yellow leaf disease (YLD) is the most destructive disease of betel palm (Areca catechu). A strong association between YLD and areca palm velarivirus 1 (APV1) has been observed. However, the causal relationship between APV1 and disease, and the transmission mode, warrant further investigation. This work showed that APV1 was transmitted by both Ferrisia virgata and Pseudococcus cryptus mealybugs and caused YLD symptoms in betel palm seedlings; therefore, we demonstrate that APV1 is a causal agent of YLD. APV1 was detected in the stylets, foreguts, midguts, and hindguts of the vectors via both immunocapture reverse transcription PCR and immunofluorescence assays. APV1 was not transmitted transovarially from viruliferous female F. virgata to their progeny. In summary, the transmission of APV1 by F. virgata may occur in a noncirculative, semipersistent manner. This study fills important gaps in our knowledge of velarivirus transmission, which is critical for developing YLD management practices.
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Affiliation(s)
- Huaiwen Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, P. R. China
| | - Xue Zhao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, P. R. China
| | - Xianmei Cao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, P. R. China
| | - Latif Ullah Khan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, P. R. China
| | - Ruibai Zhao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, P. R. China
| | - Hongxing Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, P. R. China
| | - Xi Huang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, P. R. China
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Ruiz-García AB, Canales C, Morán F, Ruiz-Torres M, Herrera-Mármol M, Olmos A. Characterization of Spanish Olive Virome by High Throughput Sequencing Opens New Insights and Uncertainties. Viruses 2021; 13:v13112233. [PMID: 34835039 PMCID: PMC8622421 DOI: 10.3390/v13112233] [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: 10/12/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 01/04/2023] Open
Abstract
The use of high throughput sequencing (HTS) for the analysis of Spanish olive trees showing leaf yellowing discoloration, defoliation, and/or decline has provided new insights into the olive viruses present in Spain and has opened discussions about the pros and cons of these technologies for diagnostic purposes. In this study, we report for the first time in Spanish orchards the presence of olive leaf yellowing-associated virus (OLYaV), for which the second full coding sequence has been determined. This virus has also been detected in a putative vector, the psyllid Euphyllura olivina. In addition, the presence in Spain of Olea europaea geminivirus (OEGV), recently reported in Italy, has been confirmed, and the full-length sequence of two isolates was obtained by HTS and Sanger sequencing. These results, as well as the detection of other viral sequences related to olive latent virus 3 (OLV-3) and olive viral satellite RNA, raises questions on the biological significance of the findings, about the requirement of standardization on the interpretation of HTS results, and the necessity of additional tests to confirm the relevance of the HTS detection of viral sequences.
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Affiliation(s)
- Ana Belén Ruiz-García
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra, Moncada-Náquera Km 4.5, 46113 Moncada, Spain; (A.B.R.-G.); (C.C.); (F.M.)
| | - Celia Canales
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra, Moncada-Náquera Km 4.5, 46113 Moncada, Spain; (A.B.R.-G.); (C.C.); (F.M.)
| | - Félix Morán
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra, Moncada-Náquera Km 4.5, 46113 Moncada, Spain; (A.B.R.-G.); (C.C.); (F.M.)
| | - Manuel Ruiz-Torres
- Laboratorio de Producción y Sanidad Vegetal de Jaén, Junta de Andalucía, Sierra Morena, 12b, 23620 Mengíbar, Spain; (M.R.-T.); (M.H.-M.)
| | - Magdalena Herrera-Mármol
- Laboratorio de Producción y Sanidad Vegetal de Jaén, Junta de Andalucía, Sierra Morena, 12b, 23620 Mengíbar, Spain; (M.R.-T.); (M.H.-M.)
| | - Antonio Olmos
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra, Moncada-Náquera Km 4.5, 46113 Moncada, Spain; (A.B.R.-G.); (C.C.); (F.M.)
- Correspondence:
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Mushtaq M, Dar AA, Basu U, Bhat BA, Mir RA, Vats S, Dar MS, Tyagi A, Ali S, Bansal M, Rai GK, Wani SH. Integrating CRISPR-Cas and Next Generation Sequencing in Plant Virology. Front Genet 2021; 12:735489. [PMID: 34759957 PMCID: PMC8572880 DOI: 10.3389/fgene.2021.735489] [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: 07/02/2021] [Accepted: 09/16/2021] [Indexed: 12/26/2022] Open
Abstract
Plant pathology has been revolutionized by the emergence and intervention of next-generation sequencing technologies (NGS) which provide a fast, cost-effective, and reliable diagnostic for any class of pathogens. NGS has made tremendous advancements in the area of research and diagnostics of plant infecting viromes and has bridged plant virology with other advanced research fields like genome editing technologies. NGS in a broader perspective holds the potential for plant health improvement by diagnosing and mitigating the new or unusual symptoms caused by novel/unidentified viruses. CRISPR-based genome editing technologies can enable rapid engineering of efficient viral/viroid resistance by directly targeting specific nucleotide sites of plant viruses and viroids. Critical genes such as eIf (iso) 4E or eIF4E have been targeted via the CRISPR platform to produce plants resistant to single-stranded RNA (ssRNA) viruses. CRISPR/Cas-based multi-target DNA or RNA tests can be used for rapid and accurate diagnostic assays for plant viruses and viroids. Integrating NGS with CRISPR-based genome editing technologies may lead to a paradigm shift in combating deadly disease-causing plant viruses/viroids at the genomic level. Furthermore, the newly discovered CRISPR/Cas13 system has unprecedented potential in plant viroid diagnostics and interference. In this review, we have highlighted the application and importance of sequencing technologies on covering the viral genomes for precise modulations. This review also provides a snapshot vision of emerging developments in NGS technologies for the characterization of plant viruses and their potential utilities, advantages, and limitations in plant viral diagnostics. Furthermore, some of the notable advances like novel virus-inducible CRISPR/Cas9 system that confers virus resistance with no off-target effects have been discussed.
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Affiliation(s)
- Muntazir Mushtaq
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Aejaz Ahmad Dar
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Umer Basu
- Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | | | - Rakeeb Ahmad Mir
- Department of Biotechnology, School of Biosciences and Biotechnology, BGSB University, Rajouri, India
| | - Sanskriti Vats
- Department of Agricultural Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - M. S. Dar
- Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Anshika Tyagi
- Department of Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Sajad Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Monika Bansal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Gyanendra Kumar Rai
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
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Reynard JS, Turco S, Brodard J, Kellenberger I, Maclot F, Schumpp O, Gugerli P, Pooggin MM. Identification and Molecular Characterization of a Novel Hordeivirus Associated With Yellow Mosaic Disease of Privet ( Ligustrum vulgare) in Europe. Front Microbiol 2021; 12:723350. [PMID: 34646247 PMCID: PMC8503643 DOI: 10.3389/fmicb.2021.723350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/31/2021] [Indexed: 11/13/2022] Open
Abstract
Wild plants serve as a large reservoir of known and yet-unknown viruses and as a source of viral pathogens of cultivated plants. Yellow mosaic disease of forest shrub Ligustrum vulgare (privet) was recurrently observed in Europe for more than 100 years. Using a universal virus identification approach based on deep sequencing and de novo assembly of viral small interfering (si)RNAs we identified a causative agent of this disease in Switzerland and reconstructed its complete 3-segmented RNA genome. Notably, a short 3'-terminal common region (CR) attached to each segment via a ∼53-71 nucleotide poly(A) tract, as determined by RT-PCR sequencing, was initially identified as an orphan siRNA contig with conserved tRNA-like secondary structure. Phylogenomic analysis classified this virus as a novel member in the genus Hordeivirus of family Virgaviridae, which we named ligustrum mosaic virus (LigMV). Similar to other hordeiviruses, LigMV formed rod-shape virions (visualized by electron microscopy), was transmitted through seeds and could also be mechanically transmitted to herbaceous hosts Chenopodium quinoa and Nicotiana benthamiana. Blot hybridization analysis identified genomic and subgenomic RNAs, sharing the 3'-CR and likely serving as monocistronic mRNAs for seven evolutionarily-conserved viral proteins including two subunits of viral RNA-dependent RNA polymerase, coat protein, triple gene block proteins mediating viral movement and cysteine-rich suppressor of RNA silencing. Analysis of size, polarity, and hotspot profiles of viral siRNAs suggested that they are produced by the plant antiviral Dicer-like (DCL) proteins DCL2 and DCL4 processing double-stranded intermediates of genomic RNA replication. Whole genome sequencing of French and Austrian isolates of LigMV revealed its genetic stability over a wide geographic range (>99% nucleotide identity to Swiss isolates and each other), suggesting its persistence and spread in Europe via seed dispersal.
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Affiliation(s)
| | - Silvia Turco
- Department of Environmental Sciences, Botany, University of Basel, Basel, Switzerland
| | - Justine Brodard
- Virology-Phytoplasmology Laboratory, Agroscope, Nyon, Switzerland
| | | | - François Maclot
- Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Olivier Schumpp
- Virology-Phytoplasmology Laboratory, Agroscope, Nyon, Switzerland
| | - Paul Gugerli
- Virology-Phytoplasmology Laboratory, Agroscope, Nyon, Switzerland
| | - Mikhail M Pooggin
- PHIM Plant Health Institute, University of Montpellier, INRAE, CIRAD, IRD, Institute Agro, Montpellier, France
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10
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Quality Assessment and Validation of High-Throughput Sequencing for Grapevine Virus Diagnostics. Viruses 2021; 13:v13061130. [PMID: 34208336 PMCID: PMC8231206 DOI: 10.3390/v13061130] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/07/2021] [Accepted: 06/10/2021] [Indexed: 12/11/2022] Open
Abstract
Development of High-Throughput Sequencing (HTS), also known as next generation sequencing, revolutionized diagnostic research of plant viruses. HTS outperforms bioassays and molecular diagnostic assays that are used to screen domestic and quarantine grapevine materials in data throughput, cost, scalability, and detection of novel and highly variant virus species. However, before HTS-based assays can be routinely used for plant virus diagnostics, performance specifications need to be developed and assessed. In this study, we selected 18 virus-infected grapevines as a test panel for measuring performance characteristics of an HTS-based diagnostic assay. Total nucleic acid (TNA) was extracted from petioles and dormant canes of individual samples and constructed libraries were run on Illumina NextSeq 500 instrument using a 75-bp single-end read platform. Sensitivity was 98% measured over 264 distinct virus and viroid infections with a false discovery rate (FDR) of approximately 1 in 5 positives. The results also showed that combining a spring petiole test with a fall cane test increased sensitivity to 100% for this TNA HTS assay. To evaluate extraction methodology, these results were compared to parallel dsRNA extractions. In addition, in a more detailed dilution study, the TNA HTS assay described here consistently performed well down to a dilution of 5%. In that range, sensitivity was 98% with a corresponding FDR of approximately 1 in 5. Repeatability and reproducibility were assessed at 99% and 93%, respectively. The protocol, criteria, and performance levels described here may help to standardize HTS for quality assurance and accreditation purposes in plant quarantine or certification programs.
