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Dantes W, Boatwright L, Cieniewicz EJ. Comparing RT-PCR of Individual Samples with High-Throughput Sequencing of Pooled Plant Samples for Field-Level Surveillance of Viruses in Blackberry and Wild Rubus. PLANT DISEASE 2024; 108:2435-2446. [PMID: 38557244 DOI: 10.1094/pdis-11-23-2428-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Blackberry production is increasing in the Southeastern United States with the availability of new cultivars. In addition to high production costs, growers are challenged by virus diseases. Blackberry yellow vein disease (BYVD) significantly limits blackberry production. BYVD is associated with the crinivirus blackberry yellow vein-associated virus in mixed infections with other viruses. The specific disease etiology and ecological factors underlying BYVD are not well understood and rely on the effective diagnosis of several viruses involved in the complex. In 2021, we collected samples from blackberry plants showing BYVD symptoms, asymptomatic blackberry plants, and wild Rosaceae spp. from nine farms across South Carolina, for a total of 372 individual plant samples. RNA from individual samples was isolated and pooled into sample groups (i.e., symptomatic, asymptomatic, and wild) from each farm for a total of 24 pooled samples. We sequenced the pooled RNA using Illumina and analyzed sequence profiles using the Virtool bioinformatics application. We also tested each plant for six viruses by reverse transcriptase PCR or reverse transcriptase quantitative PCR and compared plant (PCR)-level and field (high-throughput sequencing [HTS])-level data. Virtool detected 17 known viruses in the pooled samples, including 11 blackberry viruses. PCR testing was mostly consistent with HTS, with some notable disagreements for specific viruses. Our study demonstrates that HTS could be used as an efficient tool to detect viruses in bulked samples in blackberry fields, although limitations to using HTS for field-level surveillance are also discussed here.
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Affiliation(s)
- Wanita Dantes
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634
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Rott ME, Ghoshal K, Lerat S, Brosseau C, Clément G, Phelan J, Poojari S, Gaafar Y, Vemulapati BM, Scheer H, Ritzenthaler C, Fall ML, Moffett P. Improving grapevine virus diagnostics: Comparative analysis of three dsRNA enrichment methods for high-throughput sequencing. J Virol Methods 2024; 329:114997. [PMID: 39059502 DOI: 10.1016/j.jviromet.2024.114997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024]
Abstract
The extraction of double stranded (ds) RNA is a common enrichment method for the study, characterization, and detection of RNA viruses. In addition to RNA viruses, viroids, and some DNA viruses, can also be detected from dsRNA enriched extracts which makes it an attractive method for detecting a wide range of viruses when coupled with HTS. Several dsRNA enrichment strategies have been developed. The oldest utilizes the selective binding properties of dsRNA to cellulose. More recent methods are based on the application of anti-dsRNA antibodies and viral proteins with a specific affinity for dsRNA. All three methods have been used together with HTS for plant virus detection and study. To our knowledge, this is the first comparative study of three alternative dsRNA enrichment methods for virus and viroid detection through HTS using virus-infected, and healthy grapevine test plants. Extracts were performed in triplicate using methods based on, the anti-dsRNA antibody mAb rJ2 (Millipore Sigma Canada Ltd, Oakville, ON, Canada), the B2 dsRNA binding protein, and ReliaPrep™ Resin (Promega Corporation, Madison, WI, USA). The results show that the workflows for all three methods are effectively comparable, apart from purification steps related to antibody and binding protein construct. Both the cellulose resin and dsRNA binding protein construct methods provide highly enriched dsRNA extracts suitable for HTS with the B2 method providing a 36× and the ReliaPrep™ Resin a 163× increase in dsRNA enrichment compared to the mAb rJ2 antibody. The overall consistency and cost effectiveness of the ReliaPrep™ cellulose resin-based method and the potentially simpler adaptation to robotics made it the method of choice for future transfer to a semi-automated workflow.
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Affiliation(s)
- Michael E Rott
- Canadian Food Inspection Agency, Centre for Plant Health, Sidney Laboratory, 8801 East Saanich Rd, North Saanich, British Columbia V8L 1H3, Canada.
| | - Kankana Ghoshal
- Canadian Food Inspection Agency, Centre for Plant Health, Sidney Laboratory, 8801 East Saanich Rd, North Saanich, British Columbia V8L 1H3, Canada
| | - Sylvain Lerat
- Département de Biologie, Université de Sherbrooke, 2500 Bd de l'Université, Sherbrooke, Québec J1K 2R1, Canada
| | - Chantal Brosseau
- Département de Biologie, Université de Sherbrooke, 2500 Bd de l'Université, Sherbrooke, Québec J1K 2R1, Canada
| | - Geneviève Clément
- Département de Biologie, Université de Sherbrooke, 2500 Bd de l'Université, Sherbrooke, Québec J1K 2R1, Canada
| | - James Phelan
- Canadian Food Inspection Agency, Centre for Plant Health, Sidney Laboratory, 8801 East Saanich Rd, North Saanich, British Columbia V8L 1H3, Canada
| | - Sudarsana Poojari
- Cool Climate Oenology and Viticulture Institute, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Yahya Gaafar
- Canadian Food Inspection Agency, Centre for Plant Health, Sidney Laboratory, 8801 East Saanich Rd, North Saanich, British Columbia V8L 1H3, Canada
| | - Bhadra M Vemulapati
- Cool Climate Oenology and Viticulture Institute, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Hélène Scheer
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg 67000, France
| | - Christophe Ritzenthaler
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg 67000, France
| | - Mamadou L Fall
- Agriculture and Agri-Food Canada, 430 Gouin Boulevard, Saint-Jean-sur-Richelieu, Québec J3B 3EB, Canada
| | - Peter Moffett
- Département de Biologie, Université de Sherbrooke, 2500 Bd de l'Université, Sherbrooke, Québec J1K 2R1, Canada
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He C, Wang L, Li Y, Zhou K, Zhao K, Chen D, Li J, Song H, Tu M. Loquat ( Eriobotrya japonica) Is a New Natural Host of Tomato Mosaic Virus and Citrus Exocortis Viroid. PLANTS (BASEL, SWITZERLAND) 2024; 13:1965. [PMID: 39065492 PMCID: PMC11280522 DOI: 10.3390/plants13141965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024]
Abstract
Loquat leaves exhibiting obvious yellowing, blistering, mosaic, leaf upward cupping, crinkle, and leaf narrowing were identified in Panzhihua City, Sichuan Province, China. High-throughput sequencing (HTS) with the ribo-depleted cDNA library was employed to identify the virome in the loquat samples; only tomato mosaic virus (ToMV) and citrus exocortis viroid (CEVd) were identified in the transcriptome data. The complete genome sequence of ToMV and CEVd were obtained from the loquat leaves. The full-length genome of the ToMV-loquat is 6376 nt and comprises four open reading frames (ORFs) encoding 183 kDa protein, RNA-dependent RNA polymerase (RdRp), movement protein (MP), and coat protein (CP), respectively. A pairwise identity analysis showed that the complete sequence of the ToMV-loquat had a nucleotide identity between 98.5 and 99.3% with other ToMV isolates. A phylogenetic analysis indicated that ToMV-loquat was more closely related to ToMV-IFA9 (GenBank No. ON156781). A CEVd sequence with 361 nt in length was amplified based on the HTS contigs, sequence alignment indicated CEVd-loquat had the highest identity with the strain of CEVd-Balad (GenBank No. PP869624), phylogenetic analysis showed that CEVd-loquat was more closely related to CEVd-lettuce (GenBank No. ON993891). This significant discovery marks the first documentation and characterization of ToMV and CEVd infecting loquat plants, shedding light on potential threats to loquat cultivation and providing insights for disease management strategies.
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Affiliation(s)
- Chengyong He
- Institute of Horticulture, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (C.H.); (L.W.); (Y.L.); (K.Z.); (K.Z.); (D.C.); (J.L.); (H.S.)
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
| | - Lingli Wang
- Institute of Horticulture, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (C.H.); (L.W.); (Y.L.); (K.Z.); (K.Z.); (D.C.); (J.L.); (H.S.)
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
| | - Yarui Li
- Institute of Horticulture, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (C.H.); (L.W.); (Y.L.); (K.Z.); (K.Z.); (D.C.); (J.L.); (H.S.)
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
| | - Kangyu Zhou
- Institute of Horticulture, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (C.H.); (L.W.); (Y.L.); (K.Z.); (K.Z.); (D.C.); (J.L.); (H.S.)
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
- College of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Ke Zhao
- Institute of Horticulture, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (C.H.); (L.W.); (Y.L.); (K.Z.); (K.Z.); (D.C.); (J.L.); (H.S.)
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
| | - Dong Chen
- Institute of Horticulture, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (C.H.); (L.W.); (Y.L.); (K.Z.); (K.Z.); (D.C.); (J.L.); (H.S.)
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
| | - Jing Li
- Institute of Horticulture, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (C.H.); (L.W.); (Y.L.); (K.Z.); (K.Z.); (D.C.); (J.L.); (H.S.)
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
| | - Haiyan Song
- Institute of Horticulture, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (C.H.); (L.W.); (Y.L.); (K.Z.); (K.Z.); (D.C.); (J.L.); (H.S.)
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
| | - Meiyan Tu
- Institute of Horticulture, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (C.H.); (L.W.); (Y.L.); (K.Z.); (K.Z.); (D.C.); (J.L.); (H.S.)
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
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Marais A, Gentit P, Brans Y, Renvoisé JP, Faure C, Saison A, Cousseau P, Castaing J, Chambon F, Pion A, Calado G, Lefebvre M, Garnier S, Latour F, Bresson K, Grasseau N, Candresse T. Comparative Performance Evaluation of Double-Stranded RNA High-Throughput Sequencing for the Detection of Viral Infection in Temperate Fruit Crops. PHYTOPATHOLOGY 2024; 114:1701-1709. [PMID: 38376958 DOI: 10.1094/phyto-12-23-0480-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
There is limited information on the compared performances of biological, serological. and molecular assays with high-throughput sequencing (HTS) for viral indexing in temperate fruit crops. Here, using a range of samples of predetermined virological status, we compared two performance criteria (inclusivity and analytical sensitivity) of enzyme-linked immunosorbent assay (ELISA), molecular hybridization, reverse transcription (RT)-PCR, and double-stranded RNA (dsRNA) HTS for the detection of a total of 14 viruses (10 genera) and four viroids (three genera). When undiluted samples from individual plants were used, ELISA had the lowest performance, with an overall detection rate of 68.7%, followed by RT-PCR (82.5%) and HTS (90.7%; 100% if considering only viruses). The lower performance of RT-PCR reflected the inability to amplify some isolates as a consequence of point mutations affecting primer-binding sites. In addition, HTS identified viruses that had not been identified by other assays in nearly two-thirds of the samples. Analysis of serial dilutions of fruit tree samples allowed comparison of analytical sensitivities for various viruses. ELISA showed the lowest analytical sensitivity, but RT-PCR showed higher analytical sensitivity than HTS for most of the samples. Overall, these results confirm the superiority of HTS over biological indexing in terms of speed and inclusivity and show that while the absolute analytical sensitivity of RT-PCR tends to be higher than that of HTS, PCR inclusivity is affected by viral genetic diversity. Taken together, these results make a strong case for the implementation of HTS-based approaches in fruit tree viral testing protocols supporting quarantine and certification programs.
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Affiliation(s)
- Armelle Marais
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Pascal Gentit
- ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM, 7 rue Jean Dixméras, 49044 Angers Cedex 01, France
| | - Yoann Brans
- CTIFL, Laboratoire de virologie fruitière, Centre de Lanxade, 24130 Prigonrieux, France
| | | | - Chantal Faure
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Anne Saison
- ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM, 7 rue Jean Dixméras, 49044 Angers Cedex 01, France
| | - Pascaline Cousseau
- ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM, 7 rue Jean Dixméras, 49044 Angers Cedex 01, France
| | - Julie Castaing
- CTIFL, Laboratoire de virologie fruitière, Centre de Lanxade, 24130 Prigonrieux, France
| | - Fabien Chambon
- ANSES, Plant Health Laboratory, Unité de Quarantaine, 63370 Lempdes, France
| | - Angélique Pion
- ANSES, Plant Health Laboratory, Unité de Quarantaine, 63370 Lempdes, France
| | - Grégory Calado
- ANSES, Plant Health Laboratory, Unité de Quarantaine, 63370 Lempdes, France
| | - Marie Lefebvre
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Soraya Garnier
- ANSES, Plant Health Laboratory, Unité de Quarantaine, 63370 Lempdes, France
| | - François Latour
- CTIFL, Laboratoire de virologie fruitière, Centre de Lanxade, 24130 Prigonrieux, France
| | - Kévin Bresson
- CTIFL, Laboratoire de virologie fruitière, Centre de Lanxade, 24130 Prigonrieux, France
| | - Nathalie Grasseau
- CTIFL, Laboratoire de virologie fruitière, Centre de Lanxade, 24130 Prigonrieux, France
| | - Thierry Candresse
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
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5
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Li Z, Qin J, Zhu Y, Zhou M, Zhao N, Zhou E, Wang X, Chen X, Cui X. Occurrence, distribution, and genetic diversity of faba bean viruses in China. Front Microbiol 2024; 15:1424699. [PMID: 38962134 PMCID: PMC11219563 DOI: 10.3389/fmicb.2024.1424699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 06/06/2024] [Indexed: 07/05/2024] Open
Abstract
With worldwide cultivation, the faba bean (Vicia faba L.) stands as one of the most vital cool-season legume crops, serving as a major component of food security. China leads global faba bean production in terms of both total planting area and yield, with major production hubs in Yunnan, Sichuan, Jiangsu, and Gansu provinces. The faba bean viruses have caused serious yield losses in these production areas, but previous researches have not comprehensively investigated this issue. In this study, we collected 287 faba bean samples over three consecutive years from eight provinces/municipalities of China. We employed small RNA sequencing, RT-PCR, DNA sequencing, and phylogenetic analysis to detect the presence of viruses and examine their incidence, distribution, and genetic diversity. We identified a total of nine distinct viruses: bean yellow mosaic virus (BYMV, Potyvirus), milk vetch dwarf virus (MDV, Nanovirus), vicia cryptic virus (VCV, Alphapartitivirus), bean common mosaic virus (BCMV, Potyvirus), beet western yellows virus (BWYV, Polerovirus), broad bean wilt virus (BBWV, Fabavirus), soybean mosaic virus (SMV, Potyvirus), pea seed-borne mosaic virus (PSbMV, Potyvirus), and cucumber mosaic virus (CMV, Cucumovirus). BYMV was the predominant virus found during our sampling, followed by MDV and VCV. This study marks the first reported detection of BCMV in Chinese faba bean fields. Except for several isolates from Gansu and Yunnan provinces, our sequence analysis revealed that the majority of BYMV isolates contain highly conserved nucleotide sequences of coat protein (CP). Amino acid sequence alignment indicates that there is a conserved NAG motif at the N-terminal region of BYMV CP, which is considered important for aphid transmission. Our findings not only highlight the presence and diversity of pathogenic viruses in Chinese faba bean production, but also provide target pathogens for future antiviral resource screening and a basis for antiviral breeding.
