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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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Du X, Zhan X, Gu X, Liu X, Mao B. Evaluation of Virus-Free Chrysanthemum 'Hangju' Productivity and Response to Virus Reinfection in the Field: Molecular Insights into Virus-Host Interactions. PLANTS (BASEL, SWITZERLAND) 2024; 13:732. [PMID: 38475578 DOI: 10.3390/plants13050732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/01/2024] [Accepted: 03/03/2024] [Indexed: 03/14/2024]
Abstract
The shoot apical meristem culture has been used widely to produce virus-free plantlets which have the advantages of strong disease resistance, high yield, and prosperous growth potential. However, this virus-free plant will be naturally reinfected in the field. The physiological and metabolic responses in the reinfected plant are still unknown. The flower of chrysanthemum 'Hangju' is a traditional medicine which is unique to China. In this study, we found that the virus-free 'Hangju' (VFH) was reinfected with chrysanthemum virus B/R in the field. However, the reinfected VFH (RVFH) exhibited an increased yield and medicinal components compared with virus-infected 'Hangju' (VIH). Comparative analysis of transcriptomes was performed to explore the molecular response mechanisms of the RVFH to CVB infection. A total of 6223 differentially expressed genes (DEGs) were identified in the RVFH vs. the VIH. KEGG enrichment and physiological analyses indicated that treatment with the virus-free technology significantly mitigated the plants' lipid and galactose metabolic stress responses in the RVFH. Furthermore, GO enrichment showed that plant viral diseases affected salicylic acid (SA)-related processes in the RVFH. Specifically, we found that phenylalanine ammonia-lyase (PAL) genes played a major role in defense-related SA biosynthesis in 'Hangju'. These findings provided new insights into the molecular mechanisms underlying plant virus-host interactions and have implications for developing strategies to improve plant resistance against viruses.
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Affiliation(s)
- Xuejie Du
- Institute of Biotechnology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Xinqiao Zhan
- School of Pharmaceutical Sciences, Taizhou University, Taizhou 318000, China
| | - Xueting Gu
- Institute of Biotechnology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
- Zhejiang Tongxiang Hangbaiju Technology Academy, Tongxiang 314500, China
| | - Xinyi Liu
- Institute of Biotechnology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
- Zhejiang Tongxiang Hangbaiju Technology Academy, Tongxiang 314500, China
| | - Bizeng Mao
- Institute of Biotechnology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
- Zhejiang Tongxiang Hangbaiju Technology Academy, Tongxiang 314500, China
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Gao K, Chen Q, Pan B, Sun Y, Xu Y, Chen D, Liu H, Luo C, Chen X, Li H, Huang C. Current Achievements and Future Prospects in Virus Elimination Technology for Functional Chrysanthemum. Viruses 2023; 15:1770. [PMID: 37632112 PMCID: PMC10459880 DOI: 10.3390/v15081770] [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: 07/24/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Chrysanthemum is an important functional plant that is used for food, medicine and tea. Functional chrysanthemums become infected with viruses all around the world, seriously lowering their quality and yield. Viral infection has become an important limiting factor in chrysanthemum production. Functional chrysanthemum is often propagated asexually by cutting during production, and viral infection of seedlings is becoming increasingly serious. Chrysanthemums can be infected by a variety of viruses causing different symptoms. With the development of biotechnology, virus detection and virus-free technologies for chrysanthemum seedlings are becoming increasingly effective. In this study, the common virus species, virus detection methods and virus-free technology of chrysanthemum infection are reviewed to provide a theoretical basis for virus prevention, treatment and elimination in functional chrysanthemum.
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Affiliation(s)
- Kang Gao
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (K.G.); (D.C.); (H.L.); (C.L.); (X.C.)
| | - Qingbing Chen
- College of Architecture, North China University of Water Resources and Electric Power, Zhengzhou 450046, China; (Q.C.); (B.P.); (Y.S.); (Y.X.)
| | - Bo Pan
- College of Architecture, North China University of Water Resources and Electric Power, Zhengzhou 450046, China; (Q.C.); (B.P.); (Y.S.); (Y.X.)
| | - Yahui Sun
- College of Architecture, North China University of Water Resources and Electric Power, Zhengzhou 450046, China; (Q.C.); (B.P.); (Y.S.); (Y.X.)
| | - Yuran Xu
- College of Architecture, North China University of Water Resources and Electric Power, Zhengzhou 450046, China; (Q.C.); (B.P.); (Y.S.); (Y.X.)