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11
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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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12
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Umber M, Filloux D, Gélabale S, Gomez RM, Marais A, Gallet S, Gamiette F, Pavis C, Teycheney PY. Molecular Viral Diagnosis and Sanitation of Yam Genetic Resources: Implications for Safe Yam Germplasm Exchange. Viruses 2020; 12:v12101101. [PMID: 33003342 PMCID: PMC7650539 DOI: 10.3390/v12101101] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 01/25/2023] Open
Abstract
Yam (Dioscorea spp.) is an important crop in tropical and subtropical regions. Many viruses have been recently identified in yam, hampering genetic conservation and safe international exchanges of yam germplasm. We report on the implementation of reliable and cost-effective PCR-based detection tools targeting eight different yam-infecting viruses. Viral indexing of the in vitro yam collection maintained by the Biological Resources Center for Tropical Plants (BRC-TP) in Guadeloupe (French West Indies) unveiled a high prevalence of potyviruses, badnaviruses, Dioscorea mosaic associated virus (DMaV) and yam asymptomatic virus 1 (YaV1) and a high level of coinfections. Infected yam accessions were subjected to a combination of thermotherapy and meristem culture. Sanitation levels were monitored using PCR-based and high-throughput sequencing-based diagnosis, confirming the efficacy and reliability of PCR-based detection tools. Sanitation rates were highly variable depending on viruses. Sixteen accessions were successfully sanitized, paving the way to safe yam germplasm exchanges and the implementation of clean seed production programs worldwide.
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Affiliation(s)
- Marie Umber
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
- Correspondence: ; Tel.: +590-590-25-59-29
| | - Denis Filloux
- Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Unité Mixte de Recherche—Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France;
- Biologie et Génétique des Interactions Plante-Parasite, Univ. Montpellier, Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Institut National de Recherche pour l’Agriculture, Montpellier SupAgro, F-34060 Montpellier, France
| | - Suzia Gélabale
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
| | - Rose-Marie Gomez
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
| | - Armelle Marais
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Université de Bordeaux, Unité Mixte de Recherche Biologie du Fruit et Pathologie, F-33882 Villenave d’Ornon, France;
| | - Séverine Gallet
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
| | - Franciane Gamiette
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
| | - Claudie Pavis
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
| | - Pierre-Yves Teycheney
- Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, F-97130 Capesterre Belle-Eau, France;
- Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, Univ. Montpellier, Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Institut Agro, F-97130 Capesterre Belle-Eau, France
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13
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Khalili M, Candresse T, Faure C, Marais A. Complete genome sequence of almond luteovirus 1, a novel luteovirus infecting almond. Arch Virol 2020; 165:2123-2126. [PMID: 32617763 DOI: 10.1007/s00705-020-04715-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 05/23/2020] [Indexed: 11/27/2022]
Abstract
In this study, we report the complete genome sequence of a novel luteovirus detected in almond using high-throughput sequencing. The genome of the new luteovirus comprises 5,047 nucleotides, and its genomic organization is similar to that of the recently described nectarine stem pitting associated virus (NSPaV), with only four open reading frames, encoding replication-related proteins, the coat protein (CP), and a CP readthrough protein involved in the aphid transmission of luteovirids. Phylogenic and pairwise distance analyses showed that this virus shares 79% and 57.8% amino acid identity in the P1-P2 fusion protein and the P3-P5 protein, respectively, with the most closely related luteovirus, NSPaV, suggesting that it represents a novel species, for which the name "Almond associated luteovirus 1" is proposed. To our knowledge, this is the first report of an almond-infecting luteovirus.
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Affiliation(s)
- Maryam Khalili
- INRAE, Univ. Bordeaux, UMR BFP, 33140, Villenave d'Ornon, France
| | | | - Chantal Faure
- INRAE, Univ. Bordeaux, UMR BFP, 33140, Villenave d'Ornon, France
| | - Armelle Marais
- INRAE, Univ. Bordeaux, UMR BFP, 33140, Villenave d'Ornon, France.
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14
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Marais A, Šafářová D, Navrátil M, Faure C, Cornaggia D, Brans Y, Suchá J, Candresse T. Complete genome sequence of cherry virus T, a novel cherry-infecting tepovirus. Arch Virol 2020; 165:1711-1714. [PMID: 32409875 DOI: 10.1007/s00705-020-04656-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/12/2020] [Indexed: 10/24/2022]
Abstract
Double-stranded RNA and total RNA purified from sour cherry leaves (Prunus cerasus, cv. Amarelka Chvalkovicka) was analyzed by high-throughput sequencing. BLAST annotation identified contigs with homology to several already known cherry-infecting viruses (prune dwarf virus, prunus necrotic ringspot virus, prunus virus F, little cherry virus 1) as well as contigs with sequences more distantly related to those of members of the family Betaflexiviridae and in particular to prunus virus T of the genus Tepovirus. The full genome sequence of a putative virus (6,847 nucleotides [nt]; GenBank no. MT090966) was assembled and completed at the genome ends. The genome has a typical tepovirus organization, containing three overlapping open reading frames (ORFs), encoding a replication-associated protein, a movement protein and a capsid protein, respectively. Both its genome organization and its phylogenetic relationships show that the virus belongs to the genus Tepovirus, but considering the species demarcation criteria for the family Betaflexiviridae, it appears to represent a novel virus species, and we propose the name "cherry virus T" (ChVT) for this virus.
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Affiliation(s)
- A Marais
- INRAE, University of Bordeaux, UMR BFP, 33140, Villenave d'Ornon, France
| | - D Šafářová
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, 783 71, Olomouc-Holice, Czech Republic
| | - M Navrátil
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, 783 71, Olomouc-Holice, Czech Republic
| | - C Faure
- INRAE, University of Bordeaux, UMR BFP, 33140, Villenave d'Ornon, France
| | - D Cornaggia
- Laboratoire de Virologie et de Biologie moléculaire, CTIFL, 28 Route des Nébouts, 24130, Prigonrieux, France
| | - Y Brans
- Laboratoire de Virologie et de Biologie moléculaire, CTIFL, 28 Route des Nébouts, 24130, Prigonrieux, France
| | - J Suchá
- Research Institute of Pomology in Holovousy Ltd, Holovousy 129, 508 01, Hořice, Czech Republic
| | - T Candresse
- INRAE, University of Bordeaux, UMR BFP, 33140, Villenave d'Ornon, France.
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15
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Candresse T, Marais A, Faure C, Lefebvre M, Lacombe T, Boursiquot JM. Complete genome sequence of a novel grapevine-infecting member of the genus Polerovirus, grapevine polerovirus 1. Arch Virol 2020; 165:1683-1685. [PMID: 32372367 DOI: 10.1007/s00705-020-04640-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/28/2020] [Indexed: 10/24/2022]
Abstract
Double-stranded RNAs and total RNAs purified from grapevine (Vitis vinifera) phloem scrapings of two varieties held in the INRAE (France) grapevine germplasm collection were analyzed by high-throughput sequencing. BLAST annotation revealed contigs with homology to Polerovirus genus members. The full genome sequence of one isolate (KT) was determined (5651 nucleotides [nt]), and a partial sequence representing about half of the genome was assembled for a second isolate (KS) that was found to share 95% nt sequence identity with the KT isolate. The genome has a typical polerovirus organization, containing six open reading frames (ORFs) as well as a putative additional ORF3a. Based on genome organization and phylogenetic relationships, the new virus belongs to the genus Polerovirus but, similar to the recently described persimmon polerovirus 1, is characterized by a highly divergent coat-protein/readthrough domain. Considering the species demarcation criteria for the family Luteoviridae, these two isolates, together with a closely related sequence recently deposited in the GenBank database (LC507098), represent a new Polerovirus species for which the name "Grapevine polerovirus 1" is proposed.
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Affiliation(s)
- T Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, 72 Avenue Edouard Bourlaux, CS20032, 33882, Villenave d'Ornon cedex, France.
| | - A Marais
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, 72 Avenue Edouard Bourlaux, CS20032, 33882, Villenave d'Ornon cedex, France
| | - C Faure
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, 72 Avenue Edouard Bourlaux, CS20032, 33882, Villenave d'Ornon cedex, France
| | - M Lefebvre
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, 72 Avenue Edouard Bourlaux, CS20032, 33882, Villenave d'Ornon cedex, France
| | - T Lacombe
- UMR AGAP, INRAE, Montpellier SupAgro, TA A-108/03 Avenue Agropolis, 34398, Montpellier Cedex 5, France
- Centre de Ressources Biologiques de la Vigne, INRAE, 34340, Marseillan-Plage, France
| | - J M Boursiquot
- UMR AGAP, INRAE, Montpellier SupAgro, TA A-108/03 Avenue Agropolis, 34398, Montpellier Cedex 5, France
- Centre de Ressources Biologiques de la Vigne, INRAE, 34340, Marseillan-Plage, France
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16
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Katsiani A, Stainton D, Lamour K, Tzanetakis IE. The population structure of Rose rosette virus in the USA. J Gen Virol 2020; 101:676-684. [PMID: 32375952 DOI: 10.1099/jgv.0.001418] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rose rosette virus (RRV) (genus Emaravirus) is the causal agent of the homonymous disease, the most destructive malady of roses in the USA. Although the importance of the disease is recognized, little sequence information and no full genomes are available for RRV, a multi-segmented RNA virus. To better understand the population structure of the virus we implemented a Hi-Plex PCR amplicon high-throughput sequencing approach to sequence all 7 segments and to quantify polymorphisms in 91 RRV isolates collected from 16 states in the USA. Analysis revealed insertion/deletion (indel) polymorphisms primarily in the 5' and 3' non-coding, but also within coding regions, including some resulting in changes of protein length. Phylogenetic analysis showed little geographical structuring, suggesting that topography does not have a strong influence on virus evolution. Overall, the virus populations were homogeneous, possibly because of regular movement of plants, the recent emergence of RRV and/or because the virus is under strong purification selection to preserve its integrity and biological functions.