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Affiliation(s)
- Zongdi Li
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu, China
- Department of Economic Crops, Yanjiang Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Nantong, Jiangsu, China
| | - Jiachao Qin
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu, China
| | - Yuxiang Zhu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu, China
| | - Mimi Zhou
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu, China
| | - Na Zhao
- Department of Economic Crops, Yanjiang Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Nantong, Jiangsu, China
| | - Enqiang Zhou
- Department of Economic Crops, Yanjiang Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Nantong, Jiangsu, China
| | - Xuejun Wang
- Department of Economic Crops, Yanjiang Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Nantong, Jiangsu, China
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu, China
| | - Xiaoyan Cui
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu, China
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Iglesias D, Stevens K, Sharma A, Diaz-Lara A. A Novel Cryptic Virus Isolated from Galphimia spp. in Mexico. Pathogens 2024; 13:504. [PMID: 38921801 PMCID: PMC11207071 DOI: 10.3390/pathogens13060504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/04/2024] [Accepted: 06/09/2024] [Indexed: 06/27/2024] Open
Abstract
Galphimia spp. is a plant employed in traditional medicine in Mexico because of its anxiolytic and sedative effects. Viruses have been associated with different alterations in plants, although asymptomatic agents (i.e., cryptic viruses) are also known. High-throughput sequencing (HTS) allows for the detection of pathogenic and non-pathogenic viral agents in plants, including potential novel viruses. The aim of this study was to investigate the presence of viral agents in two populations of Galphimia spp. by HTS. Sequencing was conducted on an Illumina NextSeq 550 platform, and a putative novel virus was identified. Two contigs showed homology to partitiviruses, and these encoded the RNA-dependent RNA polymerase and coat protein. These proteins showed the highest identities with orthologs in the recently discovered Vitis cryptic virus. A phylogenetic analysis of both RNAs showed that the new virus clusters into the monophyletic genus Deltapartitivirus along with other plant-infecting viruses. The result of the HTS analysis was validated by conventional RT-PCR and Sanger sequencing. A novel virus was discovered in a symptomless Galphimia spp. plant and tentatively named the Galphimia cryptic virus (GCV). This is the first virus discovered in medicinal plants in Mexico.
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Affiliation(s)
- Dianella Iglesias
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico;
| | - Kristian Stevens
- Departments of Computer Science and Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA;
| | - Ashutosh Sharma
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico;
| | - Alfredo Diaz-Lara
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico;
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Roy SD, Ramasamy S, Obbineni JM. An evaluation of nucleic acid-based molecular methods for the detection of plant viruses: a systematic review. Virusdisease 2024; 35:357-376. [PMID: 39071869 PMCID: PMC11269559 DOI: 10.1007/s13337-024-00863-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/15/2024] [Indexed: 07/30/2024] Open
Abstract
Precise and timely diagnosis of plant viruses is a prerequisite for the implementation of efficient management strategies, considering factors like globalization of trade and climate change facilitating the spread of viruses that lead to agriculture yield losses of billions yearly worldwide. Symptomatic diagnosis alone may not be reliable due to the diverse symptoms and confusion with plant abiotic stresses. It is crucial to detect plant viruses accurately and reliably and do so with little time. A complete understanding of the various detection methods is necessary to achieve this. Enzyme-linked immunosorbent assay (ELISA), has become more popular as a method for detecting viruses but faces limitations such as antibody availability, cost, sample volume, and time. Advanced techniques like polymerase chain reaction (PCR) have surpassed ELISA with its various sensitive variants. Over the last decade, nucleic acid-based molecular methods have gained popularity and have quickly replaced other techniques, such as serological techniques for detecting plant viruses due to their specificity and accuracy. Hence, this review enables the reader to understand the strengths and weaknesses of each molecular technique starting with PCR and its variations, along with various isothermal amplification followed by DNA microarrays, and next-generation sequencing (NGS). As a result of the development of new technologies, NGS is becoming more and more accessible and cheaper, and it looks possible that this approach will replace others as a favoured approach for carrying out regular diagnosis. NGS is also becoming the method of choice for identifying novel viruses. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-024-00863-0.
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Affiliation(s)
- Subha Deep Roy
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu India
- School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, Tamil Nadu India
| | | | - Jagan M. Obbineni
- School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, Tamil Nadu India
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8
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González-Pérez E, Chiquito-Almanza E, Villalobos-Reyes S, Canul-Ku J, Anaya-López JL. Diagnosis and Characterization of Plant Viruses Using HTS to Support Virus Management and Tomato Breeding. Viruses 2024; 16:888. [PMID: 38932180 PMCID: PMC11209215 DOI: 10.3390/v16060888] [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: 04/25/2024] [Revised: 05/20/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
Viral diseases pose a significant threat to tomato crops (Solanum lycopersicum L.), one of the world's most economically important vegetable crops. The limited genetic diversity of cultivated tomatoes contributes to their high susceptibility to viral infections. To address this challenge, tomato breeding programs must harness the genetic resources found in native populations and wild relatives. Breeding efforts may aim to develop broad-spectrum resistance against the virome. To identify the viruses naturally infecting 19 advanced lines, derived from native tomatoes, high-throughput sequencing (HTS) of small RNAs and confirmation with PCR and RT-PCR were used. Single and mixed infections with tomato mosaic virus (ToMV), tomato golden mosaic virus (ToGMoV), and pepper huasteco yellow vein virus (PHYVV) were detected. The complete consensus genomes of three variants of Mexican ToMV isolates were reconstructed, potentially forming a new ToMV clade with a distinct 3' UTR. The absence of reported mutations associated with resistance-breaking to ToMV suggests that the Tm-1, Tm-2, and Tm-22 genes could theoretically be used to confer resistance. However, the high mutation rates and a 63 nucleotide insertion in the 3' UTR, as well as amino acid mutations in the ORFs encoding 126 KDa, 183 KDa, and MP of Mexican ToMV isolates, suggest that it is necessary to evaluate the capacity of these variants to overcome Tm-1, Tm-2, and Tm-22 resistance genes. This evaluation, along with the characterization of advanced lines using molecular markers linked to these resistant genes, will be addressed in future studies as part of the breeding strategy. This study emphasizes the importance of using HTS for accurate identification and characterization of plant viruses that naturally infect tomato germplasm based on the consensus genome sequences. This study provides crucial insights to select appropriate disease management strategies and resistance genes and guide breeding efforts toward the development of virus-resistant tomato varieties.
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Affiliation(s)
| | - Elizabeth Chiquito-Almanza
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Celaya, Guanajuato 38110, Mexico; (E.G.-P.); (S.V.-R.); (J.C.-K.)
| | | | | | - José Luis Anaya-López
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Celaya, Guanajuato 38110, Mexico; (E.G.-P.); (S.V.-R.); (J.C.-K.)
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Bettoni JC, Wang MR, Li JW, Fan X, Fazio G, Hurtado-Gonzales OP, Volk GM, Wang QC. Application of Biotechniques for In Vitro Virus and Viroid Elimination in Pome Fruit Crops. PHYTOPATHOLOGY 2024; 114:930-954. [PMID: 38408117 DOI: 10.1094/phyto-07-23-0232-kc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Sustainable production of pome fruit crops is dependent upon having virus-free planting materials. The production and distribution of plants derived from virus- and viroid-negative sources is necessary not only to control pome fruit viral diseases but also for sustainable breeding activities, as well as the safe movement of plant materials across borders. With variable success rates, different in vitro-based techniques, including shoot tip culture, micrografting, thermotherapy, chemotherapy, and shoot tip cryotherapy, have been employed to eliminate viruses from pome fruits. Higher pathogen eradication efficiencies have been achieved by combining two or more of these techniques. An accurate diagnosis that confirms complete viral elimination is crucial for developing effective management strategies. In recent years, considerable efforts have resulted in new reliable and efficient virus detection methods. This comprehensive review documents the development and recent advances in biotechnological methods that produce healthy pome fruit plants. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Jean Carlos Bettoni
- Independent Researcher, 35 Brasil Correia Street, Videira, SC 89560510, Brazil
| | - Min-Rui Wang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Jing-Wei Li
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang 550025, China
| | - Xudong Fan
- National Center for Eliminating Viruses from Deciduous Fruit Trees, Institute of Pomology of CAAS, Xingcheng 125100, China
| | - Gennaro Fazio
- U.S. Department of Agriculture-Agricultural Research Service Plant Genetic Resources Unit, Geneva, NY 14456, U.S.A
| | - Oscar P Hurtado-Gonzales
- U.S. Department of Agriculture-APHIS Plant Germplasm Quarantine Program, BARC-East, Beltsville, MD 20705, U.S.A
| | - Gayle M Volk
- U.S. Department of Agriculture-Agricultural Research Service National Laboratory for Genetic Resources Preservation, Fort Collins, CO 80521, U.S.A
| | - Qiao-Chun Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, China
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10
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Kim HJ, Choi SR, Cho IS, Jeong RD. Viral Metatranscriptomic Analysis to Reveal the Diversity of Viruses Infecting Satsuma Mandarin (Citrus unshiu) in Korea. THE PLANT PATHOLOGY JOURNAL 2024; 40:115-124. [PMID: 38606442 PMCID: PMC11016556 DOI: 10.5423/ppj.oa.01.2024.0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 04/13/2024]
Abstract
Citrus cultivation plays a pivotal role, making a significant contribution to global fruit production and dietary consumption. Accurate identification of viral pathogens is imperative for the effective management of plant viral disease in citrus crops. High-throughput sequencing serves as an alternative approach, enabling comprehensive pathogen identification on a large scale without requiring pre-existing information. In this study, we employed HTS to investigate viral pathogens infecting citrus in three different regions of South Korea: Jejudo (Jeju), Wando-gun (Wando), and Dangjin-si (Dangjin). The results unveiled diverse viruses and viroids that exhibited regional variations. Notably, alongside the identification of well-known citrus viruses such as satsuma dwarf virus, citrus tatter leaf virus, and citrus leaf blotch virus (CLBV), this study also uncovered several viruses and viroids previously unreported in Korean citrus. Phylogenetic analysis revealed that majority of identified viruses exhibited the closest affilations with isolates from China or Japan. However, CLBV and citrus viroid-I-LSS displayed diverse phylogenetic positions, reflecting their regional origins. This study advances our understanding of citrus virome diversity and regional dynamics through HTS, emphasizing its potential in unraveling intricate viral pathogens in agriculture. Consequently, it significantly contributes to disease management strategies, ensuring the resilience of the citrus industry.
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Affiliation(s)
- Hae-Jun Kim
- Department of Applied Biology, Chonnam National University, Gwangju 61185, Korea
| | - Se-Ryung Choi
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea
| | - In-Sook Cho
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea
| | - Rae-Dong Jeong
- Department of Applied Biology, Chonnam National University, Gwangju 61185, Korea
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11
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Wang Y, Wang Y, Li Z, Zeng Q, Xu Q, Wang Z, Zhou X. Genomic characterization of a novel cytorhabdovirus infecting Ixeris denticulata in China. Arch Virol 2024; 169:46. [PMID: 38366035 DOI: 10.1007/s00705-024-05988-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/12/2024] [Indexed: 02/18/2024]
Abstract
Ixeris denticulata is a perennial herbal plant with important medical and economic value. In this study, a novel rhabdovirus from I. denticulata with leaf curling and mottle symptoms was identified through next-generation sequencing and molecular cloning approaches. Based on the host species and properties of this virus, it was tentatively named "Ixeris denticulata-associated rhabdovirus" (IdaRV). IdaRV has a negative-sense RNA genome that is 12,705 nucleotides in length and has five open reading frames (ORFs) in the order 3'-nucleoprotein -phosphoprotein -movement protein -matrix protein -large RNA-dependent RNA polymerase-5'. Pairwise sequence comparisons showed that IdaRV had 42.2-53.0% sequence identity to members of the genera Cytorhabdovirus, Varicosavirus, Betanucleorhabdovirus, Gammanucleorhabdovirus, Dichorhavirus, and Alphanucleorhabdovirus in the subfamily Betarhabdovirinae. BLASTp searches indicated that putative products of ORF1, ORF2, ORF3, ORF4, and ORF5 of IdaRV are most closely related to those of rudbeckia virus 1 (RudV1, GenBank accession number ON185810), with 32.1%, 21.3%, 52.4%, 37.6%, and 57.1% amino acid sequence identity, respectively, at the protein level. Phylogenetic analysis showed that IdaRV forms a smaller branch with RudV1, which belongs to the genus Cytorhabdovirus. These results establish IdaRV as a novel rhabdovirus in the genus Cytorhabdovirus of the family Rhabdoviridae.