| | - Dongliang Chen
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (K.G.); (D.C.); (H.L.); (C.L.); (X.C.)
| | - Hua Liu
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (K.G.); (D.C.); (H.L.); (C.L.); (X.C.)
| | - Chang Luo
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (K.G.); (D.C.); (H.L.); (C.L.); (X.C.)
| | - Xi Chen
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (K.G.); (D.C.); (H.L.); (C.L.); (X.C.)
| | - Haiying Li
- College of Architecture, North China University of Water Resources and Electric Power, Zhengzhou 450046, China; (Q.C.); (B.P.); (Y.S.); (Y.X.)
| | - Conglin Huang
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (K.G.); (D.C.); (H.L.); (C.L.); (X.C.)
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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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Costa LC, Atha B, Hu X, Lamour K, Yang Y, O’Connell M, McFarland C, Foster JA, Hurtado-Gonzales OP. High-throughput detection of a large set of viruses and viroids of pome and stone fruit trees by multiplex PCR-based amplicon sequencing. FRONTIERS IN PLANT SCIENCE 2022; 13:1072768. [PMID: 36578329 PMCID: PMC9791224 DOI: 10.3389/fpls.2022.1072768] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
A comprehensive diagnostic method of known plant viruses and viroids is necessary to provide an accurate phytosanitary status of fruit trees. However, most widely used detection methods have a small limit on either the number of targeted viruses/viroids or the number of samples to be evaluated at a time, hampering the ability to rapidly scale up the test capacity. Here we report that by combining the power of high multiplexing PCR (499 primer pairs) of small amplicons (120-135bp), targeting 27 viruses and 7 viroids of fruit trees, followed by a single high-throughput sequencing (HTS) run, we accurately diagnosed the viruses and viroids on as many as 123 pome and stone fruit tree samples. We compared the accuracy, sensitivity, and reproducibility of this approach and contrast it with other detection methods including HTS of total RNA (RNA-Seq) and individual RT-qPCR for every fruit tree virus or viroid under the study. We argue that this robust and high-throughput cost-effective diagnostic tool will enhance the viral/viroid knowledge of fruit trees while increasing the capacity for large scale diagnostics. This approach can also be adopted for the detection of multiple viruses and viroids in other crops.
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Affiliation(s)
- Larissa Carvalho Costa
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Benjamin Atha
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Xiaojun Hu
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, United States
| | - Yu Yang
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Mary O’Connell
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Clint McFarland
- Plant Protection and Quarantine - Field Operations, Animal and Plant Health Inspection Service, United States Department of Agriculture, Raleigh, NC, United States
| | - Joseph A. Foster
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Oscar P. Hurtado-Gonzales
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
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Zhong X, Yang L, Li J, Tang Z, Wu C, Zhang L, Zhou X, Wang Y, Wang Z. Integrated next-generation sequencing and comparative transcriptomic analysis of leaves provides novel insights into the ethylene pathway of Chrysanthemum morifolium in response to a Chinese isolate of chrysanthemum virus B. Virol J 2022; 19:182. [DOI: 10.1186/s12985-022-01890-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 09/26/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Chrysanthemum virus B (CVB), a key member of the genus Carlavirus, family Betaflexiviridae, causes severe viral diseases in chrysanthemum (Chrysanthemum morifolium) plants worldwide. However, information on the mechanisms underlying the response of chrysanthemum plants to CVB is scant.
Methods
Here, an integrated next-generation sequencing and comparative transcriptomic analysis of chrysanthemum leaves was conducted to explore the molecular response mechanisms of plants to a Chinese isolate of CVB (CVB-CN) at the molecular level.
Results
In total, 4934 significant differentially expressed genes (SDEGs) were identified to respond to CVB-CN, of which 4097 were upregulated and 837 were downregulated. Gene ontology and functional classification showed that the majority of upregulated SDEGs were categorized into gene cohorts involved in plant hormone signal transduction, phenylpropanoid and flavonoid biosynthesis, and ribosome metabolism. Enrichment analysis demonstrated that ethylene pathway-related genes were significantly upregulated following CVB-CN infection, indicating a strong promotion of ethylene biosynthesis and signaling. Furthermore, disruption of the ethylene pathway in Nicotiana benthamiana, a model plant, using virus-induced gene silencing technology rendered them more susceptible to cysteine-rich protein of CVB-CN induced hypersensitive response, suggesting a crucial role of this pathway in response to CVB-CN infection.
Conclusion
This study provides evidence that ethylene pathway has an essential role of plant in response to CVB and offers valuable insights into the defense mechanisms of chrysanthemum against Carlavirus.