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Affiliation(s)
- Asimina Katsiani
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville AR 72701, USA
| | - Daisy Stainton
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville AR 72701, USA
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville AR 72701, USA
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17
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Marais A, Faure C, Theil S, Candresse T. Characterization of the virome of shallots affected by the shallot mild yellow stripe disease in France. PLoS One 2019; 14:e0219024. [PMID: 31339882 PMCID: PMC6655591 DOI: 10.1371/journal.pone.0219024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 07/09/2019] [Indexed: 11/19/2022] Open
Abstract
To elucidate the etiology of a new disease of shallot in France, double-stranded RNAs from asymptomatic and symptomatic shallot plants were analyzed using high-throughput sequencing (HTS). Annotation of contigs, molecular characterization and phylogenetic analyses revealed the presence in symptomatic plants of a virus complex consisting of shallot virus X (ShVX, Allexivirus), shallot latent virus (SLV, Carlavirus) and two novel viruses belonging to the genera Carlavirus and Potyvirus, for which the names of shallot virus S (ShVS) and shallot mild yellow stripe associated virus (SMYSaV), are proposed. Complete or near complete genomic sequences were obtained for all these agents, revealing divergent isolates of ShVX and SLV. Trials to fulfill Koch's postulates were pursued but failed to reproduce the symptoms on inoculated shallots, even though the plants were proved to be infected by the four viruses detected by HTS. Replanting of bulbs from SMYSaV-inoculated shallot plants resulted in infected plants, showing that the virus can perpetuate the infection over seasons. A survey analyzing 351 shallot samples over a four years period strongly suggests an association of SMYSaV with the disease symptoms. An analysis of SMYSaV diversity indicates the existence of two clusters of isolates, one of which is largely predominant in the field over years.
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Affiliation(s)
- Armelle Marais
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Chantal Faure
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Sébastien Theil
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Thierry Candresse
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, Villenave d’Ornon, France
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18
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Tahzima R, Foucart Y, Peusens G, Beliën T, Massart S, De Jonghe K. High-Throughput Sequencing Assists Studies in Genomic Variability and Epidemiology of Little Cherry Virus 1 and 2 infecting Prunus spp. in Belgium. Viruses 2019; 11:E592. [PMID: 31261922 PMCID: PMC6669712 DOI: 10.3390/v11070592] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/20/2019] [Accepted: 06/28/2019] [Indexed: 11/17/2022] Open
Abstract
Little cherry disease, caused by little cherry virus 1 (LChV-1) and little cherry virus 2 (LChV-2), which are both members of the family Closteroviridae, severely affects sweet (Prunus avium L.) and sour cherry (P. cerasus L.) orchards lifelong production worldwide. An intensive survey was conducted across different geographic regions of Belgium to study the disease presence on these perennial woody plants and related species. Symptomatic as well as non-symptomatic Prunus spp. trees tested positive via RT-PCR for LChV-1 and -2 in single or mixed infections, with a slightly higher incidence for LChV-1. Both viruses were widespread and highly prevalent in nearly all Prunus production areas as well as in private gardens and urban lane trees. The genetic diversity of Belgian LChV-1 and -2 isolates was assessed by Sanger sequencing of partial genomic regions. A total RNA High-Throughput Sequencing (HTS) approach confirmed the presence of both viruses, and revealed the occurrence of other Prunus-associated viruses, namely cherry virus A (CVA), prune dwarf virus (PDV) and prunus virus F (PrVF). The phylogenetic inference from full-length genomes revealed well-defined evolutionary phylogroups with high genetic variability and diversity for LChV-1 and LChV-2 Belgian isolates, yet with little or no correlation with planting area or cultivated varieties. The global diversity and the prevalence in horticultural areas of LChV-1 and -2 variants, in association with other recently described fruit tree viruses, are of particular concern. Future epidemiological implications as well as new investigation avenues are exhaustively discussed.
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Affiliation(s)
- Rachid Tahzima
- Plant Sciences, Fisheries and Food (ILVO), Flanders Research Institute for Agriculture, 9820 Merelbeke, Belgium
- Department of Integrated and Urban Phytopathology, University of Liège (ULg) - Gembloux Agro-Bio tech, 5030 Gembloux, Belgium
| | - Yoika Foucart
- Plant Sciences, Fisheries and Food (ILVO), Flanders Research Institute for Agriculture, 9820 Merelbeke, Belgium
| | - Gertie Peusens
- Department of Zoology, Proefcentrum Fruitteelt (pcfruit), 3800 Sint-Truiden, Belgium
| | - Tim Beliën
- Department of Zoology, Proefcentrum Fruitteelt (pcfruit), 3800 Sint-Truiden, Belgium
| | - Sébastien Massart
- Department of Integrated and Urban Phytopathology, University of Liège (ULg) - Gembloux Agro-Bio tech, 5030 Gembloux, Belgium
| | - Kris De Jonghe
- Plant Sciences, Fisheries and Food (ILVO), Flanders Research Institute for Agriculture, 9820 Merelbeke, Belgium.
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19
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Scussel S, Candresse T, Marais A, Claverie S, Hoareau M, Azali HA, Verdin E, Tepfer M, Filloux D, Fernandez E, Roumagnac P, Robène I, Lefeuvre P, Jourda C, Roux-Cuvelier M, Lett JM. High-throughput sequencing of complete genomes of ipomoviruses associated with an epidemic of cassava brown streak disease in the Comoros Archipelago. Arch Virol 2019; 164:2193-2196. [PMID: 31123961 DOI: 10.1007/s00705-019-04228-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 03/05/2019] [Indexed: 11/26/2022]
Abstract
Using high-throughput sequencing of small interfering RNAs (siRNAs), virion-associated nucleic acid (VANA), and double stranded RNAs (dsRNAs), we have determined the complete genome sequences of Comorian isolates of two ipomoviruses, cassava brown streak virus (CBSV) and a divergent isolate of Ugandan cassava brown streak virus (UCBSV-KM) representing a new strain of this virus. While the large ORF of CBSV shares the highest nucleotide sequence identity (95.9%) with a Tanzanian isolate of CBSV, the large UCBSV-KM ORF shares the highest nucleotide sequence identity (77.5%) with a Malawian isolate of UCBSV. This low value is near the species demarcation threshold for the family Potyviridae (<76%). Phylogenetic analysis confirms that UCBSV-KM represents a new lineage that is genetically distinct from the currently described UCBSV strains.
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Affiliation(s)
- Sarah Scussel
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Armelle Marais
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Sohini Claverie
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
- Université de La Réunion, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | - Murielle Hoareau
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | | | - Eric Verdin
- INRA, UR407 Unité de Pathologie Végétale, CS 60094, 84140, Montfavet, France
| | - Mark Tepfer
- INRA, UR407 Unité de Pathologie Végétale, CS 60094, 84140, Montfavet, France
- Institut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, CNRS, Saclay Plant Sciences (SPS), Université Paris-Saclay, 78026, Versailles, France
| | - Denis Filloux
- CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398, Montpellier Cedex-5, France
| | - Emmanuel Fernandez
- CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398, Montpellier Cedex-5, France
| | - Philippe Roumagnac
- CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398, Montpellier Cedex-5, France
| | - Isabelle Robène
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | - Pierre Lefeuvre
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | - Cyril Jourda
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | - Michel Roux-Cuvelier
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | - Jean-Michel Lett
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France.
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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: 157] [Impact Index Per Article: 31.4] [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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21
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Mann KS, Chisholm J, Sanfaçon H. Strawberry Mottle Virus (Family Secoviridae, Order Picornavirales) Encodes a Novel Glutamic Protease To Process the RNA2 Polyprotein at Two Cleavage Sites. J Virol 2019; 93:e01679-18. [PMID: 30541838 PMCID: PMC6384087 DOI: 10.1128/jvi.01679-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/19/2018] [Indexed: 01/29/2023] Open
Abstract
Strawberry mottle virus (SMoV) belongs to the family Secoviridae (order Picornavirales) and has a bipartite genome with each RNA encoding one polyprotein. All characterized secovirids encode a single protease related to the picornavirus 3C protease. The SMoV 3C-like protease was previously shown to cut the RNA2 polyprotein (P2) at a single site between the predicted movement protein and coat protein (CP) domains. However, the SMoV P2 polyprotein includes an extended C-terminal region with a coding capacity of up to 70 kDa downstream of the presumed CP domain, an unusual characteristic for this family. In this study, we identified a novel cleavage event at a P↓AFP sequence immediately downstream of the CP domain. Following deletion of the PAFP sequence, the polyprotein was processed at or near a related PKFP sequence 40 kDa further downstream, defining two protein domains in the C-terminal region of the P2 polyprotein. Both processing events were dependent on a novel protease domain located between the two cleavage sites. Mutagenesis of amino acids that are conserved among isolates of SMoV and of the related Black raspberry necrosis virus did not identify essential cysteine, serine, or histidine residues, suggesting that the RNA2-encoded SMoV protease is not related to serine or cysteine proteases of other picorna-like viruses. Rather, two highly conserved glutamic acid residues spaced by 82 residues were found to be strictly required for protease activity. We conclude that the processing of SMoV polyproteins requires two viral proteases, the RNA1-encoded 3C-like protease and a novel glutamic protease encoded by RNA2.IMPORTANCE Many viruses encode proteases to release mature proteins and intermediate polyproteins from viral polyproteins. Polyprotein processing allows regulation of the accumulation and activity of viral proteins. Many viral proteases also cleave host factors to facilitate virus infection. Thus, viral proteases are key virulence factors. To date, viruses with a positive-strand RNA genome are only known to encode cysteine or serine proteases, most of which are related to the cellular papain, trypsin, or chymotrypsin proteases. Here, we characterize the first glutamic protease encoded by a plant virus or by a positive-strand RNA virus. The novel glutamic protease is unique to a few members of the family Secoviridae, suggesting that it is a recent acquisition in the evolution of this family. The protease does not resemble known cellular proteases. Rather, it is predicted to share structural similarities with a family of fungal and bacterial glutamic proteases that adopt a lectin fold.