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Affiliation(s)
- Yaqin Wang
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yongzhi Wang
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zhenghe Li
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Qinwen Zeng
- Bureau of Agriculture and Rural Affairs of Longquan City, Longquan, 610100, China
| | - Qiqiang Xu
- Bureau of Agriculture and Rural Affairs of Longquan City, Longquan, 610100, China
| | - Zhanqi Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000, China.
| | - Xueping Zhou
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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12
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Ghorani S, Massumi H, Farhangi SH, Mansouri M, Heydarnejad J, Hosseinipour A. Metatranscriptome analysis of symptomatic bitter apple plants revealed mixed viral infections with a putative novel polerovirus. BMC Genomics 2024; 25:181. [PMID: 38360528 PMCID: PMC10868029 DOI: 10.1186/s12864-024-10057-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/27/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Next-generation Sequencing (NGS) combined with bioinformatic analyses constitutes a powerful approach for identifying and characterizing previously unknown viral genomes. In this study, leaf samples from bitter apple plants (Citrullus colocynthis (L.) Schrad) exhibiting symptoms such as dwarfing, leaf crinkling, and chlorosis were collected from the southern part of Kerman province, Iran. RESULTS Putative infecting viruses were identified through de novo assembly of sequencing reads using various tools, followed by BLAST analysis. Complete genomes for Squash vein yellowing virus (SqVYV), Citrus-associated rhabdovirus (CiaRV), and a novel polerovirus-related strain termed Bitter apple aphid-borne yellows virus (BaABYV) were assembled and characterized. Additionally, a partial genome for Watermelon mosaic virus (WMV) was assembled. The genomic organization of the BaABYV was determined to be 5'-ORF0-ORF1-ORF1,2-ORF3a-ORF3-ORF3,5-ORF4-3'. Amino acid sequence identities for inferred proteins (P0 and P1, P1,2) with known poleroviruses were found to be the 90% species delineation limit, implying that BaABYV should be considered a new member of the genus Polerovirus. Recombination events were observed in the BaABYV and WMV strains; such events were not found in the CiaRV strain. CONCLUSIONS Molecular evidence from this study suggests that C. colocynthis is a reservoir host of several plant viruses. Among them, BaABYV is proposed as a new member of the genus Polerovirus. Furthermore, the CiaRV strain has been reported for the first time from Iran.
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Affiliation(s)
- Shahrbanou Ghorani
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, 7616914111, Iran
| | - Hossein Massumi
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, 7616914111, Iran.
- Research and Technology Institute of Plant Production (RTIPP), Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Samin H Farhangi
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Mehdi Mansouri
- Department of Agricultural Biotechnology, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Jahangir Heydarnejad
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, 7616914111, Iran
| | - Akbar Hosseinipour
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, 7616914111, Iran
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13
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Keremane M, Singh K, Ramadugu C, Krueger RR, Skaggs TH. Next Generation Sequencing, and Development of a Pipeline as a Tool for the Detection and Discovery of Citrus Pathogens to Facilitate Safer Germplasm Exchange. PLANTS (BASEL, SWITZERLAND) 2024; 13:411. [PMID: 38337944 PMCID: PMC10856814 DOI: 10.3390/plants13030411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024]
Abstract
Citrus is affected by many diseases, and hence, the movement of citrus propagative materials is highly regulated in the USA. Currently used regulatory pathogen detection methods include biological and laboratory-based technologies, which are time-consuming, expensive, and have many limitations. There is an urgent need to develop alternate, rapid, economical, and reliable testing methods for safe germplasm exchange. Citrus huanglongbing (HLB) has devastated citrus industries leading to an increased need for germplasm exchanges between citrus growing regions for evaluating many potentially valuable hybrids for both HLB resistance and multilocational performance. In the present study, Next-Generation Sequencing (NGS) methods were used to sequence the transcriptomes of 21 test samples, including 15 well-characterized pathogen-positive plants. A workflow was designed in the CLC Genomics Workbench software, v 21.0.5 for bioinformatics analysis of the sequence data for the detection of pathogens. NGS was rapid and found to be a valuable technique for the detection of viral and bacterial pathogens, and for the discovery of new citrus viruses, complementary to the existing array of biological and laboratory assays. Using NGS methods, we detected beet western yellows virus, a newly reported citrus virus, and a variant of the citrus yellow vein-associated virus associated with the "fatal yellows" disease.
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Affiliation(s)
- Manjunath Keremane
- USDA ARS, National Clonal Germplasm Repository for Citrus and Dates, Riverside, CA 92507, USA;
| | - Khushwant Singh
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA;
| | - Chandrika Ramadugu
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA;
| | - Robert R. Krueger
- USDA ARS, National Clonal Germplasm Repository for Citrus and Dates, Riverside, CA 92507, USA;
| | - Todd H. Skaggs
- USDA ARS, U.S. Salinity Laboratory, Riverside, CA 92507, USA;
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14
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Tarquini G, Maestri S, Ermacora P, Martini M. The Oxford Nanopore MinION as a Versatile Technology for the Diagnosis and Characterization of Emerging Plant Viruses. Methods Mol Biol 2024; 2732:235-249. [PMID: 38060129 DOI: 10.1007/978-1-0716-3515-5_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
The emergence of novel viral epidemics that could affect major crops represents a serious threat to global food security. The early and accurate identification of the causative viral agent is the most important step for a rapid and effective response to disease outbreaks. Over the last years, the Oxford Nanopore Technologies (ONT) MinION sequencer has been proposed as an effective diagnostic tool for the early detection and identification of emerging viruses in plants, providing many advantages compared with different high-throughput sequencing (HTS) technologies. Here, we provide a step-by-step protocol that we optimized to obtain the virome of "Lamon bean" plants (Phaseolus vulgaris L.), an agricultural product with Protected Geographical Indication (PGI) in North-East of Italy, which is frequently subjected to multiple infections caused by different RNA viruses. The conversion of viral RNA in ds-cDNA enabled the use of Genomic DNA Ligation Sequencing Kit and Native Barcoding DNA Kit, which have been originally developed for DNA sequencing. This allowed the simultaneous diagnosis of both DNA- and RNA-based pathogens, providing a more versatile alternative to the use of direct RNA and/or direct cDNA sequencing kits.
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Affiliation(s)
- Giulia Tarquini
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Simone Maestri
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milano, Italy
| | - Paolo Ermacora
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Marta Martini
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy.
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15
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Bester R, Maree HJ. Validation of High-Throughput Sequencing (HTS) for Routine Detection of Citrus Viruses and Viroids. Methods Mol Biol 2024; 2732:199-219. [PMID: 38060127 DOI: 10.1007/978-1-0716-3515-5_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
The management of plant diseases relies on the accurate identification of pathogens that requires a robust and validated tool in terms of specificity, sensitivity, repeatability, and reproducibility. High-throughput sequencing (HTS) has become the method of choice for virus detection when either a complete viral status of a plant is required in a single assay or if an unknown viral agent is expected. To ensure that the most accurate diagnosis is made from an HTS data analysis, a standardized protocol per pathosystem is required. This chapter presents a detailed protocol for the detection of viruses and viroids infecting citrus using HTS. The protocol describes all the steps from sample processing, nucleic acid extraction, and bioinformatic analyses validated to be an efficient method for detection in this pathosystem. The protocol also includes a section on citrus tristeza virus (CTV) genotype differentiation using HTS data.
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Affiliation(s)
- Rachelle Bester
- Citrus Research International, Stellenbosch, South Africa
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Hans J Maree
- Citrus Research International, Stellenbosch, South Africa.
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa.
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16
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Donaire L, Aranda MA. Computational Pipeline for the Detection of Plant RNA Viruses Using High-Throughput Sequencing. Methods Mol Biol 2024; 2724:1-20. [PMID: 37987894 DOI: 10.1007/978-1-0716-3485-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
In this chapter, we describe a computational pipeline for the in silico detection of plant viruses by high-throughput sequencing (HTS) from total RNA samples. The pipeline is designed for the analysis of short reads generated using an Illumina platform and free-available software tools. First, we provide advice for high-quality total RNA purification, library preparation, and sequencing. The bioinformatics pipeline begins with the raw reads obtained from the sequencing machine and performs some curation steps to obtain long contigs. Contigs are blasted against a local database of reference nucleotide viral sequences to identify the viruses in the samples. Then, the search is refined by applying specific filters. We also provide the code to re-map the short reads against the viruses found to get information on sequencing depth and read coverage for each virus. No previous bioinformatics background is required, but basic knowledge of the Unix command line and R language is recommended.
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Affiliation(s)
- Livia Donaire
- Abiopep S.L., Parque Científico de Murcia, Complejo de Espinardo, Murcia, Spain.
- Department of Stress Biology and Plant Pathology, Centro de Edafología y Biología Aplicada del Segura (CEBAS)-CSIC, Murcia, Spain.
| | - Miguel A Aranda
- Department of Stress Biology and Plant Pathology, Centro de Edafología y Biología Aplicada del Segura (CEBAS)-CSIC, Murcia, Spain
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17
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Singh S, Stainton D, Tzanetakis IE. Development of Rapid and Affordable Virus-Mimicking Artificial Positive Controls. PLANT DISEASE 2024; 108:30-34. [PMID: 37578360 DOI: 10.1094/pdis-06-23-1072-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
A major bottleneck in the development of detection assays is the availability of positive controls. Their acquisition can be problematic, their maintenance is expensive, and without them, assays cannot be validated. Herein, we present a novel strategy for the development of virus-mimicking artificial positive controls (ViMAPCs). The time between design and application is less than 5 days, unlike alternatives which normally take several weeks to obtain and implement. The ViMAPCs provide a realistic representation of natural infection unlike alternatives and allow for an effortless recognition of laboratory-based contamination. The feasibility and adaptability of the strategy was evaluated using several RNA and DNA plant viruses. ViMAPCs can be used in diagnostics laboratories but also in the monitoring of pathogen outbreaks where rapid response is of utmost importance.
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Affiliation(s)
- Shivani Singh
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - Daisy Stainton
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
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18
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Hu X, Hurtado-Gonzales OP, Adhikari BN, French-Monar RD, Malapi M, Foster JA, McFarland CD. PhytoPipe: a phytosanitary pipeline for plant pathogen detection and diagnosis using RNA-seq data. BMC Bioinformatics 2023; 24:470. [PMID: 38093207 PMCID: PMC10717670 DOI: 10.1186/s12859-023-05589-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Detection of exotic plant pathogens and preventing their entry and establishment are critical for the protection of agricultural systems while securing the global trading of agricultural commodities. High-throughput sequencing (HTS) has been applied successfully for plant pathogen discovery, leading to its current application in routine pathogen detection. However, the analysis of massive amounts of HTS data has become one of the major challenges for the use of HTS more broadly as a rapid diagnostics tool. Several bioinformatics pipelines have been developed to handle HTS data with a focus on plant virus and viroid detection. However, there is a need for an integrative tool that can simultaneously detect a wider range of other plant pathogens in HTS data, such as bacteria (including phytoplasmas), fungi, and oomycetes, and this tool should also be capable of generating a comprehensive report on the phytosanitary status of the diagnosed specimen. RESULTS We have developed an open-source bioinformatics pipeline called PhytoPipe (Phytosanitary Pipeline) to provide the plant pathology diagnostician community with a user-friendly tool that integrates analysis and visualization of HTS RNA-seq data. PhytoPipe includes quality control of reads, read classification, assembly-based annotation, and reference-based mapping. The final product of the analysis is a comprehensive report for easy interpretation of not only viruses and viroids but also bacteria (including phytoplasma), fungi, and oomycetes. PhytoPipe is implemented in Snakemake workflow with Python 3 and bash scripts in a Linux environment. The source code for PhytoPipe is freely available and distributed under a BSD-3 license. CONCLUSIONS PhytoPipe provides an integrative bioinformatics pipeline that can be used for the analysis of HTS RNA-seq data. PhytoPipe is easily installed on a Linux or Mac system and can be conveniently used with a Docker image, which includes all dependent packages and software related to analyses. It is publicly available on GitHub at https://github.com/healthyPlant/PhytoPipe and on Docker Hub at https://hub.docker.com/r/healthyplant/phytopipe .
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Affiliation(s)
- Xiaojun Hu
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA.
| | - Oscar P Hurtado-Gonzales
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA
| | - Bishwo N Adhikari
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA
| | - Ronald D French-Monar
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA
| | - Martha Malapi
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA
- American Seed Trade Association (ASTA), Alexandria, VA, USA
| | - Joseph A Foster
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA
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19
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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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20
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Nery FMB, Batista JG, Melo FFS, Ribeiro SG, Boiteux LS, Melo FL, Silva JGI, Reis LDNA, Pereira-Carvalho RC. Novel plant-associated genomoviruses from the Brazilian Cerrado biome. Arch Virol 2023; 168:286. [PMID: 37940763 DOI: 10.1007/s00705-023-05892-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 08/19/2023] [Indexed: 11/10/2023]
Abstract
The discovery rate of new plant viruses has increased due to studies involving high-throughput sequencing (HTS), particularly for single-stranded DNA viruses of the family Genomoviridae. We carried out an HTS-based survey of genomoviruses in a wide range of native and exotic trees grown in the Brazilian Cerrado biome, and the complete genome sequences of two novel members of the family Genomoviridae from two distinct genera were determined. Specific primers were designed to detect these genomoviruses in individual samples. A new gemykolovirus (Tecoma stans associated gemykolovirus) was detected in Tecoma stans, and a new gemykibivirus (Ouratea duparquetiana associated gemykibivirus) was detected in Ouratea duparquetiana. A gemykrogvirus related to Gila monster associated gemykrogvirus (80% pairwise identity) was also detected in foliar samples of Trembleya parviflora. Our pilot study paves the way for a better characterization of this diverse collection of genomoviruses as well as their interactions with the associated tree species.