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Chavhan R, Sable S, Narwade A, Hinge V, Kalbande B, Mukherjee A, Chakrabarty P, Kadam US. Multiplex molecular marker-assisted analysis of significant pathogens of cotton (Gossypium sp.). BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Rashid S, Wani F, Ali G, Sofi TA, Dar ZA, Hamid A. Viral metatranscriptomic approach to study the diversity of virus(es) associated with Common Bean (Phaseolus vulgaris L.) in the North-Western Himalayan region of India. Front Microbiol 2022; 13:943382. [PMID: 36212886 PMCID: PMC9532741 DOI: 10.3389/fmicb.2022.943382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Plant viruses are a major threat to legume production worldwide. In recent years, new virus strains have emerged with increasing frequencies in various legume cropping systems, which demands the development of cutting-edge virus surveillance techniques. In this study, we surveyed the common bean fields of Kashmir valley for virus infection using a total of 140 symptomatic and non-symptomatic leaf samples collected from different locations. The genetic diversity of viruses was examined by high-throughput sequencing (HTS) with three viruses being identified, namely, Bean Common Mosaic Virus (BCMV), Bean Common Mosaic Necrosis Virus (BCMNV), and Clover Yellow Vein Virus (ClYVV). BCMNV and ClYVV are new reports from India. De novo assembly of transcriptome constructed near-complete genomes of these viruses. RT-PCR results confirmed the presence of these viruses with an emerge incidence of 56. 4% for BCMV, 27.1% for BCMNV and 16.4 for ClYVV in the valley. Several samples were found to contain multiple virus infections with BCMV being the most predominant. Recombination events were detected in the genomes of BCMV and ClYVV, but not BCMNV. Phylogenetic and pairwise identity matrix evidence suggests viral import from multiple countries. Our results demonstrate that HTS followed by multiplex PCR assay is a simple, rapid, and reliable approach for simultaneous diagnosis of plant viruses.
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Affiliation(s)
- Shahjahan Rashid
- Department of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Srinagar, India
| | - Farhana Wani
- Department of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Srinagar, India
| | - Gowhar Ali
- Department of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Srinagar, India
| | - Tariq A. Sofi
- Department of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Srinagar, India
| | - Zahoor Ahmed Dar
- Department of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Srinagar, India
| | - Aflaq Hamid
- Department of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Srinagar, India
- *Correspondence: Aflaq Hamid
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Ye J, Song J, Gao Y, Lu X, Pei W, Li F, Feng H, Yang W. An automatic fluorescence phenotyping platform to evaluate dynamic infection process of Tobacco mosaic virus-green fluorescent protein in tobacco leaves. FRONTIERS IN PLANT SCIENCE 2022; 13:968855. [PMID: 36119566 PMCID: PMC9478445 DOI: 10.3389/fpls.2022.968855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
Tobacco is one of the important economic crops all over the world. Tobacco mosaic virus (TMV) seriously affects the yield and quality of tobacco leaves. The expression of TMV in tobacco leaves can be analyzed by detecting green fluorescence-related traits after inoculation with the infectious clone of TMV-GFP (Tobacco mosaic virus - green fluorescent protein). However, traditional methods for detecting TMV-GFP are time-consuming and laborious, and mostly require a lot of manual procedures. In this study, we develop a low-cost machine-vision-based phenotyping platform for the automatic evaluation of fluorescence-related traits in tobacco leaf based on digital camera and image processing. A dynamic monitoring experiment lasting 7 days was conducted to evaluate the efficiency of this platform using Nicotiana tabacum L. with a total of 14 samples, including the wild-type strain SR1 and 4 mutant lines generated by RNA interference technology. As a result, we found that green fluorescence area and brightness generally showed an increasing trend over time, and the trends were different among these SR1 and 4 mutant lines samples, where the maximum and minimum of green fluorescence area and brightness were mutant-4 and mutant-1 respectively. In conclusion, the platform can full-automatically extract fluorescence-related traits with the advantage of low-cost and high accuracy, which could be used in detecting dynamic changes of TMV-GFP in tobacco leaves.