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Affiliation(s)
- Krin S Mann
- Agriculture and Agri-Food Canada, Summerland Research and Development Centre, Summerland, British Columbia, Canada
| | - Joan Chisholm
- Agriculture and Agri-Food Canada, Summerland Research and Development Centre, Summerland, British Columbia, Canada
| | - Hélène Sanfaçon
- Agriculture and Agri-Food Canada, Summerland Research and Development Centre, Summerland, British Columbia, Canada
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Nourinejhad Zarghani S, Hily JM, Glasa M, Marais A, Wetzel T, Faure C, Vigne E, Velt A, Lemaire O, Boursiquot JM, Okic A, Ruiz-Garcia AB, Olmos A, Lacombe T, Candresse T. Grapevine virus T diversity as revealed by full-length genome sequences assembled from high-throughput sequence data. PLoS One 2018; 13:e0206010. [PMID: 30376573 PMCID: PMC6207325 DOI: 10.1371/journal.pone.0206010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/04/2018] [Indexed: 12/13/2022] Open
Abstract
RNASeq or double-stranded RNA based approaches allowed the reconstruction of a total of 9 full-length or near full-length genomes of the recently discovered grapevine virus T (GVT). In addition, datamining of publicly available grapevine RNASeq transcriptome data allowed the reconstruction of a further 14 GVT genomes from five grapevine sources. Together with four GVT sequences available in Genbank, these novel sequences were used to analyse GVT diversity. GVT shows a very limited amount of indels variation but a high level of nucleotide and aminoacid polymorphism. This level is comparable to that shown in the closely related grapevine rupestris stem pitting-associated virus (GRSPaV). Further analyses showed that GVT mostly evolves under conservative selection pressure and that recombination has contributed to its evolutionary history. Phylogenetic analyses allow to identify at least seven clearly separated groups of GVT isolates. Analysis of the only reported PCR GVT-specific detection primer pair indicates that it is likely to fail to amplify some GVT isolates. Taken together these results point at the distinctiveness of GVT but also at the many points it shares with GRSPaV. They constitute the first pan-genomic analysis of the diversity of this novel virus.
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Affiliation(s)
- Shaheen Nourinejhad Zarghani
- DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse, Germany
- Department of Plant Protection, College of Abouraihan, University of Tehran, Tehran, Iran
| | | | - Miroslav Glasa
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Armelle Marais
- Equipe de Virologie, UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | - Thierry Wetzel
- DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse, Germany
| | - Chantal Faure
- Equipe de Virologie, UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | | | - Amandine Velt
- Université de Strasbourg, INRA, SVQV UMR-A 1131, Colmar, France
| | - Olivier Lemaire
- Université de Strasbourg, INRA, SVQV UMR-A 1131, Colmar, France
| | - Jean Michel Boursiquot
- UMR 1334 AGAP, INRA, Montpellier SupAgro, Montpellier, France
- Centre de Ressources Biologiques de la Vigne, INRA, Marseillan-Plage, France
| | - Arnela Okic
- University of Sarajevo, Faculty of Agriculture and Food Science, Sarajevo, Bosnia and Herzegovina
| | | | - Antonio Olmos
- Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
| | - Thierry Lacombe
- UMR 1334 AGAP, INRA, Montpellier SupAgro, Montpellier, France
- Centre de Ressources Biologiques de la Vigne, INRA, Marseillan-Plage, France
| | - Thierry Candresse
- Equipe de Virologie, UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
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23
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Svanella-Dumas L, Τsarmpopoulos Ι, Marais A, Theil S, Faure C, Gaudin J, Candresse T. Complete genome sequence of lettuce chordovirus 1 isolated from cultivated lettuce in France. Arch Virol 2018; 163:2543-2545. [PMID: 29730706 DOI: 10.1007/s00705-018-3858-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/27/2018] [Indexed: 10/17/2022]
Abstract
Double-stranded RNAs purified from cultivated (Lactuca sativa) or wild (L. serriola) lettuce from southwest France were analyzed by high-throughput sequencing. For both samples, BLAST annotation revealed contigs with homology to Betaflexiviridae family members. The full genome sequence of the isolate from cultivated lettuce (JG1) was completed (8,536 nucleotides [nt], excluding the poly(A) tail). The sequence of the 3' half of the genome (4,800 nt) of a wild lettuce isolate (P22) was determined and found to share 95.1% nt sequence identity with the JG1 isolate. The JG1 genome contains four open reading frames, encoding a replicase, a movement protein, a capsid protein, and a protein of unknown function, respectively. Based on genome organization and phylogenetic relationships, the lettuce virus is most closely related to the recently described carrot chordoviruses 1 and 2 in the family Betaflexiviridae. Considering the species demarcation criteria in this family, the two lettuce viruses represent isolates of a new chordovirus species for which the name "lettuce chordovirus 1" (LeCV1) is proposed.
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Affiliation(s)
- Laurence Svanella-Dumas
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Ιason Τsarmpopoulos
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Armelle Marais
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Sébastien Theil
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Chantal Faure
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Jonathan Gaudin
- UMR 1065, Santé et Agroécologie du Vignoble, INRA, Bordeaux Sciences Agro, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Thierry Candresse
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France.
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24
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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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Svanella-Dumas L, Marais A, Faure C, Theil S, Lefebvre M, Candresse T. Genome characterization of a divergent isolate of the mycovirus Botrytis virus F from a grapevine metagenome. Arch Virol 2018; 163:3181-3183. [PMID: 30074093 DOI: 10.1007/s00705-018-3975-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 07/23/2018] [Indexed: 11/28/2022]
Abstract
As part of a grapevine metagenome study, total RNA extracted from grapevine phloem scrapings was analyzed by Illumina sequencing. For one 420A rootstock sample, reads mapping against a reference database and BLAST annotation of contigs identified the presence of a divergent isolate of Botrytis virus F (BVF). The full genome sequence of this isolate (IVC-5-77) was determined (6,828 nucleotides [nt], excluding the poly(A) tail) and shown to be collinear with that of the BVF reference isolate, with the two open reading frames encoding a replication-associated protein (REP) and a coat protein (CP). The IVC-5-77 isolate, however, is very divergent, showing only 81.3-81.6% nucleotide sequence identity to the two other sequenced BVF isolates. The internal non-coding region was also found to be highly variable between BVF isolates. Analysis of the RNASeq reads demonstrated that close to 20% of them belong to Botrytis cinerea, the putative host of the IVC-5-77 isolate. These results extend our knowledge of the diversity and variability of BVF and demonstrate its detectability, together with that of its B. cinerea host, in total RNA RNASeq data from grapevine phloem scrapings.
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Affiliation(s)
- Laurence Svanella-Dumas
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Armelle Marais
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Chantal Faure
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Sébastien Theil
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Marie Lefebvre
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France.
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26
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Verdin E, Marais A, Wipf-Scheibel C, Faure C, Pelletier B, David P, Svanella-Dumas L, Poisblaud C, Lecoq H, Candresse T. Biological and Genetic Characterization of New and Known Necroviruses Causing an Emerging Systemic Necrosis Disease of Corn Salad (Valerianella locusta) in France. PHYTOPATHOLOGY 2018; 108:1002-1010. [PMID: 29490195 DOI: 10.1094/phyto-08-17-0284-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: 06/08/2023]
Abstract
An emerging systemic necrosis disease of corn salad was first observed in the Nantes region of France in the late 2000s. Classical virology and high-throughput sequencing approaches demonstrated that the disease is associated with four different necroviruses: tobacco necrosis virus A (TNVA), tobacco necrosis virus D (TNVD), olive mild mosaic virus (OMMV), and a novel recombinant Alphanecrovirus for which the name corn salad necrosis virus (CSNV) is proposed. Satellite tobacco necrosis virus was also frequently observed. Koch's postulates were completed for all four agents, each one alone being able to cause systemic necrosis of varying severity in corn salad. OMMV was the most frequently observed virus and causes the most severe symptoms. TNVA was the second, both in terms of prevalence and symptom severity while TNVD and CSNV were only rarely observed and caused the less severe symptoms. The emergence of this systemic disease may have been favored by the short and repeated cropping cycles used for corn salad, possibly allowing the selection of necrovirus isolates with an improved ability to systemically invade this specialty crop.