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Affiliation(s)
- Flávia Milene B Nery
- Departamento de Fitopatologia, Universidade de Brasília (UnB), Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Josiane G Batista
- Departamento de Fitopatologia, Universidade de Brasília (UnB), Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Felipe Fochat S Melo
- Departamento de Fitopatologia, Universidade de Brasília (UnB), Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Simone G Ribeiro
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, 70770-017, Brazil
| | - Leonardo S Boiteux
- Embrapa Vegetable Crops (Hortaliças), National Center for Vegetable Crops Research (CNPH), Brasília, DF, 70275-970, Brazil
| | - Fernando L Melo
- Departamento de Fitopatologia, Universidade de Brasília (UnB), Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Juliana Gabrielle I Silva
- Departamento de Fitopatologia, Universidade de Brasília (UnB), Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Luciane de Nazaré A Reis
- Departamento de Fitopatologia, Universidade de Brasília (UnB), Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Rita C Pereira-Carvalho
- Departamento de Fitopatologia, Universidade de Brasília (UnB), Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil.
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21
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Zhao Z, Wang S, Dong Z, Fan Q, Lei R, Kuang R, Zhang Y. One-Step Reverse-Transcription Recombinase-Aided Amplification CRISPR/Cas12a-Based Lateral Flow Assay for Fast Field Screening and Accurate Differentiation of Four Major Tobamoviruses Infecting Tomato and Pepper. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37916776 DOI: 10.1021/acs.jafc.3c05268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Several tobamoviruses cause substantial economic losses to tomato and pepper crops globally, especially the pepper mild mosaic virus (PMMoV), tomato brown rugose fruit virus (ToBRFV), tomato mosaic virus (ToMV), and tomato mottle mosaic virus (ToMMV). A fast and accurate detection method is essential for virus identification. An all-in-one reaction method combining a one-step reverse-transcription recombinase-aided amplification (RT-RAA) and CRISPR/Cas12a-based lateral flow assay in one mixture was developed to rapidly screen and accurately differentiate among these four tobamoviruses for field detection in tomato and pepper plants. With a generic RT-RAA primer set and a mix of four specific crRNAs, along with a portable metal incubator and the use of a crude extraction method, this method screened for PMMoV, ToBRFV, ToMV, and ToMMV concurrently in less than 1 h, enabling field workers to take action immediately. The accurate differentiation of these four viruses could be achieved by later adding a single specific crRNA.
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Affiliation(s)
- Zhenxing Zhao
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Siyuan Wang
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Zheng Dong
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Qixuan Fan
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, Department of Plant Pathology, China Agricultural University, 100193 Beijing, China
| | - Rong Lei
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Ruirui Kuang
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, Department of Plant Pathology, China Agricultural University, 100193 Beijing, China
| | - Yongjiang Zhang
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China
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22
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Jo Y, Choi H, Lee BC, Hong JS, Kim SM, Cho WK. Exploring Tomato Fruit Viromes through Transcriptome Data Analysis. Viruses 2023; 15:2139. [PMID: 38005817 PMCID: PMC10674750 DOI: 10.3390/v15112139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
This study delves into the complex landscape of viral infections in tomatoes (Solanum lycopersicum) using available transcriptome data. We conducted a virome analysis, revealing 219 viral contigs linked to four distinct viruses: tomato chlorosis virus (ToCV), southern tomato virus (STV), tomato yellow leaf curl virus (TYLCV), and cucumber mosaic virus (CMV). Among these, ToCV predominated in contig count, followed by STV, TYLCV, and CMV. A notable finding was the prevalence of coinfections, emphasizing the concurrent presence of multiple viruses in tomato plants. Despite generally low viral levels in fruit transcriptomes, STV emerged as the primary virus based on viral read count. We delved deeper into viral abundance and the contributions of RNA segments to replication. While initially focused on studying the impact of sound treatment on tomato fruit transcriptomes, the unexpected viral presence underscores the importance of considering viruses in plant research. Geographical variations in virome communities hint at potential forensic applications. Phylogenetic analysis provided insights into viral origins and genetic diversity, enhancing our understanding of the Korean tomato virome. In conclusion, this study advances our knowledge of the tomato virome, stressing the need for robust pest control in greenhouse-grown tomatoes and offering insights into virus management and crop protection.
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Affiliation(s)
- Yeonhwa Jo
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea;
| | - Hoseong Choi
- Plant Health Center, Seoul National University, Seoul 08826, Republic of Korea;
| | - Bong Choon Lee
- Crop Protection Division, National Academy of Agricultural Science, Rural Development Administration, Wanju 55365, Republic of Korea;
| | - Jin-Sung Hong
- Department of Applied Biology, Kangwon National University, Chuncheon 24341, Republic of Korea;
| | - Sang-Min Kim
- Crop Foundation Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Won Kyong Cho
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea;
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23
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Elwan EA, Rabie M, Aleem EEA, Fattouh FA, Kagda MS, Zaghloul HAH. Exploring virus presence in field-collected potato leaf samples using RNA sequencing. J Genet Eng Biotechnol 2023; 21:106. [PMID: 37861927 PMCID: PMC10589165 DOI: 10.1186/s43141-023-00561-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 10/11/2023] [Indexed: 10/21/2023]
Abstract
BACKGROUND The quick and accurate identification of viruses is essential for plant disease management. Next-generation sequencing (NGS) technology may allow the discovery, detection, and identification of plant pathogens. This study adopted RNA-sequencing (RNA-Seq) technology to explore the viruses in three potato plants (S3, S4, and S6) growing under field conditions. RESULTS Potato-known infecting viruses, such as alfalfa mosaic virus (AMV), potato leafroll virus (PLRV), and potato virus Y (PVY), were identified using bioinformatics programs and validated using RT-PCR. The presence of these potato viruses was also confirmed by visual inspection of host symptoms. In addition, the nearly complete genome of PLRV and the complete or partial genome sequence of multipartite virus segments have been identified. Besides the three major potato viruses that BLASTn analysis revealed were present in our samples, BLASTx analysis revealed some reads are derived from other potato viruses, such as potato virus V (PVV), Andean potato latent virus (APLV), and tomato chlorosis virus (ToCV), which are not frequently reported in potato field screenings in Egypt. Other microbial agents, such as bacteria and fungi, were also identified in the examined sample sequences. Some mycovirus sequences derived from ourmia-like viruses and Alternaria alternata chrysovirus were also identified in sample S4, confirming the complexity of the potato microbiome under field conditions. CONCLUSION NGS quickly and accurately identifies potato plant viruses under field conditions. Implementing this technology on a larger scale is recommended to explore potato fields and imported plants, where symptoms may be absent, unspecific, or only triggered under certain conditions.
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Affiliation(s)
- Esraa A Elwan
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Alexandria, 21511, Egypt
| | - Mona Rabie
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Alexandria, 21511, Egypt
| | - Engy E Abdel Aleem
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Alexandria, 21511, Egypt
| | - Faiza A Fattouh
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Alexandria, 21511, Egypt
| | - Meenakshi S Kagda
- Genetics Department, School of Medicine, Stanford University, Stanford, CA, USA
| | - Heba A H Zaghloul
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Alexandria, 21511, Egypt.
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Morán F, Olmos A, Candresse T, Ruiz-García AB. Complete Genome Characterization of Penicillimonavirus gammaplasmoparae, a Bipartite Member of the Family Mymonaviridae. PLANTS (BASEL, SWITZERLAND) 2023; 12:3300. [PMID: 37765464 PMCID: PMC10538141 DOI: 10.3390/plants12183300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 08/29/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023]
Abstract
In this study, we identified Plasmopara-viticola-lesion-associated mononegaambi virus 3 (recently classified as Penicillimonavirus gammaplasmoparae), a fungi-associated mymonavirus, in grapevine plants showing an unusual upward curling symptomatology on the leaves and premature decline. Mymonaviridae is a family comprising nine genera of negative-sense single-stranded RNA viruses infecting filamentous fungi, although few of them have been associated with oomycetes, plants, and insects. Although the first mymonavirus genome description was reported a decade ago, the genome organization of several genera in the family, including the genus Penicillimonavirus, has remained unclear to date. We have determined the complete genome of P. gammaplasmoparae, which represents the first complete genomic sequence for this genus. Moreover, we provide strong evidence that P. gammaplasmoparae genome is bipartite and comprises two RNA molecules of around 6150 and 4560 nt. Our results indicate that the grapevine powdery mildew pathogen, Erysiphe necator, was also present in the analyzed plants and suggest P. gammaplasmoparae could be infecting this fungus. However, whether the fungus and/or the mycovirus are associated with the symptomatology that initially prompted these efforts remains to be determined.
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Affiliation(s)
- Félix Morán
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113 Valencia, Spain; (F.M.); (A.O.)
| | - Antonio Olmos
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113 Valencia, Spain; (F.M.); (A.O.)
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, University Bordeaux, CEDEX, 33882 Villenave d’Ornon, France;
| | - Ana Belén Ruiz-García
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113 Valencia, Spain; (F.M.); (A.O.)
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Choi H, Jo Y, Chung H, Choi SY, Kim SM, Hong JS, Lee BC, Cho WK. Investigating Variability in Viral Presence and Abundance across Soybean Seed Development Stages Using Transcriptome Analysis. PLANTS (BASEL, SWITZERLAND) 2023; 12:3257. [PMID: 37765420 PMCID: PMC10535271 DOI: 10.3390/plants12183257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/05/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
Plant transcriptomes offer a valuable resource for studying viral communities (viromes). In this study, we explore how plant transcriptome data can be applied to virome research. We analyzed 40 soybean transcriptomes across different growth stages and identified six viruses: broad bean wilt virus 2 (BBWV2), brassica yellow virus (BrYV), beet western yellow virus (BWYV), cucumber mosaic virus (CMV), milk vetch dwarf virus (MDV), and soybean mosaic virus (SMV). SMV was the predominant virus in both Glycine max (GM) and Glycine soja (GS) cultivars. Our analysis confirmed its abundance in both, while BBWV2 and CMV were more prevalent in GS than GM. The viral proportions varied across developmental stages, peaking in open flowers. Comparing viral abundance measured by viral reads and fragments per kilobase of transcript per million (FPKM) values revealed insights. SMV showed similar FPKM values in GM and GS, but BBWV2 and CMV displayed higher FPKM proportions in GS. Notably, the differences in viral abundance between GM and GS were generally insignificant based on the FPKM values across developmental stages, except for the apical bud stage in four GM cultivars. We also detected MDV, a multi-segmented virus, in two GM samples, with variable proportions of its segments. In conclusion, our study demonstrates the potential of plant transcriptomes for virome research, highlighting their strengths and limitations.
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Affiliation(s)
- Hoseong Choi
- Plant Health Center, Seoul National University, Seoul 08826, Republic of Korea;
| | - Yeonhwa Jo
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea;
| | - Hyunjung Chung
- Crop Foundation Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea; (H.C.); (S.Y.C.); (S.-M.K.)
| | - Soo Yeon Choi
- Crop Foundation Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea; (H.C.); (S.Y.C.); (S.-M.K.)
| | - Sang-Min Kim
- Crop Foundation Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea; (H.C.); (S.Y.C.); (S.-M.K.)
| | - Jin-Sung Hong
- Department of Applied Biology, Kangwon National University, Chuncheon 24341, Republic of Korea;
| | - Bong Choon Lee
- Crop Protection Division, National Academy of Agricultural Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Won Kyong Cho
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea;
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26
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Kreuze JF, Cuellar WJ, Kumar PL, Boddupalli P, Omondi AB. New Technologies Provide Innovative Opportunities to Enhance Understanding of Major Virus Diseases Threatening Global Food Security. PHYTOPATHOLOGY 2023; 113:1622-1629. [PMID: 37311729 DOI: 10.1094/phyto-12-22-0457-v] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Plant viruses pose a continuous and serious threat to crop production worldwide, and globalization and climate change are exacerbating the establishment and rapid spread of new viruses. Simultaneously, developments in genome sequencing technology, nucleic acid amplification methods, and epidemiological modeling are providing plant health specialists with unprecedented opportunities to confront these major threats to the food security and livelihoods of millions of resource-constrained smallholders. In this perspective, we have used recent examples of integrated application of these technologies to enhance understanding of the emergence of plant viral diseases of key food security crops in low- and middle-income countries. We highlight how international funding and collaboration have enabled high-throughput sequencing-based surveillance approaches, targeted field and lab-based diagnostic tools, and modeling approaches that can be effectively used to support surveillance and preparedness against existing and emerging plant viral threats. The importance of national and international collaboration and the future role of CGIAR in further supporting these efforts, including building capabilities to make optimal use of these technologies in low- and middle-income countries, are discussed. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Jan F Kreuze
- One CGIAR Plant Health Initiative
- International Potato Center, Apartado 1558, Lima 15024, Peru
| | - Wilmer J Cuellar
- One CGIAR Plant Health Initiative
- One CGIAR Accelerated Breeding Initiative
- Alliance of Bioversity International and CIAT, Km 17 Recta Cali-Palmira, Cali 763537, Colombia
| | - P Lava Kumar
- One CGIAR Plant Health Initiative
- International Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan, Nigeria
| | - Prasanna Boddupalli
- One CGIAR Plant Health Initiative
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF Campus, UN Avenue, Gigiri, Nairobi, Kenya
| | - Aman B Omondi
- One CGIAR Plant Health Initiative
- Alliance of Bioversity International and CIAT, IPGRI Building, 08BP 0932-Cotonou, Republic of Benin
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27
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Choi H, Jo Y, Cho WK. In Silico Virome Analysis of Chinese Narcissus Transcriptomes Reveals Diverse Virus Species and Genetic Diversity at Different Flower Development Stages. BIOLOGY 2023; 12:1094. [PMID: 37626980 PMCID: PMC10452245 DOI: 10.3390/biology12081094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023]
Abstract
Viromes of Chinese narcissus flowers were explored using transcriptome data from 20 samples collected at different flower development stages. Quality controlled raw data underwent de novo assembly, resulting in 5893 viral contigs that matched the seven virus species. The most abundant viruses were narcissus common latent virus (NCLV), narcissus yellow stripe virus (NYSV), and narcissus mottling-associated virus (NMaV). As flower development stages advanced, white tepal plants showed an increase in the proportion of viral reads, while the variation in viral proportion among yellow tepal plants was relatively small. Narcissus degeneration virus (NDV) dominated the white tepal samples, whereas NDV and NYSV prevailed in the yellow tepal samples. Potyviruses, particularly NDV, are the primary infectious viruses. De novo assembly generated viral contigs for five viruses, yielding complete genomes for NCLV, NDV, narcissus late season yellow virus (NLSYV), and NYSV. Phylogenetic analysis revealed genetic diversity, with distinct NCLV, NMaV, NDV, NLSYV, and NYSV groups. This study provides valuable insights into the viromes and genetic diversity of viruses in Chinese narcissus flowers.