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Affiliation(s)
- Junli Ye
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jingyan Song
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yuan Gao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xu Lu
- Key Laboratory of Horticulture Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - Wenyue Pei
- Key Laboratory of Horticulture Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Feng Li
- Key Laboratory of Horticulture Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Hui Feng
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
| | - Wanneng Yang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
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Tobacco Mosaic Virus Infection of Chrysanthemums in Thailand: Development of Colorimetric Reverse-Transcription Loop-Mediated Isothermal Amplification (RT–LAMP) Technique for Sensitive and Rapid Detection. PLANTS 2022; 11:plants11141788. [PMID: 35890422 PMCID: PMC9325109 DOI: 10.3390/plants11141788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 11/23/2022]
Abstract
We detected tobacco mosaic virus (TMV), a member of the genus Tobamovirus and one of the most significant plant-infecting viruses, for the first time in a chrysanthemum in Thailand using reverse-transcription polymerase chain reaction (RT–PCR). The TMV-infected chrysanthemum leaves exhibited mosaic symptoms. We conducted a sequence analysis of the coat protein (CP) gene and found that the TMV detected in the chrysanthemum had 98% identity with other TMV isolates in GenBank. We carried out bioassays and showed that TMV induced mosaic and stunting symptoms in inoculated chrysanthemums. We observed the rigid rod structure of TMV under a transmission electron microscope (TEM). To enhance the speed and sensitivity of detection, we developed a colorimetric RT loop-mediated isothermal amplification (LAMP) technique. We achieved LAMP detection after 30 min incubation in isothermal conditions at 65 °C, and distinguished the positive results according to the color change from pink to yellow. The sensitivity of the LAMP technique was 1000-fold greater than that of RT–PCR, and we found no cross-reactivity with other viruses or viroids. This is the first reported case of a TMV-infected chrysanthemum in Thailand, and our colorimetric RT–LAMP TMV detection method is the first of its kind.
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Miljanić V, Jakše J, Rusjan D, Škvarč A, Štajner N. Small RNA Sequencing and Multiplex RT-PCR for Diagnostics of Grapevine Viruses and Virus-Like Organisms. Viruses 2022; 14:v14050921. [PMID: 35632662 PMCID: PMC9145883 DOI: 10.3390/v14050921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 12/18/2022] Open
Abstract
Metagenomic approaches used for virus diagnostics allow for rapid and accurate detection of all viral pathogens in the plants. In order to investigate the occurrence of viruses and virus-like organisms infecting grapevine from the Ampelographic collection Kromberk in Slovenia, we used Ion Torrent small RNA sequencing (sRNA-seq) and the VirusDetect pipeline to analyze the sRNA-seq data. The used method revealed the presence of: Grapevine leafroll-associated virus 1 (GLRaV-1), Grapevine leafroll-associated virus 2 (GLRaV-2), Grapevine leafroll-associated virus 3 (GLRaV-3), Grapevine rupestris stem pitting-associated virus (GRSPaV), Grapevine fanleaf virus (GFLV) and its satellite RNA (satGFLV), Grapevine fleck virus (GFkV), Grapevine rupestris vein feathering virus (GRVFV), Grapevine Pinot gris virus (GPGV), Grapevine satellite virus (GV-Sat), Hop stunt viroid (HSVd), and Grapevine yellow speckle viroid 1 (GYSVd-1). Multiplex reverse transcription-polymerase chain reaction (mRT-PCR) was developed for validation of sRNA-seq predicted infections, including various combinations of viruses or viroids and satellite RNA. mRT-PCR could further be used for rapid and cost-effective routine molecular diagnosis, including widespread, emerging, and seemingly rare viruses, as well as viroids which testing is usually overlooked.
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Affiliation(s)
- Vanja Miljanić
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Denis Rusjan
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Andreja Škvarč
- Chamber of Agriculture and Forestry of Slovenia, Agriculture and Forestry Institute Nova Gorica, 5000 Nova Gorica, Slovenia
| | - Nataša Štajner
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
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Abstract
Amplification of different nucleic acid targets in the same reaction (multiplex polymerase chain reaction) is challenging but an extremely useful tool especially for viroid diagnosis. In the amplification mixtures, several pairs of primers work together in the same conditions to detect different targets. Here, we describe the development and use of a multiplex reverse transcription polymerase chain reaction protocol highlighting the most crucial factors that can significantly affect the quality of the method. First, particular attention must be paid to primer design. Then, the amplification mixture and temperature conditions must be calibrated precisely to avoid cross reactivity or loss in sensitivity. Finally, the detection system of the amplification results must allow a specific identification of the amplified target(s).