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Affiliation(s)
- E Verdin
- First, third, and ninth authors: Unité de Pathologie Végétale, INRA, Domaine Saint Maurice, 67, allée des chênes, CS 60094, F84143 Montfavet Cedex, France; second, fourth, seventh, and tenth authors: Equipe de Virologie, UMR 1332 BFP, INRA, University of Bordeaux, 71 Avenue Edouard Bourleaux, CS20032, F33882 Villenave d'Ornon Cedex, France; fifth author: Comité Départemental de Développement Maraîcher (CDDM), Maisons des maraîchers, La métairie neuve, F44860 Pont St Martin, France; and sixth and eighth authors: HM.CLAUSE, 1 Chemin du Moulin des Ronzières, 49800 La Bohalle, France
| | - A Marais
- First, third, and ninth authors: Unité de Pathologie Végétale, INRA, Domaine Saint Maurice, 67, allée des chênes, CS 60094, F84143 Montfavet Cedex, France; second, fourth, seventh, and tenth authors: Equipe de Virologie, UMR 1332 BFP, INRA, University of Bordeaux, 71 Avenue Edouard Bourleaux, CS20032, F33882 Villenave d'Ornon Cedex, France; fifth author: Comité Départemental de Développement Maraîcher (CDDM), Maisons des maraîchers, La métairie neuve, F44860 Pont St Martin, France; and sixth and eighth authors: HM.CLAUSE, 1 Chemin du Moulin des Ronzières, 49800 La Bohalle, France
| | - C Wipf-Scheibel
- First, third, and ninth authors: Unité de Pathologie Végétale, INRA, Domaine Saint Maurice, 67, allée des chênes, CS 60094, F84143 Montfavet Cedex, France; second, fourth, seventh, and tenth authors: Equipe de Virologie, UMR 1332 BFP, INRA, University of Bordeaux, 71 Avenue Edouard Bourleaux, CS20032, F33882 Villenave d'Ornon Cedex, France; fifth author: Comité Départemental de Développement Maraîcher (CDDM), Maisons des maraîchers, La métairie neuve, F44860 Pont St Martin, France; and sixth and eighth authors: HM.CLAUSE, 1 Chemin du Moulin des Ronzières, 49800 La Bohalle, France
| | - C Faure
- First, third, and ninth authors: Unité de Pathologie Végétale, INRA, Domaine Saint Maurice, 67, allée des chênes, CS 60094, F84143 Montfavet Cedex, France; second, fourth, seventh, and tenth authors: Equipe de Virologie, UMR 1332 BFP, INRA, University of Bordeaux, 71 Avenue Edouard Bourleaux, CS20032, F33882 Villenave d'Ornon Cedex, France; fifth author: Comité Départemental de Développement Maraîcher (CDDM), Maisons des maraîchers, La métairie neuve, F44860 Pont St Martin, France; and sixth and eighth authors: HM.CLAUSE, 1 Chemin du Moulin des Ronzières, 49800 La Bohalle, France
| | - B Pelletier
- First, third, and ninth authors: Unité de Pathologie Végétale, INRA, Domaine Saint Maurice, 67, allée des chênes, CS 60094, F84143 Montfavet Cedex, France; second, fourth, seventh, and tenth authors: Equipe de Virologie, UMR 1332 BFP, INRA, University of Bordeaux, 71 Avenue Edouard Bourleaux, CS20032, F33882 Villenave d'Ornon Cedex, France; fifth author: Comité Départemental de Développement Maraîcher (CDDM), Maisons des maraîchers, La métairie neuve, F44860 Pont St Martin, France; and sixth and eighth authors: HM.CLAUSE, 1 Chemin du Moulin des Ronzières, 49800 La Bohalle, France
| | - P David
- First, third, and ninth authors: Unité de Pathologie Végétale, INRA, Domaine Saint Maurice, 67, allée des chênes, CS 60094, F84143 Montfavet Cedex, France; second, fourth, seventh, and tenth authors: Equipe de Virologie, UMR 1332 BFP, INRA, University of Bordeaux, 71 Avenue Edouard Bourleaux, CS20032, F33882 Villenave d'Ornon Cedex, France; fifth author: Comité Départemental de Développement Maraîcher (CDDM), Maisons des maraîchers, La métairie neuve, F44860 Pont St Martin, France; and sixth and eighth authors: HM.CLAUSE, 1 Chemin du Moulin des Ronzières, 49800 La Bohalle, France
| | - L Svanella-Dumas
- First, third, and ninth authors: Unité de Pathologie Végétale, INRA, Domaine Saint Maurice, 67, allée des chênes, CS 60094, F84143 Montfavet Cedex, France; second, fourth, seventh, and tenth authors: Equipe de Virologie, UMR 1332 BFP, INRA, University of Bordeaux, 71 Avenue Edouard Bourleaux, CS20032, F33882 Villenave d'Ornon Cedex, France; fifth author: Comité Départemental de Développement Maraîcher (CDDM), Maisons des maraîchers, La métairie neuve, F44860 Pont St Martin, France; and sixth and eighth authors: HM.CLAUSE, 1 Chemin du Moulin des Ronzières, 49800 La Bohalle, France
| | - C Poisblaud
- First, third, and ninth authors: Unité de Pathologie Végétale, INRA, Domaine Saint Maurice, 67, allée des chênes, CS 60094, F84143 Montfavet Cedex, France; second, fourth, seventh, and tenth authors: Equipe de Virologie, UMR 1332 BFP, INRA, University of Bordeaux, 71 Avenue Edouard Bourleaux, CS20032, F33882 Villenave d'Ornon Cedex, France; fifth author: Comité Départemental de Développement Maraîcher (CDDM), Maisons des maraîchers, La métairie neuve, F44860 Pont St Martin, France; and sixth and eighth authors: HM.CLAUSE, 1 Chemin du Moulin des Ronzières, 49800 La Bohalle, France
| | - H Lecoq
- First, third, and ninth authors: Unité de Pathologie Végétale, INRA, Domaine Saint Maurice, 67, allée des chênes, CS 60094, F84143 Montfavet Cedex, France; second, fourth, seventh, and tenth authors: Equipe de Virologie, UMR 1332 BFP, INRA, University of Bordeaux, 71 Avenue Edouard Bourleaux, CS20032, F33882 Villenave d'Ornon Cedex, France; fifth author: Comité Départemental de Développement Maraîcher (CDDM), Maisons des maraîchers, La métairie neuve, F44860 Pont St Martin, France; and sixth and eighth authors: HM.CLAUSE, 1 Chemin du Moulin des Ronzières, 49800 La Bohalle, France
| | - T Candresse
- First, third, and ninth authors: Unité de Pathologie Végétale, INRA, Domaine Saint Maurice, 67, allée des chênes, CS 60094, F84143 Montfavet Cedex, France; second, fourth, seventh, and tenth authors: Equipe de Virologie, UMR 1332 BFP, INRA, University of Bordeaux, 71 Avenue Edouard Bourleaux, CS20032, F33882 Villenave d'Ornon Cedex, France; fifth author: Comité Départemental de Développement Maraîcher (CDDM), Maisons des maraîchers, La métairie neuve, F44860 Pont St Martin, France; and sixth and eighth authors: HM.CLAUSE, 1 Chemin du Moulin des Ronzières, 49800 La Bohalle, France
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27
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Beuve M, Hily JM, Alliaume A, Reinbold C, Le Maguet J, Candresse T, Herrbach E, Lemaire O. A complex virome unveiled by deep sequencing analysis of RNAs from a French Pinot Noir grapevine exhibiting strong leafroll symptoms. Arch Virol 2018; 163:2937-2946. [PMID: 30033497 DOI: 10.1007/s00705-018-3949-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 05/11/2018] [Indexed: 11/25/2022]
Abstract
We have characterized the virome of a grapevine Pinot Noir accession (P70) that displayed, over the year, very stable and strong leafroll symptoms. For this, we have used two extraction methods (dsRNA and total RNA) coupled with the high throughput sequencing (HTS) Illumina technique. While a great disparity in viral sequences were observed, both approaches gave similar results, revealing a very complex infection status. Five virus and viroid isolates [Grapevine leafroll-associated viruse-1 (GLRaV-1), Grapevine virus A (GVA), Grapevine rupestris stem pitting-associated virus (GRSPaV), Hop stunt viroid (HSVd) and Grapevine yellow speckle viroid 1 (GYSVd1)] were detected in P70 with a grand total of eleven variants being identified and de novo assembled. A comparison between both extraction methods regarding their power to detect viruses and the ease of genome assembly is also provided.
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Affiliation(s)
- Monique Beuve
- SVQV, Université de Strasbourg, 68000, Colmar, France
| | | | | | | | - Jean Le Maguet
- SVQV, Université de Strasbourg, 68000, Colmar, France
- Institut Français des Productions Cidricoles (IFPC), 61500, Sées, France
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Villenave d'Ornon Cedex, France
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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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29
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Baráth D, Jaksa-Czotter N, Molnár J, Varga T, Balássy J, Szabó LK, Kirilla Z, Tusnády GE, Preininger É, Várallyay É. Small RNA NGS Revealed the Presence of Cherry Virus A and Little Cherry Virus 1 on Apricots in Hungary. Viruses 2018; 10:E318. [PMID: 29891760 PMCID: PMC6024520 DOI: 10.3390/v10060318] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/08/2018] [Accepted: 06/09/2018] [Indexed: 12/14/2022] Open
Abstract
Fruit trees, such as apricot trees, are constantly exposed to the attack of viruses. As they are propagated in a vegetative way, this risk is present not only in the field, where they remain for decades, but also during their propagation. Metagenomic diagnostic methods, based on next generation sequencing (NGS), offer unique possibilities to reveal all the present pathogens in the investigated sample. Using NGS of small RNAs, a special field of these techniques, we tested leaf samples of different varieties of apricot originating from an isolator house or open field stock nursery. As a result, we identified Cherry virus A (CVA) and little cherry virus 1 (LChV-1) for the first time in Hungary. The NGS results were validated by RT-PCR and also by Northern blot in the case of CVA. Cloned and Sanger sequenced viral-specific PCR products enabled us to investigate their phylogenetic relationships. However, since these pathogens have not been described in our country before, their role in symptom development and modification during co-infection with other viruses requires further investigation.
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Affiliation(s)
- Dániel Baráth
- Agricultural Biotechnology Institute, NARIC, 2100 Gödöllő, Hungary.
| | | | - János Molnár
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, 7632 Pécs, Hungary.
| | - Tünde Varga
- Agricultural Biotechnology Institute, NARIC, 2100 Gödöllő, Hungary.
| | - Júlia Balássy
- Agricultural Biotechnology Institute, NARIC, 2100 Gödöllő, Hungary.
| | | | - Zoltán Kirilla
- Fruitculture Research Institute, NARIC, 1223 Budapest, Hungary.
| | - Gábor E Tusnády
- Institute of Enzymology, Research Center of Natural Sciences, HAS, 1117 Budapest, Hungary.
| | - Éva Preininger
- Fruitculture Research Institute, NARIC, 1223 Budapest, Hungary.
| | - Éva Várallyay
- Agricultural Biotechnology Institute, NARIC, 2100 Gödöllő, Hungary.