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Affiliation(s)
- Hoseong Choi
- Plant Health Center, Seoul National University, Seoul 08826, Republic of Korea;
| | - Yeonhwa Jo
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea;
| | - Won Kyong Cho
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea;
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28
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Tuo D, Yao Y, Yan P, Chen X, Qu F, Xue W, Liu J, Kong H, Guo J, Cui H, Dai Z, Shen W. Development of cassava common mosaic virus-based vector for protein expression and gene editing in cassava. PLANT METHODS 2023; 19:78. [PMID: 37537660 PMCID: PMC10399001 DOI: 10.1186/s13007-023-01055-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 07/15/2023] [Indexed: 08/05/2023]
Abstract
BACKGROUND Plant virus vectors designed for virus-mediated protein overexpression (VOX), virus-induced gene silencing (VIGS), and genome editing (VIGE) provide rapid and cost-effective tools for functional genomics studies, biotechnology applications and genome modification in plants. We previously reported that a cassava common mosaic virus (CsCMV, genus Potexvirus)-based VIGS vector was used for rapid gene function analysis in cassava. However, there are no VOX and VIGE vectors available in cassava. RESULTS In this study, we developed an efficient VOX vector (CsCMV2-NC) for cassava by modifying the CsCMV-based VIGS vector. Specifically, the length of the duplicated putative subgenomic promoter (SGP1) of the CsCMV CP gene was increased to improve heterologous protein expression in cassava plants. The modified CsCMV2-NC-based VOX vector was engineered to express genes encoding green fluorescent protein (GFP), bacterial phytoene synthase (crtB), and Xanthomonas axonopodis pv. manihotis (Xam) type III effector XopAO1 for viral infection tracking, carotenoid biofortification and Xam virulence effector identification in cassava. In addition, we used CsCMV2-NC to deliver single guide RNAs (gMePDS1/2) targeting two loci of the cassava phytoene desaturase gene (MePDS) in Cas9-overexpressing transgenic cassava lines. The CsCMV-gMePDS1/2 efficiently induced deletion mutations of the targeted MePDS with the albino phenotypes in systemically infected cassava leaves. CONCLUSIONS Our results provide a useful tool for rapid and efficient heterologous protein expression and guide RNA delivery in cassava. This expands the potential applications of CsCMV-based vector in gene function studies, biotechnology research, and precision breeding for cassava.
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Affiliation(s)
- Decai Tuo
- National Key Laboratory for Tropical Crops Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops (Ministry of Agriculture and Rural Affairs), Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou & Sanya, Hainan, China
| | - Yuan Yao
- National Key Laboratory for Tropical Crops Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops (Ministry of Agriculture and Rural Affairs), Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou & Sanya, Hainan, China
| | - Pu Yan
- National Key Laboratory for Tropical Crops Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops (Ministry of Agriculture and Rural Affairs), Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou & Sanya, Hainan, China
| | - Xin Chen
- National Key Laboratory for Tropical Crops Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops (Ministry of Agriculture and Rural Affairs), Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou & Sanya, Hainan, China
| | - Feihong Qu
- School of Tropical Agriculture and Forestry, Sanya Nanfan Research Institute, Hainan University, Haikou & Sanya, Hainan, China
| | - Weiqian Xue
- School of Tropical Agriculture and Forestry, Sanya Nanfan Research Institute, Hainan University, Haikou & Sanya, Hainan, China
| | - Jinping Liu
- School of Tropical Agriculture and Forestry, Sanya Nanfan Research Institute, Hainan University, Haikou & Sanya, Hainan, China
| | - Hua Kong
- National Key Laboratory for Tropical Crops Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops (Ministry of Agriculture and Rural Affairs), Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou & Sanya, Hainan, China
| | - Jianchun Guo
- National Key Laboratory for Tropical Crops Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops (Ministry of Agriculture and Rural Affairs), Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou & Sanya, Hainan, China
| | - Hongguang Cui
- School of Tropical Agriculture and Forestry, Sanya Nanfan Research Institute, Hainan University, Haikou & Sanya, Hainan, China
| | - Zhaoji Dai
- School of Tropical Agriculture and Forestry, Sanya Nanfan Research Institute, Hainan University, Haikou & Sanya, Hainan, China
| | - Wentao Shen
- National Key Laboratory for Tropical Crops Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops (Ministry of Agriculture and Rural Affairs), Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou & Sanya, Hainan, China.
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Svanella-Dumas L, Tsarmpopoulos I, Marais A, Faure C, Theil S, Glasa M, Predajna L, Gaudin J, Tian S, Porcher L, Gentit P, De Oliveira ML, Krause-Sakate R, Candresse T. Molecular and Biological Characterization of Novel and Known Family Secoviridae Members Infecting Lettuce. PHYTOPATHOLOGY 2023; 113:1595-1604. [PMID: 37081712 DOI: 10.1094/phyto-03-23-0095-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
High-throughput sequencing of two lettuces showing virus-like symptoms in France provided evidence of infection by members of the family Secoviridae. One plant (JG1) had a complex mixed infection that involved, among others, a novel waikavirus (lettuce waikavirus 1) and two isolates of a sequivirus related to lettuce mottle virus (LeMoV). The second lettuce plant (JG2) was singly infected by LeMoV. Complete genomic sequences were obtained for all four isolates and, in addition, near complete genome sequences were obtained for other LeMoV or LeMoV-related isolates (from French cultivated and wild lettuces and from a Brazilian cultivated lettuce) and for two isolates of another family Asteraceae-infecting sequivirus, dandelion yellow mosaic virus (DaYMV). Analysis of these genomic sequences allows the proposal of tentative genome organization for the various viruses and clarification of their phylogenetic relationships. Sequence and host range comparisons point to significant differences between the two sequivirus isolates identified in the JG1 plant and LeMoV isolates from France and Brazil, suggesting they belong to a novel species for which the name lettuce star mosaic virus is proposed.
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Affiliation(s)
- Laurence Svanella-Dumas
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Iason Tsarmpopoulos
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Armelle Marais
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Chantal Faure
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Sébastien Theil
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Miroslav Glasa
- Biomedical Research Center of the Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 84505 Bratislava, Slovak Republic
| | - Lukas Predajna
- Biomedical Research Center of the Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 84505 Bratislava, Slovak Republic
| | - Jonathan Gaudin
- INRAE, Bordeaux Sciences Agro, UMR Santé et Agroécologie du Vignoble, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Sixing Tian
- ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM, 7 rue Jean Dixméras, 49044 Angers Cedex 01, France
| | - Laëtitia Porcher
- ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM, 7 rue Jean Dixméras, 49044 Angers Cedex 01, France
| | - Pascal Gentit
- ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM, 7 rue Jean Dixméras, 49044 Angers Cedex 01, France
| | - Milena Leite De Oliveira
- Laboratorio Central Multisuarios (LACEM), Faculdade de Ciências Agronômicas, School of Agriculture, Sao Paulo State University (UNESP), Botucatu, Brazil
| | - Renate Krause-Sakate
- Department of Plant Protection, Faculdade de Ciências Agronômicas, School of Agriculture, Sao Paulo State University (UNESP), Botucatu, Brazil
| | - Thierry Candresse
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
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Stainton D, Villamor DEV, Sierra Mejia A, Srivastava A, Mollov D, Martin RR, Tzanetakis IE. Genomic analyses of a widespread blueberry virus in the United States. Virus Res 2023; 333:199143. [PMID: 37271421 PMCID: PMC10352716 DOI: 10.1016/j.virusres.2023.199143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/06/2023]
Abstract
Screening of blueberry accessions using high throughput sequencing revealed the presence of a new virus. Genomic structure and sequence are similar to that of nectarine stem pitting associated virus (NSPaV), a member of the genus Luteovirus, family Tombusviridae. The full genome of the new luteovirus, tentatively named blueberry virus L (BlVL), was characterized and analyzed. Similar to NSPaV, BlVL does not contain readily identifiable movement proteins in any of the seven isolates sequenced. More than 600 samples collected from five states were screened and 79% were found infected, making BlVL the most widespread blueberry virus in the United States.
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Affiliation(s)
- Daisy Stainton
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA
| | - Dan E V Villamor
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA
| | - Andrea Sierra Mejia
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA
| | - Ashish Srivastava
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA
| | - Dimitre Mollov
- USDA-ARS, Horticultural Crops Disease and Pest Management Research Unit, 3420 NW Orchard Ave, Corvallis, OR 97330; Oregon State University, Corvallis, OR 97330, USA
| | | | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA.
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Diaz-Lara A, Stevens K, Aguilar-Molina VH, Fernández-Cortés JM, Chabacano León VM, De Donato M, Sharma A, Erickson TM, Al Rwahnih M. High-Throughput Sequencing of Grapevine in Mexico Reveals a High Incidence of Viruses including a New Member of the Genus Enamovirus. Viruses 2023; 15:1561. [PMID: 37515247 PMCID: PMC10386000 DOI: 10.3390/v15071561] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/08/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
This is the first viral metagenomic analysis of grapevine conducted in Mexico. During the summer of 2021, 48 plants displaying virus-like symptoms were sampled in Queretaro, an important grapevine-producing area of Mexico, and analyzed for the presence of viruses via high-throughput sequencing (HTS). The results of HTS were verified by real-time RT-PCR following a standardized testing scheme (Protocol 2010). Fourteen different viruses were identified, including grapevine asteroid mosaic-associated virus (GAMaV), grapevine Cabernet Sauvignon reovirus (GCSV), grapevine fanleaf virus (GFLV), grapevine fleck virus (GFkV), grapevine Pinot gris virus (GPGV), grapevine red globe virus (GRGV), grapevine rupestris stem pitting-associated virus (GRSPaV), grapevine rupestris vein feathering virus (GRVFV), grapevine Syrah virus 1 (GSyV-1), grapevine virus B (GVB), and grapevine leafroll-associated viruses 1, 2, 3, 4 (GLRaV1, 2, 3, 4). Additionally, divergent variants of GLRaV4 and GFkV, and a novel Enamovirus-like virus were discovered. This is the first report of GAMaV, GCSV, GLRaV4, GPGV, GRGV, GRVFV, and GSyV-1 infecting grapevines in Mexico; the impact of these pathogens on production is unknown.
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Affiliation(s)
- Alfredo Diaz-Lara
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico
| | - Kristian Stevens
- Departments of Computer Science and Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA
- Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA
| | | | | | | | - Marcos De Donato
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico
| | - Ashutosh Sharma
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico
| | - Teresa M Erickson
- Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA
| | - Maher Al Rwahnih
- Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA
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Koloniuk I, Matyášová A, Brázdová S, Veselá J, Přibylová J, Várallyay E, Fránová J. Analysis of Virus-Derived siRNAs in Strawberry Plants Co-Infected with Multiple Viruses and Their Genotypes. PLANTS (BASEL, SWITZERLAND) 2023; 12:2564. [PMID: 37447124 DOI: 10.3390/plants12132564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023]
Abstract
Plants can be infected with multiple viruses. High-throughput sequencing tools have enabled numerous discoveries of multi-strain infections, when more than one viral strain or divergent genomic variant infects a single plant. Here, we investigated small interfering RNAs (siRNAs) in a single strawberry plant co-infected with several strains of strawberry mottle virus (SMoV), strawberry crinkle virus (SCV) and strawberry virus 1 (StrV-1). A range of plants infected with subsets of the initial viral species and strains that were obtained by aphid-mediated transmission were also evaluated. Using high-throughput sequencing, we characterized the small RNA fractions associated with different genotypes of these three viruses and determined small RNA hotspot regions in viral genomes. A comparison of virus-specific siRNA (vsiRNA) abundance with relative viral concentrations did not reveal any consistent agreement. Strawberry mottle virus strains exhibiting considerable variations in concentrations were found to be associated with comparable quantities of vsiRNAs. Additionally, by estimating the specificity of siRNAs to different viral strains, we observed that a substantial pool of vsiRNAs could target all SMoV strains, while strain-specific vsiRNAs predominantly targeted rhabdoviruses, SCV and StrV-1. This highlights the intricate nature and potential interference of the antiviral response within a single infected plant when multiple viruses are present.