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30
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Katsiani AT, Pappi P, Olmos A, Efthimiou KE, Maliogka VI, Katis NI. Development of a Real-Time RT-PCR for the Universal Detection of LChV1 and Study of the Seasonal Fluctuation of the Viral Titer in Sweet Cherry Cultivars. PLANT DISEASE 2018; 102:899-904. [PMID: 30673385 DOI: 10.1094/pdis-01-17-0107-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Little cherry virus 1 (LChV1) is a sweet cherry pathogen which has lately been reported in other Prunus spp. LChV1 variability makes reliable detection a challenging undertaking. The objective of this work was to develop a rapid, sensitive, and reliable one-tube, real-time reverse-transcription polymerase chain reaction (RT-PCR) for the detection and quantification of LChV1. Primers and a TaqMan probe were designed, using conserved regions of the capsid protein gene. Detection range was evaluated using several divergent viral isolates. The amplification efficiency of the method was estimated at 96.7%, whereas the detection limit was about 100 RNA copies. The protocol was applied in the study of virus fluctuation within leaves and phloem tissue throughout the year and the best periods to test and plant tissues to sample were determined. Comparative analysis of this method with a previously published nested RT-PCR revealed the higher analytical and diagnostic sensitivity of the new test, making it a reliable tool that can be used in routine testing and certification programs.
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Affiliation(s)
- Asimina T Katsiani
- Plant Pathology Laboratory, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Polyxeni Pappi
- Plant Pathology Laboratory, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Antonio Olmos
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain
| | - Konstantinos E Efthimiou
- Plant Pathology Laboratory, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki
| | - Varvara I Maliogka
- Plant Pathology Laboratory, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki
| | - Nikolaos I Katis
- Plant Pathology Laboratory, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki
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31
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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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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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33
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Svanella-Dumas L, Theil S, Barret M, Candresse T. Complete genomic sequence of Raphanus sativus cryptic virus 4 (RsCV4), a novel alphapartitivirus from radish. Arch Virol 2018; 163:1097-1100. [PMID: 29302793 DOI: 10.1007/s00705-017-3693-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/10/2017] [Indexed: 11/30/2022]
Abstract
The present work reports the discovery and complete genome sequencing of a virus from symptomless radish seedlings, classifiable as a novel member of the genus Alphapartitivirus, family Partitiviridae. Total RNA extracted from germinating seedlings was sequenced using Illumina technology. Bioinformatic analysis of the RNA-seq data revealed two contigs representing the near full-length genomic sequences of two genomic RNAs representing a new virus. Analysis of the genome sequence (excluding the polyA tail, RNA1: 1976 nt and RNA2: 1751 nt, respectively) showed a genomic organization typical of viruses classed within the Partitiviridae, with each genomic RNA encoding a single open reading frame (ORF). Phylogenetic analysis of the RNA dependent RNA polymerase (RNA1 ORF) and of the capsid protein (RNA2 ORF) clearly showed the new virus can be classified within the genus Alphapartitivirus, but sequence divergence establishes it as a new species, for which the name "Raphanus sativus cryptic virus 4" is proposed.
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Affiliation(s)
- Laurence Svanella-Dumas
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Sébastien Theil
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Matthieu Barret
- IRHS, INRA, University of Angers, 42 rue Georges Morel, 49071, Beaucouzé, France
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS 20032, 33882, Villenave d'Ornon Cedex, France.
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Marais A, Faure C, Bergey B, Candresse T. Viral Double-Stranded RNAs (dsRNAs) from Plants: Alternative Nucleic Acid Substrates for High-Throughput Sequencing. Methods Mol Biol 2018; 1746:45-53. [PMID: 29492885 DOI: 10.1007/978-1-4939-7683-6_4] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
High-throughput sequencing (or next-generation sequencing-NGS) is an emerging technology that allows the detection of plant viruses without any prior knowledge. Various sequencing techniques and various templates can be used as substrate for NGS. This chapter describes an optimized protocol for the extraction of double-stranded RNAs (dsRNAs) from a wide range of plants and for their random amplification prior to NGS sequencing.
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Affiliation(s)
- Armelle Marais
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Villenave d'Ornon, France.
| | - Chantal Faure
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Villenave d'Ornon, France
| | - Bernard Bergey
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Villenave d'Ornon, France
| | - Thierry Candresse
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Villenave d'Ornon, France
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35
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Rolland M, Villemot J, Marais A, Theil S, Faure C, Cadot V, Valade R, Vitry C, Rabenstein F, Candresse T. Classical and next generation sequencing approaches unravel Bymovirus diversity in barley crops in France. PLoS One 2017; 12:e0188495. [PMID: 29182661 PMCID: PMC5705140 DOI: 10.1371/journal.pone.0188495] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 11/08/2017] [Indexed: 11/18/2022] Open
Abstract
Despite the generalized use of cultivars carrying the rym4 resistance gene, the impact of viral mosaic diseases on winter barleys increased in recent years in France. This change could reflect i) an increased prevalence of the rym4 resistance-breaking pathotype of Barley yellow mosaic virus Y (BaYMV-2), ii) the emergence of rym4 resistance-breaking pathotypes of Barley mild mosaic virus (BaMMV) or iii) the emergence of other viruses. A study was undertaken to determine the distribution and diversity of viruses causing yellow mosaic disease. A collection of 241 symptomatic leaf samples from susceptible, rym4 and rym5 varieties was gathered from 117 sites. The viruses present in all samples were identified by specific RT-PCR assays and, for selected samples, by double-stranded RNA next-generation sequencing (NGS). The results show that BaYMV-2 is responsible for the symptoms observed in varieties carrying the resistance gene rym4. In susceptible varieties, both BaYMV-1 and BaYMV-2 were detected, together with BaMMV. Phylogenetic analyses indicate that the rym4 resistance-breaking ability independently evolved in multiple genetic backgrounds. Parallel analyses revealed a similar scenario of multiple independent emergence events in BaMMV for rym5 resistance-breaking, likely involving multiple amino acid positions in the viral-linked genome protein. NGS analyses and classical techniques provided highly convergent results, highlighting and validating the power of NGS approaches for diagnostics and viral population characterization.
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Affiliation(s)
- Mathieu Rolland
- Groupe d'Etude et de contrôle des Variétés Et des Semences, Beaucouzé, France
| | - Julie Villemot
- Groupe d'Etude et de contrôle des Variétés Et des Semences, Beaucouzé, France
| | - Armelle Marais
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Université de Bordeaux, Villenave d’Ornon, France
| | - Sébastien Theil
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Université de Bordeaux, Villenave d’Ornon, France
| | - Chantal Faure
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Université de Bordeaux, Villenave d’Ornon, France
| | - Valérie Cadot
- Groupe d'Etude et de contrôle des Variétés Et des Semences, Beaucouzé, France
| | - Romain Valade
- ARVALIS–Institut du végétal, Thiverval-Grignon, France
| | - Cindy Vitry
- ARVALIS–Institut du végétal, Thiverval-Grignon, France
| | | | - Thierry Candresse
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Université de Bordeaux, Villenave d’Ornon, France
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36
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Šafářová D, Candresse T, Navrátil M. Complete genome sequence of a novel bromovirus infecting elderberry (Sambucus nigra L.) in the Czech Republic. Arch Virol 2017; 163:567-570. [PMID: 29094240 DOI: 10.1007/s00705-017-3629-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/05/2017] [Indexed: 10/18/2022]
Abstract
The genus Bromovirus currently contains six species whose members have relatively narrow host ranges. In the present work, a new bromovirus infecting elderberry (Sambucus nigra L.) is reported. dsRNA was purified and sequenced by next-generation sequencing, and with minimal additional completion by Sanger sequencing, the full tripartite genome was obtained. RNA1 is 3241 nt long and contains ORF1 (1a protein), RNA2 is 2810 nt long and contains ORF2 (2a protein), and RNA3 is 2244 nt long and contains ORF3a (movement protein) and ORF3b (coat protein, CP), separated by an intercistronic poly(A) stretch. Proteins 1a and 2a showed highest sequence identity (69.9% and 69.4%) to the corresponding proteins of melandrium yellow fleck virus. The coat protein showed highest sequence identity (67.9%) to that of brome mosaic virus. The genome shows a typical bromovirus organisation comprising of all the conserved protein domains within the genus. Phylogenetic analysis supports the assignment of this virus as a new member of the genus Bromovirus, for which the name "sambucus virus S" (SVS) is proposed.
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Affiliation(s)
- Dana Šafářová
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71, Olomouc-Holice, Czech Republic.
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Milan Navrátil
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71, Olomouc-Holice, Czech Republic
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37
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Candresse T, Theil S, Faure C, Marais A. Determination of the complete genomic sequence of grapevine virus H, a novel vitivirus infecting grapevine. Arch Virol 2017; 163:277-280. [DOI: 10.1007/s00705-017-3587-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/21/2017] [Indexed: 10/18/2022]
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38
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Two novel Alphaflexiviridae members revealed by deep sequencing of the Vanilla (Orchidaceae) virome. Arch Virol 2017; 162:3855-3861. [DOI: 10.1007/s00705-017-3540-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/04/2017] [Indexed: 02/05/2023]
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39
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Marais A, Nivault A, Faure C, Theil S, Comont G, Candresse T, Corio-Costet MF. Determination of the complete genomic sequence of Neofusicoccum luteum mitovirus 1 (NLMV1), a novel mitovirus associated with a phytopathogenic Botryosphaeriaceae. Arch Virol 2017; 162:2477-2480. [PMID: 28451899 PMCID: PMC5506512 DOI: 10.1007/s00705-017-3338-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 02/13/2017] [Indexed: 01/24/2023]
Abstract
Neofusicoccum luteum species belongs to the Botryosphaeriaceae family and is involved in grapevine wood decay diseases. The present study reports the discovery and the molecular characterization of a novel mitovirus infecting this fungus. Double-stranded RNAs were purified from cultivated N. luteum and analysed by next generation sequencing. Using contigs showing BlastX homology with the RNA-dependent RNA polymerase (RdRp) gene of various members of the family Narnaviridae, a single contig of approximately 1.2 kb was constructed. The genomic sequence was completed and phylogenetic analyses indicated that this virus represents a new member of the genus Mitovirus, for which the name of "Neofusicoccum luteum mitovirus 1" is proposed. The genome is 2,389 nucleotides long and, based on the fungal mitochondrial genetic code, it encodes a putative protein of 710 amino acids, homologous to the RdRps of members of the Narnaviridae family. The neofusicoccum luteus mitovirus 1 (NLMV1) RdRp contains the six conserved motifs previously reported for mitoviral RdRps. Our findings represent the first evidence that a mycovirus can infect N. luteum, an important pathogenic fungus of grapevine.