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Affiliation(s)
- Igor Koloniuk
- Institute of Plant Molecular Biology, Department of Plant Virology, Biology Centre CAS, 370 05 Ceske Budejovice, Czech Republic
| | - Alena Matyášová
- Institute of Plant Molecular Biology, Department of Plant Virology, Biology Centre CAS, 370 05 Ceske Budejovice, Czech Republic
| | - Sára Brázdová
- Institute of Plant Molecular Biology, Department of Plant Virology, Biology Centre CAS, 370 05 Ceske Budejovice, Czech Republic
- Faculty of Agriculture, University of South Bohemia, 370 05 Ceske Budejovice, Czech Republic
| | - Jana Veselá
- Institute of Plant Molecular Biology, Department of Plant Virology, Biology Centre CAS, 370 05 Ceske Budejovice, Czech Republic
| | - Jaroslava Přibylová
- Institute of Plant Molecular Biology, Department of Plant Virology, Biology Centre CAS, 370 05 Ceske Budejovice, Czech Republic
| | - Eva Várallyay
- Genomics Research Group, Institute of Plant Protection, Department of Plant Pathology, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, 2100 Gödöllő, Hungary
| | - Jana Fránová
- Institute of Plant Molecular Biology, Department of Plant Virology, Biology Centre CAS, 370 05 Ceske Budejovice, Czech Republic
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Reyes-Proaño EG, Cañada-Bautista MG, Cornejo-Franco JF, Alvarez-Quinto RA, Mollov D, Sanchez-Timm E, Quito-Avila DF. The Virome of Babaco ( Vasconcellea × heilbornii) Expands to Include New Members of the Rhabdoviridae and Bromoviridae. Viruses 2023; 15:1380. [PMID: 37376679 DOI: 10.3390/v15061380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Babaco (Vasconcellea × heilbornii) is a subtropical species in the Caricaceae family. The plant is native to Ecuador and represents an important crop for hundreds of families. The objective of this study was to characterize, at the genomic level, two new babaco viruses identified by high-throughput sequencing. The viruses, an ilarvirus and a nucleorhabdovirus, were found in a symptomatic babaco plant from a commercial nursery in the Azuay province of Ecuador. The tripartite genome of the new ilarvirus, provisionally named babaco ilarvirus 1 (BabIV-1), is related to subgroup 3 ilarviruses, including apple mosaic virus, apple necrotic mosaic virus, and prunus necrotic ringspot virus as the closest relatives. The genome of the nucleorhabdovirus, provisionally named babaco nucleorhabdovirus 1 (BabRV-1), showed the closest relation with joa yellow blotch-associated virus and potato yellow dwarf nucleorhabdovirus. Molecular-based detection methods found BabIV-1 and BabRV-1 in 21% and 36%, respectively, of plants surveyed in a commercial babaco nursery, highlighting the importance of enforcing virus testing and nursery certification programs for babaco.
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Affiliation(s)
- Edison G Reyes-Proaño
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Km 30.5 Vía Perimetral Campus Gustavo Galindo, Guayaquil 090902, Ecuador
- Department of Entomology and Plant Pathology, University of Idaho, Moscow, ID 83843, USA
| | - Maria G Cañada-Bautista
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Km 30.5 Vía Perimetral Campus Gustavo Galindo, Guayaquil 090902, Ecuador
| | - Juan F Cornejo-Franco
- Centro de Investigaciones Biotecnológicas del Ecuador, Escuela Superior Politécnica del Litoral, CIBE-ESPOL, Km 30.5 Vía Perimetral Campus Gustavo Galindo, Guayaquil 090902, Ecuador
| | | | | | - Eduardo Sanchez-Timm
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Km 30.5 Vía Perimetral Campus Gustavo Galindo, Guayaquil 090902, Ecuador
- Centro de Investigaciones Biotecnológicas del Ecuador, Escuela Superior Politécnica del Litoral, CIBE-ESPOL, Km 30.5 Vía Perimetral Campus Gustavo Galindo, Guayaquil 090902, Ecuador
| | - Diego F Quito-Avila
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Km 30.5 Vía Perimetral Campus Gustavo Galindo, Guayaquil 090902, Ecuador
- Centro de Investigaciones Biotecnológicas del Ecuador, Escuela Superior Politécnica del Litoral, CIBE-ESPOL, Km 30.5 Vía Perimetral Campus Gustavo Galindo, Guayaquil 090902, Ecuador
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Izhaki-Tavor LS, Yechezkel IG, Alter J, Dessau M. RNA Encapsulation Mode and Evolutionary Insights from the Crystal Structure of Emaravirus Nucleoprotein. Microbiol Spectr 2023; 11:e0501822. [PMID: 37039649 PMCID: PMC10269810 DOI: 10.1128/spectrum.05018-22] [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: 12/07/2022] [Accepted: 02/27/2023] [Indexed: 04/12/2023] Open
Abstract
Enveloped RNA viruses are rare among plant viruses. Fimoviridae is a newly founded family of plant viruses within the Bunyavirales order that inflicts diverse crop losses worldwide. The fig mosaic virus (FMV), the representative member of the Fimoviridae family, was shown to be a causative agent for the fig mosaic disease. Like all bunyaviruses, FMV has a segmented, negative-sense, single-stranded RNA (ssRNA) genome that is encapsulated by the viral nucleoprotein (N). Here, we present high-resolution crystal structures of FMV N in its RNA-free and RNA-bound forms, revealing a "paper fortune teller" structural transition between the two states. The tightly packed tetramer of FNV N is similar to the structures of other N proteins of different members of the Bunyavirales order. In its RNA-bound form, the tetramer reorganizes to adopt a more open state that allows the accommodation of the RNA. Despite the low sequence similarity to N proteins of animal-infecting bunyaviruses, there is a striking structural resemblance between FMV N and nucleoproteins from members of the Peribunyaviridae, an animal-infecting family of viruses. This structural homology implies that enveloped plant viruses and animal-infecting viruses might have a common ancestor from which they diverged. IMPORTANCE Most insect-born viruses circulate within the Animalia kingdom, whereas plant-infecting RNA viruses are cross-kingdom pathogens. Many plant-infecting viruses cause devastating crop damage that leads to food security endangerment. The evolutionary crossroads of interkingdom circulation and infection are poorly understood. Thus, we took the structural approach to understand the similarities and differences between interkingdom-infecting viruses and viruses that circulate within one kingdom of life. Using our structures of FMV N in its free form and in complex with a single-stranded RNA (ssRNA), we dissected the mechanism by which FMV N binds to the RNA and revealed the conformational changes associated with the binding. The resemblance of our structure to N proteins from members of the Peribunyaviridae family and their recently published ribonucleoprotein (RNP) pseudoatomic resolution assembly model suggests that the FMV genome is similarly encapsulated. Thus, our finding unveils yet another bridge by which plant- and animal-infecting viruses are interconnected.
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Affiliation(s)
- Lee S. Izhaki-Tavor
- Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Itai G. Yechezkel
- Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Joel Alter
- Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Moshe Dessau
- Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
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Lei Y, Yang F, Yu Z, Xu T, Zhang W, Tian F, Chen X. One-Step Reverse-Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) Assay for the Detection of Canna Yellow Streak Virus. PLANT DISEASE 2023:PDIS04220780RE. [PMID: 36480737 DOI: 10.1094/pdis-04-22-0780-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Canna yellow streak virus (CaYSV) is a potyvirus that causes severe damage to the ornamental plant canna in the United Kingdom and Brazil. Here, we identified CaYSV in China by isolating total RNA from an infected plant, amplifying the virus genome segments, and cloning and sequencing the amplicons. After assembly, the full-length genome of the virus was obtained and uploaded to the NCBI database. Phylogenetic analysis results showed that the Guizhou isolate (OL546222) was most closely related to the KS isolate (MG545919.1). Virus detection is essential for virus disease control but the subclinical infection of CaYSV on canna in its early development increases the difficulty of CaYSV diagnosis. The goal of this study was to develop an efficient method for detection of CaYSV. We designed the primers, optimized the reaction conditions, and finally established a one-step reverse-transcription loop-mediated isothermal amplification (RT-LAMP) method. The product of RT-LAMP can be analyzed by both agarose gel electrophoresis and visible color change. The established one-step RT-LAMP assay showed high specificity and sensitivity in detecting CaYSV. This RT-LAMP method was also applied in analysis of 61 field samples collected from Guizhou and Jiangsu Provinces. The results showed that the infection rates of CaYSV on canna samples from these two provinces were very high (63 and 96% respectively).
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Affiliation(s)
- Yunting Lei
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, P.R. China
| | - Fuhan Yang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, P.R. China
| | - Zhaoyao Yu
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, P.R. China
| | - Tengzhi Xu
- College of Agriculture, Guizhou University, Guiyang 550025, P.R. China
| | - Wene Zhang
- College of Agriculture, Guizhou University, Guiyang 550025, P.R. China
| | - Fenghua Tian
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, P.R. China
| | - Xiangru Chen
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, P.R. China
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Li J, Wu X, Liu H, Wang X, Yi S, Zhong X, Wang Y, Wang Z. Identification and Molecular Characterization of a Novel Carlavirus Infecting Chrysanthemum morifolium in China. Viruses 2023; 15:v15041029. [PMID: 37113009 PMCID: PMC10141686 DOI: 10.3390/v15041029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023] Open
Abstract
Chrysanthemum (Chrysanthemum morifolium) is an important ornamental and medicinal plant suffering from many viruses and viroids worldwide. In this study, a new carlavirus, tentatively named Chinese isolate of Carya illinoinensis carlavirus 1 (CiCV1-CN), was identified from chrysanthemum plants in Zhejiang Province, China. The genome sequence of CiCV1-CN was 8795 nucleotides (nt) in length, with a 68-nt 5'-untranslated region (UTR) and a 76-nt 3'-UTR, which contained six predicted open reading frames (ORFs) that encode six corresponding proteins of various sizes. Phylogenetic analyses based on full-length genome and coat protein sequences revealed that CiCV1-CN is in an evolutionary branch with chrysanthemum virus R (CVR) in the Carlavirus genus. Pairwise sequence identity analysis showed that, except for CiCV1, CiCV1-CN has the highest whole-genome sequence identity of 71.3% to CVR-X6. At the amino acid level, the highest identities of predicted proteins encoded by the ORF1, ORF2, ORF3, ORF4, ORF5, and ORF6 of CiCV1-CN were 77.1% in the CVR-X21 ORF1, 80.3% in the CVR-X13 ORF2, 74.8% in the CVR-X21 ORF3, 60.9% in the CVR-BJ ORF4, 90.2% in the CVR-X6 and CVR-TX ORF5s, and 79.4% in the CVR-X21 ORF6. Furthermore, we also found a transient expression of the cysteine-rich protein (CRP) encoded by the ORF6 of CiCV1-CN in Nicotiana benthamiana plants using a potato virus X-based vector, which can result in a downward leaf curl and hypersensitive cell death over the time course. These results demonstrated that CiCV1-CN is a pathogenic virus and C. morifolium is a natural host of CiCV1.
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Affiliation(s)
- Jiapeng Li
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Xiaoyin Wu
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Hui Liu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xiaomei Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Shaokui Yi
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Xueting Zhong
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhanqi Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
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Xiao J, Zhu K, Ma R, Zhang C, Lv K, Ge D, Liu R. Full genome sequence of a novel iflavirus from the aster leafhopper Macrosteles fascifrons. Virus Genes 2023; 59:338-342. [PMID: 36508145 DOI: 10.1007/s11262-022-01962-0] [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: 11/01/2022] [Accepted: 12/04/2022] [Indexed: 12/14/2022]
Abstract
The aster leafhopper Macrosteles fascifrons is a common insect pest that feeds on rice and other plants and may serve as a vector to transmit various viruses. Here, we discovered a novel virus from M. fascifrons using metagenomic sequencing. We obtained its complete genome sequence by contig assembly and rapid amplification of cDNA ends, and verified the genome sequence by Sanger sequencing of overlapping segments. Based on homology search and phylogenetic analysis, the new virus belongs to the family Iflaviridae and it is tentatively named "Macrosteles fascifrons iflavirus 1" (MfIV1). Excluding the poly(A) tail, the MfIV1 genome is 10,581 nucleotides in length and it is predicted to encode a polyprotein of 3119 amino acids long, which is likely further processed to several polypeptides with conserved domains, including two rhinovirus like (rhv-like) capsid domains, a cricket paralysis virus (CRPV) capsid domain, a helicase domain, and an RNA-dependent RNA polymerase (RdRp) domain. BLAST searches show that the highest amino acid sequence identity between the capsid proteins of MfIV1 and those of other reported iflaviruses is 60.22%, indicating that MfIV1 is a new member in the family Iflaviridae.
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Affiliation(s)
- Jiajing Xiao
- Center for Agroforestry Mega Data Science, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Kai Zhu
- Center for Agroforestry Mega Data Science, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Rui Ma
- Center for Agroforestry Mega Data Science, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chunmin Zhang
- Center for Agroforestry Mega Data Science, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Keliang Lv
- Center for Agroforestry Mega Data Science, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Danfeng Ge
- Center for Agroforestry Mega Data Science, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Renyi Liu
- Center for Agroforestry Mega Data Science, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Wang X, Larrea-Sarmiento A, Olmedo-Velarde A, Al Rwahnih M, Borth W, Suzuki JY, Wall MM, Melzer M, Hu J. Survey of Viruses Infecting Basella alba in Hawaii. PLANT DISEASE 2023; 107:1022-1026. [PMID: 36167515 DOI: 10.1094/pdis-02-22-0449-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Malabar spinach plants (Basella alba, Basellaceae) with leaves exhibiting symptoms of mosaic, rugosity, and malformation were found in a community garden on Oahu, HI in 2018. Preliminary studies using enzyme-linked immunosorbent assay and reverse-transcription (RT)-PCR identified Basella rugose mosaic virus (BaRMV) in symptomatic plants. However, nucleotide sequence analysis of RT-PCR amplicons indicated that additional potyviruses were also present in the symptomatic Malabar spinach. High-throughput sequencing (HTS) analysis was conducted on ribosomal RNA-depleted composite RNA samples of potyvirus-positive plants from three locations. Assembled contigs shared sequences similar to BaRMV, chilli veinal mottle virus (ChiVMV), Alternanthera mosaic virus (AltMV), Basella alba endornavirus (BaEV), broad bean wilt virus 2 (BBWV2), and Iresine viroid 1. Virus- and viroid-specific primers were designed based on HTS sequencing results and used in RT-PCR and Sanger sequencing to confirm the presence of these viruses and the viroid. We tested 63 additional samples from six community gardens for a survey of viruses in Malabar spinach and found that 21 of them were positive for BaRMV, 57 for ChiVMV, 21 for AltMV, 19 for BaEV, and 14 for BBWV2. This is the first characterization of the virome from B. alba.