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Affiliation(s)
- Armelle Marais
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS 20032, 33882, Villenave d'Ornon Cedex, France.
| | - Aurélia Nivault
- UMR 1035 Santé et Agroécologie du Vignoble, INRA, Bordeaux Sciences Agro, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Chantal Faure
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Sébastien Theil
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Gwenaëlle Comont
- UMR 1035 Santé et Agroécologie du Vignoble, INRA, Bordeaux Sciences Agro, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Marie-France Corio-Costet
- UMR 1035 Santé et Agroécologie du Vignoble, INRA, Bordeaux Sciences Agro, CS 20032, 33882, Villenave d'Ornon Cedex, France
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40
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Complete Nucleotide Sequence of an Isolate of Grapevine Satellite Virus and Evidence for the Presence of Multimeric Forms in an Infected Grapevine. GENOME ANNOUNCEMENTS 2017; 5:5/16/e01703-16. [PMID: 28428317 PMCID: PMC5399276 DOI: 10.1128/genomea.01703-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The complete nucleotide sequence of an isolate of grapevine satellite virus (GV-Sat) was determined by next-generation sequencing (NGS) and compared with the single available complete sequence. The NGS data unexpectedly provided evidence for the existence of multimeric forms of GV-Sat, which were experimentally confirmed, allowing the redefinition of GV-Sat genomic ends.
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41
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Sabbadin F, Glover R, Stafford R, Rozado-Aguirre Z, Boonham N, Adams I, Mumford R, Edwards R. Transcriptome sequencing identifies novel persistent viruses in herbicide resistant wild-grasses. Sci Rep 2017; 7:41987. [PMID: 28165016 PMCID: PMC5292734 DOI: 10.1038/srep41987] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/04/2017] [Indexed: 11/23/2022] Open
Abstract
Herbicide resistance in wild grasses is widespread in the UK, with non-target site resistance (NTSR) to multiple chemistries being particularly problematic in weed control. As a complex trait, NTSR is driven by complex evolutionary pressures and the growing awareness of the role of the phytobiome in plant abiotic stress tolerance, led us to sequence the transcriptomes of herbicide resistant and susceptible populations of black-grass and annual rye-grass for the presence of endophytes. Black-grass (Alopecurus myosuroides; Am) populations, displaying no overt disease symptoms, contained three previously undescribed viruses belonging to the Partititiviridae (AMPV1 and AMPV2) and Rhabdoviridae (AMVV1) families. These infections were widespread in UK black-grass populations and evidence was obtained for similar viruses being present in annual rye grass (Lolium rigidum), perennial rye-grass (Lolium perenne) and meadow fescue (Festuca pratensis). In black-grass, while no direct causative link was established linking viral infection to herbicide resistance, transcriptome sequencing showed a high incidence of infection in the NTSR Peldon population. The widespread infection of these weeds by little characterised and persistent viruses and their potential evolutionary role in enhancing plant stress tolerance mechanisms including NTSR warrants further investigation.
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Affiliation(s)
- Federico Sabbadin
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD UK
| | | | - Rebecca Stafford
- School of Agriculture, Food and Rural Development, Newcastle University, NE1 7RU UK
| | | | - Neil Boonham
- Fera Science Ltd., Sand Hutton, York YO41 1LZ UK
| | - Ian Adams
- Fera Science Ltd., Sand Hutton, York YO41 1LZ UK
| | - Rick Mumford
- Fera Science Ltd., Sand Hutton, York YO41 1LZ UK
| | - Robert Edwards
- School of Agriculture, Food and Rural Development, Newcastle University, NE1 7RU UK
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Cho IS, Igori D, Lim S, Choi GS, Hammond J, Lim HS, Moon JS. Deep Sequencing Analysis of Apple Infecting Viruses in Korea. THE PLANT PATHOLOGY JOURNAL 2016; 32:441-451. [PMID: 27721694 PMCID: PMC5051563 DOI: 10.5423/ppj.oa.04.2016.0104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 05/16/2016] [Accepted: 05/23/2016] [Indexed: 05/18/2023]
Abstract
Deep sequencing has generated 52 contigs derived from five viruses; Apple chlorotic leaf spot virus (ACLSV), Apple stem grooving virus (ASGV), Apple stem pitting virus (ASPV), Apple green crinkle associated virus (AGCaV), and Apricot latent virus (ApLV) were identified from eight apple samples showing small leaves and/or growth retardation. Nucleotide (nt) sequence identity of the assembled contigs was from 68% to 99% compared to the reference sequences of the five respective viral genomes. Sequences of ASPV and ASGV were the most abundantly represented by the 52 contigs assembled. The presence of the five viruses in the samples was confirmed by RT-PCR using specific primers based on the sequences of each assembled contig. All five viruses were detected in three of the samples, whereas all samples had mixed infections with at least two viruses. The most frequently detected virus was ASPV, followed by ASGV, ApLV, ACLSV, and AGCaV which were withal found in mixed infections in the tested samples. AGCaV was identified in assembled contigs ID 1012480 and 93549, which showed 82% and 78% nt sequence identity with ORF1 of AGCaV isolate Aurora-1. ApLV was identified in three assembled contigs, ID 65587, 1802365, and 116777, which showed 77%, 78%, and 76% nt sequence identity respectively with ORF1 of ApLV isolate LA2. Deep sequencing assay was shown to be a valuable and powerful tool for detection and identification of known and unknown virome in infected apple trees, here identifying ApLV and AGCaV in commercial orchards in Korea for the first time.
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Affiliation(s)
- In-Sook Cho
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea
| | - Davaajargal Igori
- Molecular Biofarming Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; Biosystems and Bioengineering Program, University of Science and Technology, Daejeon 34113, Korea
| | - Seungmo Lim
- Molecular Biofarming Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; Biosystems and Bioengineering Program, University of Science and Technology, Daejeon 34113, Korea
| | - Gug-Seoun Choi
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea
| | - John Hammond
- Floral and Nursery Plants Unit, United States National Arboretum, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705, USA
| | - Hyoun-Sub Lim
- Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Jae Sun Moon
- Molecular Biofarming Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; Biosystems and Bioengineering Program, University of Science and Technology, Daejeon 34113, Korea
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Complete Nucleotide Sequence of a French Isolate of Maize rough dwarf virus, a Fijivirus Member in the Family Reoviridae. GENOME ANNOUNCEMENTS 2016; 4:4/4/e00623-16. [PMID: 27445367 PMCID: PMC4956440 DOI: 10.1128/genomea.00623-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The complete nucleotide sequence of a French isolate of Maize rough dwarf virus (MRDV) was determined by next-generation sequencing and compared with the single available complete sequence and with the partial sequences of two additional isolates available in online databases.
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Miguel S, Biteau F, Mignard B, Marais A, Candresse T, Theil S, Bourgaud F, Hehn A. Beet western yellows virus infects the carnivorous plant Nepenthes mirabilis. Arch Virol 2016; 161:2273-8. [DOI: 10.1007/s00705-016-2891-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 05/07/2016] [Indexed: 10/21/2022]
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Colcol JF, Baudoin AB. Sensitivity of Erysiphe necator and Plasmopara viticola in Virginia to QoI Fungicides, Boscalid, Quinoxyfen, Thiophanate Methyl, and Mefenoxam. PLANT DISEASE 2016; 100:337-344. [PMID: 30694148 DOI: 10.1094/pdis-01-15-0012-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The sensitivity of downy mildew (DM, Plasmopara viticola) and powdery mildew (PM, Erysiphe necator) of grape (Vitis sp.) to commonly used nondemethylation inhibitor, single-site fungicides in and near Virginia was determined from 2005 to 2007, with more limited additional sampling in subsequent years. In grape leaf disc bioassays, 92% of the P. viticola isolates were quinone outside inhibitor (QoI, azoxystrobin) resistant but none were resistant to mefenoxam. In all, 82% of the E. necator isolates were QoI resistant. Most of the QoI-resistant P. viticola and E. necator isolates contained >95% of the G143A point mutation, which confers high levels of QoI resistance. In contrast, QoI-sensitive P. viticola isolates contained less than 1% of G143A. In total, 1 of 145 and 14 of 154 QoI-resistant P. viticola and E. necator isolates (able to grow on azoxystrobin concentration ≥1 μg/ml), respectively, contained <1% G143A. In total, 61 E. necator isolates from 23 locations were tested against thiophanate methyl, and the majority grew well on leaf tissue treated with 50 and 250 μg/ml. Through 2012, none of the E. necator isolates were resistant to boscalid and quinoxyfen. However, in 2013, quinoxyfen-resistant E. necator was detected in one vineyard experiencing difficulties with powdery mildew control. No 50% effective concentration value could be calculated but these isolates tolerated labeled rates with only limited inhibition. QoI (E. necator and P. viticola) and benzimidazole (E. necator) resistance were widespread in Virginia, rendering these materials inadvisable for control of these diseases. The practical importance and current distribution of quinoxyfen resistance needs further investigation.
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Affiliation(s)
| | - Anton B Baudoin
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
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46
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Wang J, Zhu D, Tan Y, Zong X, Wei H, Hammond RW, Liu Q. Complete nucleotide sequence of little cherry virus 1 (LChV-1) infecting sweet cherry in China. Arch Virol 2016; 161:749-53. [PMID: 26733294 DOI: 10.1007/s00705-015-2737-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 12/19/2015] [Indexed: 11/29/2022]
Abstract
Little cherry virus 1 (LChV-1), associated with little cherry disease (LCD), has a significant impact on fruit quality of infected sweet cherry trees. We report the full genome sequence of an isolate of LChV-1 from Taian, China (LChV-1-TA), detected by small-RNA deep sequencing and amplified by overlapping RT-PCR. The LChV-1-TA genome was 16,932 nt in length and contained nine open reading frames (ORFs), with sequence identity at the overall genome level of 76%, 76%, and 78% to LChV-1 isolates Y10237 (UW2 isolate), EU715989 (ITMAR isolate) and JX669615 (V2356 isolate), respectively. Based on the phylogenetic analysis of HSP70h amino acid sequences of Closteroviridae family members, LChV-1-TA was grouped into a well-supported cluster with the members of the genus Velarivirus and was also closely related to other LChV-1 isolates. This is the first report of the complete nucleotide sequence of LChV-1 infecting sweet cherry in China.