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Affiliation(s)
- Xupeng Wang
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
| | - Adriana Larrea-Sarmiento
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
| | - Alejandro Olmedo-Velarde
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
| | - Maher Al Rwahnih
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - Wayne Borth
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
| | - Jon Y Suzuki
- United States Department of Agriculture, Agricultural Research Service, Pacific Basin Agricultural Research Center, Hilo, HI 96720
| | - Marisa M Wall
- United States Department of Agriculture, Agricultural Research Service, Pacific Basin Agricultural Research Center, Hilo, HI 96720
| | - Michael Melzer
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
| | - John Hu
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
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Wu Y, Yang M, Yang H, Qiu Y, Xuan Z, Xing F, Cao M. Identification and molecular characterization of a novel cytorhabdovirus from rose plants (Rosa chinensis Jacq.). Arch Virol 2023; 168:118. [PMID: 36952055 DOI: 10.1007/s00705-023-05742-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/06/2023] [Indexed: 03/24/2023]
Abstract
A novel negative-sense single-stranded RNA virus, tentatively named "rose-associated cytorhabdovirus" (RaCV), was identified by high-throughput sequencing. RaCV is 16,067 nucleotides in length and contains eight open reading frames (ORFs 1-8) encoding a nucleocapsid protein (N), a putative phosphoprotein (P), a putative P3 protein (P3), a putative P4 protein (P4), a putative matrix protein (M), a glycoprotein (G), a putative P7 protein (P7), and an RNA-dependent RNA polymerase (L), respectively. The coding genes are flanked by a 3' leader sequence (228 nt) and a 5' trailer sequence (251 nt) and are separated by conserved intergenic junctions (3'-AUUCUUUUUG(N)nCUN-5'). Phylogenetic analysis showed that RaCV clustered with yerba mate virus A (YmVA) within the cytorhabdovirus clade, and it exhibited low a degree of nt sequence similarity (<40% identity) to other rhabdoviruses. Amino acid sequence comparisons between the putative proteins of RaCV and the corresponding proteins of other cytorhabdoviruses showed that the sequence identity levels were far below the species demarcation cutoff of 80% for cytorhabdoviruses. These results suggest that RaCV should be classified as a new member of the genus Cytorhabdovirus.
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Affiliation(s)
- Yujiao Wu
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Mengxue Yang
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Han Yang
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Yuanjian Qiu
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Zhiyou Xuan
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Fei Xing
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Mengji Cao
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China.
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Alcalá Briseño RI, Batuman O, Brawner J, Cuellar WJ, Delaquis E, Etherton BA, French-Monar RD, Kreuze JF, Navarrete I, Ogero K, Plex Sulá AI, Yilmaz S, Garrett KA. Translating virome analyses to support biosecurity, on-farm management, and crop breeding. FRONTIERS IN PLANT SCIENCE 2023; 14:1056603. [PMID: 36998684 PMCID: PMC10043385 DOI: 10.3389/fpls.2023.1056603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/14/2023] [Indexed: 06/19/2023]
Abstract
Virome analysis via high-throughput sequencing (HTS) allows rapid and massive virus identification and diagnoses, expanding our focus from individual samples to the ecological distribution of viruses in agroecological landscapes. Decreases in sequencing costs combined with technological advances, such as automation and robotics, allow for efficient processing and analysis of numerous samples in plant disease clinics, tissue culture laboratories, and breeding programs. There are many opportunities for translating virome analysis to support plant health. For example, virome analysis can be employed in the development of biosecurity strategies and policies, including the implementation of virome risk assessments to support regulation and reduce the movement of infected plant material. A challenge is to identify which new viruses discovered through HTS require regulation and which can be allowed to move in germplasm and trade. On-farm management strategies can incorporate information from high-throughput surveillance, monitoring for new and known viruses across scales, to rapidly identify important agricultural viruses and understand their abundance and spread. Virome indexing programs can be used to generate clean germplasm and seed, crucial for the maintenance of seed system production and health, particularly in vegetatively propagated crops such as roots, tubers, and bananas. Virome analysis in breeding programs can provide insight into virus expression levels by generating relative abundance data, aiding in breeding cultivars resistant, or at least tolerant, to viruses. The integration of network analysis and machine learning techniques can facilitate designing and implementing management strategies, using novel forms of information to provide a scalable, replicable, and practical approach to developing management strategies for viromes. In the long run, these management strategies will be designed by generating sequence databases and building on the foundation of pre-existing knowledge about virus taxonomy, distribution, and host range. In conclusion, virome analysis will support the early adoption and implementation of integrated control strategies, impacting global markets, reducing the risk of introducing novel viruses, and limiting virus spread. The effective translation of virome analysis depends on capacity building to make benefits available globally.
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Affiliation(s)
- Ricardo I. Alcalá Briseño
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
- Global Food Systems Institute, University of Florida, Gainesville, FL, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
- Plant Pathology Department, Oregon State University, Corvallis, OR, United States
| | - Ozgur Batuman
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
- Southwest Florida Research and Education Center (SWFREC), Immokalee, FL, United States
| | - Jeremy Brawner
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
| | - Wilmer J. Cuellar
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Erik Delaquis
- International Center for Tropical Agriculture (CIAT), Vientiane, Laos
| | - Berea A. Etherton
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
- Global Food Systems Institute, University of Florida, Gainesville, FL, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
| | | | - Jan F. Kreuze
- Crop and System Sciences Division, International Potato Center (CIP), Lima, Peru
| | - Israel Navarrete
- Crop and System Sciences Division, International Potato Center (CIP), Quito, Ecuador
| | - Kwame Ogero
- Crop and System Sciences Division, International Potato Center (CIP), Mwanza, Tanzania
| | - Aaron I. Plex Sulá
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
- Global Food Systems Institute, University of Florida, Gainesville, FL, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
| | - Salih Yilmaz
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
- Southwest Florida Research and Education Center (SWFREC), Immokalee, FL, United States
| | - Karen A. Garrett
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
- Global Food Systems Institute, University of Florida, Gainesville, FL, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
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Song X, Cao J, Xie S, Wang Y, Yin X, Guo Y, Xu C, Guo L, Wu H, Zhang M. Molecular characterization of a novel ourmia‑like virus from the phytopathogenic fungus Botryosphaeria dothidea. Arch Virol 2023; 168:106. [PMID: 36899128 DOI: 10.1007/s00705-023-05739-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 02/16/2023] [Indexed: 03/12/2023]
Abstract
Here, we describe a novel ourmia-like virus, Botryosphaeria dothidea ourmia-like virus 2 (BdOLV2), derived from the phytopathogenic fungus Botryosphaeria dothidea strain ZM180192-1 infecting maize in Henan province of China. The complete genome sequence of BdOLV2 consists of a positive-sense single-stranded RNA (+ ssRNA) segment with a length of 2,532 nucleotides (nt). The sequence contains a large open reading frame (ORF) encoding a putative RNA-dependent RNA polymerase (RdRp) consisting of 605 amino acids (aa) with a molecular mass of 68.59 kDa. This RdRp protein contains eight typical conserved motifs associated with ourmia-like viruses. BLASTp analysis revealed that the RdRp protein of BdOLV2 had the highest similarity (62.10%, 58.15%, and 55.75% identity, respectively) to a virus previously identified as "Botourmiaviridae sp.", Macrophomina phaseolina ourmia-like virus 2, and Macrophomina phaseolina ourmia-like virus 2-A. Phylogenetic analysis based on the RdRp aa sequence indicated that BdOLV2 is a new member of the genus Magoulivirus in the family Botourmiaviridae.
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Affiliation(s)
- Xinzheng Song
- College of Plant Protection, Henan Agricultural University, 450002, Zhengzhou, China
| | - Jiayuan Cao
- College of Plant Protection, Henan Agricultural University, 450002, Zhengzhou, China
| | - Shunpei Xie
- College of Plant Protection, Henan Agricultural University, 450002, Zhengzhou, China
| | - Yanfen Wang
- College of Plant Protection, Henan Agricultural University, 450002, Zhengzhou, China
| | - Xinming Yin
- College of Plant Protection, Henan Agricultural University, 450002, Zhengzhou, China
| | - Yashuang Guo
- College of Plant Protection, Henan Agricultural University, 450002, Zhengzhou, China
| | - Chao Xu
- College of Plant Protection, Henan Agricultural University, 450002, Zhengzhou, China
| | - Lihua Guo
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, 100193, Beijing, China
| | - Haiyan Wu
- Analytical Instrument Center, Henan Agricultural University, 450002, Zhengzhou, China.
| | - Meng Zhang
- College of Plant Protection, Henan Agricultural University, 450002, Zhengzhou, China.
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Ranabhat NB, Fellers JP, Bruce MA, Rupp JLS. Brome mosaic virus detected in Kansas wheat co-infected with other common wheat viruses. FRONTIERS IN PLANT SCIENCE 2023; 14:1096249. [PMID: 36938011 PMCID: PMC10022736 DOI: 10.3389/fpls.2023.1096249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Wheat breeders are developing new virus-resistant varieties; however, it is assumed that only a few viruses or well-known viruses are present in the field. New sequencing technology is allowing for better determination of natural field virus populations. For three years, 2019-2021, Kansas wheat field surveys were conducted to determine the constituents of natural field virus populations using nanopore sequencing. During analysis, brome mosaic virus (BMV) was identified for the first time in Kansas but was in association with other wheat viruses. Brome mosaic virus was identified from 29 out of 47 different Kansas counties sampled and 44% of the total samples. BMV was found co-infected with wheat streak mosaic virus (WSMV) and Triticum mosaic virus (TriMV) in 27.8% of the samples, with WSMV only (13.9%) and co-infected with WSMV + TriMV + High Plains wheat mosaic emaravirus (HPWMoV) (13.9%). RNA genomes of Kansas BMV isolates had 99.4 to 100% nucleotide and amino acid sequence identity, respectively, to each other. RNA2a possessed relatively high divergence (π = 0.01) compared to RNA1a and RNA3a (π = 0.004). Coding regions of all BMV RNAs were considered negative for purifying selection pressure as nonsynonymous and synonymous nucleotide ratio was less than one (dNs/dS >1). The identification of BMV in Kansas virus populations adds another layer of complexity to plant breeding. This work provides information to improve tools to aid in monitoring, detecting, and determining the variation within BMV.
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Affiliation(s)
- Nar B. Ranabhat
- Department of Plant Pathology, Throckmorton Plant Science Center, Kansas State University, Manhattan, KS, United States
| | - John P. Fellers
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, United States
| | - Myron A. Bruce
- Department of Plant Pathology, Throckmorton Plant Science Center, Kansas State University, Manhattan, KS, United States
| | - Jessica L. Shoup Rupp
- Department of Plant Pathology, Throckmorton Plant Science Center, Kansas State University, Manhattan, KS, United States
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Reinhold LA, Pscheidt JW. Diagnostic and Historical Surveys of Sweet Cherry ( Prunus avium) Virus and Virus-Like Diseases in Oregon. PLANT DISEASE 2023; 107:633-643. [PMID: 36018551 DOI: 10.1094/pdis-02-21-0327-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
There are over 35 known virus and virus-like diseases of sweet cherry (Prunus avium), some with potential to cause severe economic impact by reducing vegetative growth, vigor, or fruit quality. Oregon is the second-ranked state for sweet cherry production in the United States. Statewide surveys were conducted in Oregon sweet cherry orchards for virus and virus-like diversity and distribution. Orchards in key production regions with suspected virus disease symptoms were sampled. Virus-specific enzyme-linked immunosorbent assay, isothermal amplification, or quantitative real-time PCR were used to test for the presence of common or economically important sweet cherry pathogens, including cherry leaf roll virus (CLRV), little cherry virus 2 (LChV2), prune dwarf virus (PDV), prunus necrotic ringspot virus (PNRSV), tomato ringspot virus (ToRSV), and 'Candidatus Phytoplasma pruni'. CLRV, a new virus of sweet cherry in Oregon, was found associated with enation and dieback symptoms in The Dalles. Some viruses were found in new regions, which included Hood River (PDV, PNRSV, and ToRSV) and the Umpqua Valley (PDV and PNRSV). A subsequent survey was conducted in the Mid-Columbia production region for the presence of little cherry symptoms associated with little cherry and X-Diseases. All symptomatic samples from The Dalles and Mosier, OR, or Dallesport, WA, tested positive for 'Ca. P. pruni' but not LChV2. These findings provide a foundation for the current understanding and management of virus and virus-like diseases of sweet cherry in Oregon and context for further studies into these pathogens and their vectors.
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Affiliation(s)
- Lauri A Reinhold
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Jay W Pscheidt
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
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Morán F, Olmos A, Glasa M, Silva MBD, Maliogka V, Wetzel T, Ruiz-García AB. A Novel and Highly Inclusive Quantitative Real-Time RT-PCR Method for the Broad and Efficient Detection of Grapevine Leafroll-Associated Virus 1. PLANTS (BASEL, SWITZERLAND) 2023; 12:876. [PMID: 36840223 PMCID: PMC9962094 DOI: 10.3390/plants12040876] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/20/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Grapevine (Vitis vinifera L.) is one of the most important crops in the world due to its economic and social impact. Like many other crops, grapevine is susceptible to different types of diseases caused by pathogenic microorganisms. Grapevine leafroll-associated virus 1 (GLRaV-1) is a virus associated with grapevine leafroll disease and it is considered at the national and European level as a pathogen that must be absent in propagative plant material. For this reason, the availability of specific, sensitive and reliable detection techniques to ascertain the sanitary status of the plants is of great importance. The objective of this research was the development of a new GLRaV-1 detection method based on a TaqMan quantitative real-time RT-PCR targeted to the coat protein genomic region and including a host internal control in a duplex reaction. To this end, three new GLRaV-1 full genomes were recovered by HTS and aligned with all sequences available in the databases. The method has been validated following EPPO standards and applied for the diagnosis of field plant material and transmission vectors. The new protocol designed has turned out to be highly sensitive as well as much more specific than the current available methods for the detection and absolute quantitation of GLRaV-1 viral titer.
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Affiliation(s)
- Félix Morán
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, Moncada, 46113 Valencia, Spain
| | - Antonio Olmos
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, Moncada, 46113 Valencia, Spain
| | - Miroslav Glasa
- Biomedical Research Center of the Slovak Academy of Sciences, Institute of Virology, Dúbravská Cesta 9, 84505 Bratislava, Slovakia
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Nám. J. Herdu 2, 91701 Trnava, Slovakia
| | - Marilia Bueno Da Silva
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, Moncada, 46113 Valencia, Spain
| | - Varvara Maliogka
- Plant Pathology Laboratory, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Thierry Wetzel
- DLR Rheinpfalz, Institute of Plant Protection, Breitenweg, 71, 67435 Neustadt an der Weinstrasse, Germany
| | - Ana Belén Ruiz-García
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, Moncada, 46113 Valencia, Spain
- Departamento de Microbiología y Ecología, C/Doctor Moliner 50, Burjasot, 46100 Valencia, Spain
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Special Issue: "Evolution, Ecology and Diversity of Plant Virus". Viruses 2023; 15:v15020487. [PMID: 36851700 PMCID: PMC9962861 DOI: 10.3390/v15020487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
The next-generation sequencing method was developed in the second half of the 2000s and marked the beginning of high-throughput sequencing (HTS) analyses of viral communities [...].
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Tatineni S, Hein GL. Plant Viruses of Agricultural Importance: Current and Future Perspectives of Virus Disease Management Strategies. PHYTOPATHOLOGY 2023; 113:117-141. [PMID: 36095333 DOI: 10.1094/phyto-05-22-0167-rvw] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Plant viruses cause significant losses in agricultural crops worldwide, affecting the yield and quality of agricultural products. The emergence of novel viruses or variants through genetic evolution and spillover from reservoir host species, changes in agricultural practices, mixed infections with disease synergism, and impacts from global warming pose continuous challenges for the management of epidemics resulting from emerging plant virus diseases. This review describes some of the most devastating virus diseases plus select virus diseases with regional importance in agriculturally important crops that have caused significant yield losses. The lack of curative measures for plant virus infections prompts the use of risk-reducing measures for managing plant virus diseases. These measures include exclusion, avoidance, and eradication techniques, along with vector management practices. The use of sensitive, high throughput, and user-friendly diagnostic methods is crucial for defining preventive and management strategies against plant viruses. The advent of next-generation sequencing technologies has great potential for detecting unknown viruses in quarantine samples. The deployment of genetic resistance in crop plants is an effective and desirable method of managing virus diseases. Several dominant and recessive resistance genes have been used to manage virus diseases in crops. Recently, RNA-based technologies such as dsRNA- and siRNA-based RNA interference, microRNA, and CRISPR/Cas9 provide transgenic and nontransgenic approaches for developing virus-resistant crop plants. Importantly, the topical application of dsRNA, hairpin RNA, and artificial microRNA and trans-active siRNA molecules on plants has the potential to develop GMO-free virus disease management methods. However, the long-term efficacy and acceptance of these new technologies, especially transgenic methods, remain to be established.
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Affiliation(s)
- Satyanarayana Tatineni
- U.S. Department of Agriculture-Agricultural Research Service and Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583
| | - Gary L Hein
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583
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Verhoeven A, Kloth KJ, Kupczok A, Oymans GH, Damen J, Rijnsburger K, Jiang Z, Deelen C, Sasidharan R, van Zanten M, van der Vlugt RAA. Arabidopsis latent virus 1, a comovirus widely spread in Arabidopsis thaliana collections. THE NEW PHYTOLOGIST 2023; 237:1146-1153. [PMID: 36073550 PMCID: PMC10087574 DOI: 10.1111/nph.18466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
Transcriptome studies of Illumina RNA-Seq datasets of different Arabidopsis thaliana natural accessions and T-DNA mutants revealed the presence of two virus-like RNA sequences which showed the typical two-segmented genome characteristics of a comovirus. This comovirus did not induce any visible symptoms in infected A. thaliana plants cultivated under standard laboratory conditions. Hence it was named Arabidopsis latent virus 1 (ArLV1). Virus infectivity in A. thaliana plants was confirmed by quantitative reverse transcription polymerase chain reaction, transmission electron microscopy and mechanical inoculation. Arabidopsis latent virus 1 can also mechanically infect Nicotiana benthamiana, causing distinct mosaic symptoms. A bioinformatics investigation of A. thaliana RNA-Seq repositories, including nearly 6500 Sequence Read Archives (SRAs) in the NCBI SRA database, revealed the presence of ArLV1 in 25% of all archived natural A. thaliana accessions and in 8.5% of all analyzed SRAs. Arabidopsis latent virus 1 could also be detected in A. thaliana plants collected from the wild. Arabidopsis latent virus 1 is highly seed-transmissible with up to 40% incidence on the progeny derived from infected A. thaliana plants. This has probably led to a worldwide distribution in the model plant A. thaliana with as yet unknown effects on plant performance in a substantial number of studies.
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Affiliation(s)
- Ava Verhoeven
- Laboratory of VirologyWageningen University and ResearchDroevendaalsesteeg 16708PBWageningenthe Netherlands
- Plant‐Environment SignalingUtrecht UniversityPadualaan 83584 CHUtrechtthe Netherlands
- Plant Stress ResilienceUtrecht UniversityPadualaan 83584 CHUtrechtthe Netherlands
| | - Karen J. Kloth
- Laboratory of EntomologyWageningen University and ResearchDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Anne Kupczok
- Bioinformatics GroupWageningen University and ResearchDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Geert H. Oymans
- Laboratory of VirologyWageningen University and ResearchDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Janna Damen
- Laboratory of VirologyWageningen University and ResearchDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Karin Rijnsburger
- Laboratory of VirologyWageningen University and ResearchDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Zhang Jiang
- Plant‐Environment SignalingUtrecht UniversityPadualaan 83584 CHUtrechtthe Netherlands
- Plant Stress ResilienceUtrecht UniversityPadualaan 83584 CHUtrechtthe Netherlands
| | - Cas Deelen
- Plant‐Environment SignalingUtrecht UniversityPadualaan 83584 CHUtrechtthe Netherlands
| | - Rashmi Sasidharan
- Plant‐Environment SignalingUtrecht UniversityPadualaan 83584 CHUtrechtthe Netherlands
- Plant Stress ResilienceUtrecht UniversityPadualaan 83584 CHUtrechtthe Netherlands
| | - Martijn van Zanten
- Plant Stress ResilienceUtrecht UniversityPadualaan 83584 CHUtrechtthe Netherlands
- Molecular Plant PhysiologyUtrecht UniversityPadualaan 83584 CHUtrechtthe Netherlands
| | - René A. A. van der Vlugt
- Laboratory of VirologyWageningen University and ResearchDroevendaalsesteeg 16708PBWageningenthe Netherlands
- Biointeractions and Plant HealthWageningen Plant ResearchDroevendaalsesteeg 16708PBWageningenthe Netherlands
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Padmanabhan C, Nunziata S, Leon M. G, Rivera Y, Mavrodieva VA, Nakhla MK, Roy A. High-throughput sequencing application in the detection and discovery of viruses associated with the regulated citrus leprosis disease complex. FRONTIERS IN PLANT SCIENCE 2023; 13:1058847. [PMID: 36762187 PMCID: PMC9907091 DOI: 10.3389/fpls.2022.1058847] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/24/2022] [Indexed: 06/18/2023]
Abstract
Citrus leprosis (CiL) is one of the destructive emerging viral diseases of citrus in the Americas. Leprosis syndrome is associated with two taxonomically distinct groups of Brevipalpus-transmitted viruses (BTVs), that consist of positive-sense Cilevirus, Higrevirus, and negative-sense Dichorhavirus. The localized CiL symptoms observed in multiple citrus species and other alternate hosts indicates that these viruses might have originated from the mites and eventually adopted citrus as a secondary host. Genetic diversity in the genomes of viruses associated with the CiL disease complex have complicated current detection and diagnostic measures that prompted the application of High-Throughput Sequencing (HTS) protocols for improved detection and diagnosis. Two cileviruses are known to infect citrus, and among them only citrus leprosis virus C2 (CiLV-C2) hibiscus strain (CiLV-C2H) has been reported in hibiscus and passion fruit in the US. Based on our current CiL disease complex hypothesis, there is a high probability that CiL disease is associated with more viruses/strains that have not yet been identified but exist in nature. To protect the citrus industry, a Ribo-Zero HTS protocol was utilized for detection of cileviruses infecting three different hosts: Citrus spp., Swinglea glutinosa, and Hibiscus rosa-sinensis. Real-time RT-PCR assays were used to identify plants infected with CiLV-C2 or CiLV-C2H or both in mixed infection in all the above-mentioned plant genera. These results were further confirmed by bioinformatic analysis using HTS generated data. In this study, we utilized HTS assay in confirmatory diagnostics to screen BTVs infecting Dieffenbachia sp. (family: Araceae), Passiflora edulis (Passifloraceae), and Smilax auriculata (Smilacaceae). Through the implementation of HTS and downstream data analysis, we detected not only the known cileviruses in the studied hosts but also discovered a new strain of CiLV-C2 in hibiscus from Colombia. Phylogenetically, the new hibiscus strain is more closely related to CiLV-C2 than the known hibiscus strain, CiLV-C2H. We propose this strain to be named as CiLV-C2 hibiscus strain 2 (CiLV-C2H2). The findings from the study are critical for citrus growers, industry, regulators, and researchers. The possible movement of CiLV-C2H2 from hibiscus to citrus by the Brevipalpus spp. warrants further investigation.
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Affiliation(s)
- Chellappan Padmanabhan
- United States Department of Agriculture (USDA), Animal Plant Health Inspection Service, Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, MD, United States
| | - Schyler Nunziata
- United States Department of Agriculture (USDA), Animal Plant Health Inspection Service, Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, MD, United States
| | | | - Yazmín Rivera
- United States Department of Agriculture (USDA), Animal Plant Health Inspection Service, Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, MD, United States
| | - Vessela A. Mavrodieva
- United States Department of Agriculture (USDA), Animal Plant Health Inspection Service, Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, MD, United States
| | - Mark K. Nakhla
- United States Department of Agriculture (USDA), Animal Plant Health Inspection Service, Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, MD, United States
| | - Avijit Roy
- United States Department of Agriculture (USDA), Animal Plant Health Inspection Service, Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, MD, United States
- United States Department of Agriculture (USDA), Agricultural Research Service, Molecular Plant Pathology Laboratory, Beltsville Agricultural Research Center, Beltsville, MD, United States
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Discovery of a Closterovirus Infecting Jujube Plants Grown at Aksu Area in Xinjiang of China. Viruses 2023; 15:v15020267. [PMID: 36851483 PMCID: PMC9958854 DOI: 10.3390/v15020267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/05/2023] [Accepted: 01/15/2023] [Indexed: 01/19/2023] Open
Abstract
Chinese jujube (Ziziphus jujuba Mill.) is a widely grown fruit crop at Aksu in Xinjiang Uygur Autonomous Region of China. Viral disease-like symptoms are common on jujube plants. Here, for the first time, we report a virus tentatively named persimmon ampelovirus jujube isolate (PAmpV-Ju) infecting jujube plants. The virus was identified using high-throughput sequencing from a jujube plant (ID: AKS15) and molecularly related to viruses in the family Closteroviridae. The genomic sequences of two PAmpV-Ju variants named AKS15-20 and AKS15-17 were determined by RT-PCR amplifications. The genome structure of PAmpV-Ju was identical to that of a recently reported persimmon ampelovirus (PAmpV) and consisted of seven open reading frames. The genomes of AKS15-20 and AKS15-17 shared 83.7% nt identity with each other, and the highest nt sequence identity of 79% with two variants of PAmpV. The incidence of PAmpV-Ju on Aksu jujube plants was evaluated by RT-PCR assays. The phylogenetic analysis of amplified partial sequences coding for polymerase, HSP70h, and CP revealed two phylogenetic clades represented by AKS15-20 and AKS15-17. Our study provides important evidence for understanding viruses infecting jujube plants and establishing efficient measures to prevent virus spread.
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Villamor DEV, Mejia AS, Martin RR, Tzanetakis IE. Genomic Analysis and Development of Infectious Clone of a Novel Carlavirus Infecting Blueberry. PHYTOPATHOLOGY 2023; 113:98-103. [PMID: 35852469 DOI: 10.1094/phyto-05-22-0186-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A new blueberry virus was discovered using high-throughput sequencing. Using sequence identity values, phylogenetics, and serological and biological properties, we propose the virus, putatively named blueberry virus S (BluVS), to be a distinct species within the genus Carlavirus (family Betaflexiviridae). The genome was analyzed in depth, and an infectious clone was developed to initiate studies on virus pathogenicity. Agroinfiltration of the binary vector construct produced severe systemic symptoms in Nicotiana occidentalis. Back-inoculation using sap from agroinfiltrated N. occidentalis produced identical symptoms to the recipient plants (N. occidentalis), and virus purification yielded flexuous carlavirus-like particles. However, unlike blueberry scorch virus (BlScV), BluVS caused symptomless infection in Chenopodium quinoa and reacted weakly to BlScV antibodies in an enzyme-linked immunosorbent assay. Collectively, the results provide evidence for the distinct speciation of BluVS. The availability of an infectious clone provides tools for future studies on the biology of the virus.
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Affiliation(s)
- D E V Villamor
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - A Sierra Mejia
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - R R Martin
- Oregon State University and U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330
| | - I E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
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