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Affiliation(s)
- Jiawei Wang
- Key Laboratory for Fruit Biotechnology Breeding of Shandong Province, Shandong Institute of Pomology, Taian, 271000, Shandong, People's Republic of China
| | - Dongzi Zhu
- Key Laboratory for Fruit Biotechnology Breeding of Shandong Province, Shandong Institute of Pomology, Taian, 271000, Shandong, People's Republic of China
| | - Yue Tan
- Key Laboratory for Fruit Biotechnology Breeding of Shandong Province, Shandong Institute of Pomology, Taian, 271000, Shandong, People's Republic of China
| | - Xiaojuan Zong
- Key Laboratory for Fruit Biotechnology Breeding of Shandong Province, Shandong Institute of Pomology, Taian, 271000, Shandong, People's Republic of China
| | - Hairong Wei
- Key Laboratory for Fruit Biotechnology Breeding of Shandong Province, Shandong Institute of Pomology, Taian, 271000, Shandong, People's Republic of China
| | - Rosemarie W Hammond
- US Department of Agriculture, ARS, Molecular Plant Pathology Laboratory, Room 214, Building 004 BARC West, Beltsville, MD, 20705, USA.
| | - Qingzhong Liu
- Key Laboratory for Fruit Biotechnology Breeding of Shandong Province, Shandong Institute of Pomology, Taian, 271000, Shandong, People's Republic of China.
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New Insights into Asian Prunus Viruses in the Light of NGS-Based Full Genome Sequencing. PLoS One 2016; 11:e0146420. [PMID: 26741704 PMCID: PMC4704818 DOI: 10.1371/journal.pone.0146420] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 12/16/2015] [Indexed: 11/20/2022] Open
Abstract
Double stranded RNAs were purified from five Prunus sources of Asian origin and submitted to 454 pyrosequencing after a random, whole genome amplification. Four complete genomes of Asian prunus virus 1 (APV1), APV2 and APV3 were reconstructed from the sequencing reads, as well as four additional, near-complete genome sequences. Phylogenetic analyses confirmed the close relationships of these three viruses and the taxonomical position previously proposed for APV1, the only APV so far completely sequenced. The genetic distances in the respective polymerase and coat protein genes as well as their gene products suggest that APV2 should be considered as a distinct viral species in the genus Foveavirus, even if the amino acid identity levels in the polymerase are very close to the species demarcation criteria for the family Betaflexiviridae. However, the situation is more complex for APV1 and APV3, for which opposite conclusions are obtained depending on the gene (polymerase or coat protein) analyzed. Phylogenetic and recombination analyses suggest that recombination events may have been involved in the evolution of APV. Moreover, genome comparisons show that the unusually long 3’ non-coding region (3' NCR) is highly variable and a hot spot for indel polymorphisms. In particular, two APV3 variants differing only in their 3’ NCR were identified in a single Prunus source, with 3' NCRs of 214–312 nt, a size similar to that observed in other foveaviruses, but 567–850 nt smaller than in other APV3 isolates. Overall, this study provides critical genome information of these viruses, frequently associated with Prunus materials, even though their precise role as pathogens remains to be elucidated.
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Candresse T, Marais A, Sorrentino R, Faure C, Theil S, Cadot V, Rolland M, Villemot J, Rabenstein F. Complete genomic sequence of barley (Hordeum vulgare) endornavirus (HvEV) determined by next-generation sequencing. Arch Virol 2015; 161:741-3. [PMID: 26666441 DOI: 10.1007/s00705-015-2709-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 11/30/2015] [Indexed: 11/24/2022]
Abstract
Endornaviruses are unusual plant-, fungus- and oomycete-infecting viruses with a large, ca 14- to 17-kb linear double-stranded RNA (dsRNA) genome and a persistent lifestyle. The complete genome sequence of an endornavirus from the barley (Hordeum vulgare) Nerz variety was determined from paired Illumina MySeq reads derived from purified dsRNAs. The genome is 14,243 nt long, with 5' and 3' non-coding regions of 207 and 47 nt, respectively. It encodes a single large protein of 4663 amino acids that carries conserved motifs for a methyltransferase, a helicase and an RNA-dependent RNA polymerase. The sequence of Hordeum vulgare endornavirus (HvEV) carries all the hallmarks of a typical member of the genus Endornavirus, with the exception of an UDP-glycosyltransferase motif observed in many, but not all, endornaviral genomes.
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Affiliation(s)
- Thierry Candresse
- INRA, UMR 1332 Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon Cedex, France. .,Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon Cedex, France.
| | - Armelle Marais
- INRA, UMR 1332 Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon Cedex, France.,Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Roberto Sorrentino
- Dipartimento di Agraria, Università degli Studi di Napoli "Federico II", 80055, Portici, Italy
| | - Chantal Faure
- INRA, UMR 1332 Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon Cedex, France.,Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Sébastien Theil
- INRA, UMR 1332 Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon Cedex, France.,Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Valérie Cadot
- GEVES, 25 rue Georges Morel, CS 90024, 49071, Beaucouzé Cedex, France
| | - Mathieu Rolland
- GEVES, 25 rue Georges Morel, CS 90024, 49071, Beaucouzé Cedex, France
| | - Julie Villemot
- GEVES, 25 rue Georges Morel, CS 90024, 49071, Beaucouzé Cedex, France
| | - Frank Rabenstein
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kuhn-Institute, Federal Research Institute for Cultivated Plants, Erwin-Baur-Straße 27, 06484, Quedlinburg, Germany
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49
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Reynard JS, Schneeberger PHH, Frey JE, Schaerer S. Biological, Serological, and Molecular Characterization of a Highly Divergent Strain of Grapevine leafroll-associated virus 4 Causing Grapevine Leafroll Disease. PHYTOPATHOLOGY 2015; 105:1262-1269. [PMID: 25822183 DOI: 10.1094/phyto-12-14-0386-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The complete genome sequence of a highly divergent strain of Grapevine leafroll-associated virus 4 (GLRaV-4) was determined using 454 pyrosequencing technology. This virus, designated GLRaV-4 Ob, was detected in Vitis vinifera 'Otcha bala' from our grapevine virus collection at Agroscope. The GLRaV-4 Ob genome length and organization share similarities with members of subgroup II in the genus Ampelovirus (family Closteroviridae). Otcha bala was graft-inoculated onto indicator plants of cultivar Gamay to evaluate the biological properties of this new strain, and typical leafroll symptoms were induced. A monoclonal antibody for the rapid detection of GLRaV-4 Ob by enzyme-linked immunosorbent assay is available, thus facilitating large-scale diagnostics of this virus. Based on the relatively small size of the coat protein, the reduced amino acid identity and the distinct serological properties, our study clearly shows that GLRaV-4 Ob is a divergent strain of GLRaV-4. Furthermore, molecular and serological data revealed that the AA42 accession from which GLRaV-7 was originally reported is in fact co-infected with GLRaV-4 Ob and GLRaV-7. This finding challenges the idea that GLRaV-7 is a leafroll-causing agent.
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Affiliation(s)
- Jean-Sébastien Reynard
- First and fourth authors: Agroscope-Virology and Phytoplasmology, Nyon, Switzerland; second author: Swiss Tropical and Public Health Institute-Virology, Basel, Switzerland; and third author: Agroscope-Molecular Diagnostics, Genomics and Bioinformatics, Waedenswil, Switzerland
| | - Pierre H H Schneeberger
- First and fourth authors: Agroscope-Virology and Phytoplasmology, Nyon, Switzerland; second author: Swiss Tropical and Public Health Institute-Virology, Basel, Switzerland; and third author: Agroscope-Molecular Diagnostics, Genomics and Bioinformatics, Waedenswil, Switzerland
| | - Jürg Ernst Frey
- First and fourth authors: Agroscope-Virology and Phytoplasmology, Nyon, Switzerland; second author: Swiss Tropical and Public Health Institute-Virology, Basel, Switzerland; and third author: Agroscope-Molecular Diagnostics, Genomics and Bioinformatics, Waedenswil, Switzerland
| | - Santiago Schaerer
- First and fourth authors: Agroscope-Virology and Phytoplasmology, Nyon, Switzerland; second author: Swiss Tropical and Public Health Institute-Virology, Basel, Switzerland; and third author: Agroscope-Molecular Diagnostics, Genomics and Bioinformatics, Waedenswil, Switzerland
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50
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Genomic detection and characterization of a Korean isolate of Little cherry virus 1 sampled from a peach tree. Virus Genes 2015; 51:260-6. [PMID: 26315329 DOI: 10.1007/s11262-015-1225-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/02/2015] [Indexed: 10/23/2022]
Abstract
A peach tree (Prunus persica) showing yellowing and mild mottle symptoms was analyzed using high-throughput RNA sequencing to determine the causal agent. A total of nine contigs similar to Little cherry virus 1 (LChV-1) were produced, and all the contigs showed nucleotide sequence identity (lower than 83 %) and query coverage (higher than 73 %) with LChV-1. The symptomatic peach sample was confirmed to be infected with LChV-1-like virus as a result of reverse transcription-polymerase chain reaction using primers designed based on sequences of the contigs. Occurrence of diseases caused by LChV-1 in Prunus species has been reported. Complete 16,931-nt genome of the peach virus composed of eight open reading frames was determined, and conserved domains including viral methyltransferase, viral helicase 1, RNA-dependent RNA polymerase (RdRp), heat shock protein 70 homologue (HSP70h), HSP90h and closterovirus coat protein (CP) were identified. Phylogenetic trees based on amino acid sequence alignments between the peach virus and members in the family Closteroviridae showed that the virus was most similar to LChV-1. Pairwise comparisons based on amino acid sequence alignments of three genes (RdRp, HSP70h and CP) between the peach virus and LChV-1 isolates showed the highest amino acid sequence identities, with 84.32 % for RdRp, 85.48 % for HSP70h and 80.45 % for CP. These results indicate that this is the first report for the presence of LChV-1 in South Korea and may be one of the first reports of natural infection of peach by LChV-1. Although it is not clear if LChV-1 YD isolate was responsible for specific symptoms observed, detection and characterization of the peach tree-infecting LChV-1 in South Korea would be useful in terms of the epidemiology of LChV-1.
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