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Affiliation(s)
- Francesco Faggioli
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'Economia agraria (CREA)-Centro di Ricerca Difesa e Certificazione (CREA-DC), Rome, Italy.
| | - Marta Luigi
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'Economia agraria (CREA)-Centro di Ricerca Difesa e Certificazione (CREA-DC), Rome, Italy
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13
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Yan K, Du X, Mao B. Production of Virus-Free Chrysanthemum (Chrysanthemum morifolium Ramat) by Tissue Culture Techniques. Methods Mol Biol 2022; 2400:171-186. [PMID: 34905201 DOI: 10.1007/978-1-0716-1835-6_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Almost all plants in their natural environment are commonly infected by viruses. These viral infections can cause devastating diseases and result in severe yield and economic losses, making viral diseases an important limiting factor for agricultural production and sustainable development. However, these losses can be effectively reduced through the productions and applications of virus-free plantlets. In vitro culture techniques are the most successful approaches for efficient eradication of various viruses from almost all the most economically important crops. Techniques for producing virus-free plantlets include meristem tip culture, somatic embryogenesis, chemotherapy, thermotherapy, electrotherapy, shoot tip cryotherapy, and micrografting. Among them, meristem tip culture is currently the most widely used. Here, we describe a detailed protocol for producing virus-free plantlets of Chrysanthemum morifolium Ramat using tissue culture techniques.
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Affiliation(s)
- Keru Yan
- Institute of Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Hangzhou, China
| | - Xuejie Du
- Institute of Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Hangzhou, China
| | - Bizeng Mao
- Institute of Biotechnology, Zhejiang University, Hangzhou, China.
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Hangzhou, China.
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14
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Maina S, Zheng L, Rodoni BC. Targeted Genome Sequencing (TG-Seq) Approaches to Detect Plant Viruses. Viruses 2021; 13:583. [PMID: 33808381 PMCID: PMC8066983 DOI: 10.3390/v13040583] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/22/2021] [Accepted: 03/27/2021] [Indexed: 12/18/2022] Open
Abstract
Globally, high-throughput sequencing (HTS) has been used for virus detection in germplasm certification programs. However, sequencing costs have impeded its implementation as a routine diagnostic certification tool. In this study, the targeted genome sequencing (TG-Seq) approach was developed to simultaneously detect multiple (four) viral species of; Pea early browning virus (PEBV), Cucumber mosaic virus (CMV), Bean yellow mosaic virus (BYMV) and Pea seedborne mosaic virus (PSbMV). TG-Seq detected all the expected viral amplicons within multiplex PCR (mPCR) reactions. In contrast, the expected PCR amplicons were not detected by gel electrophoresis (GE). For example, for CMV, GE only detected RNA1 and RNA2 while TG-Seq detected all the three RNA components of CMV. In an mPCR to amplify all four viruses, TG-Seq readily detected each virus with more than 732,277 sequence reads mapping to each amplicon. In addition, TG-Seq also detected all four amplicons within a 10-8 serial dilution that were not detectable by GE. Our current findings reveal that the TG-Seq approach offers significant potential and is a highly sensitive targeted approach for detecting multiple plant viruses within a given biological sample. This is the first study describing direct HTS of plant virus mPCR products. These findings have major implications for grain germplasm healthy certification programs and biosecurity management in relation to pathogen entry into Australia and elsewhere.
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Affiliation(s)
- Solomon Maina
- Microbial Sciences, Pests & Diseases, Agriculture Victoria, 110 Natimuk Road, Horsham, Victoria 3400, Australia
- Australian Grains Genebank, Agriculture Victoria, 110 Natimuk Road, Horsham, Victoria 3400, Australia
| | - Linda Zheng
- Microbial Sciences, Pests & Diseases, Agriculture Victoria, AgriBio, 5 Ring Road, Bundoora, Victoria 3083, Australia; (L.Z.); (B.C.R.)
| | - Brendan C. Rodoni
- Microbial Sciences, Pests & Diseases, Agriculture Victoria, AgriBio, 5 Ring Road, Bundoora, Victoria 3083, Australia; (L.Z.); (B.C.R.)
- School of Applied Systems Biology (SASB), La Trobe University, Bundoora, Victoria 3083, Australia
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15
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Maurastoni M, Sá-Antunes TF, Oliveira SA, Santos AMC, Ventura JA, Fernandes PMB. A multiplex RT-PCR method to detect papaya meleira virus complex in adult pre-flowering plants. Arch Virol 2020; 165:1211-1214. [PMID: 32170392 DOI: 10.1007/s00705-020-04588-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/10/2020] [Indexed: 12/16/2022]
Abstract
Papaya sticky disease (PSD), which can destroy orchards, was first attributed to papaya meleira virus (PMeV). However, the discovery of papaya meleira virus 2 (PMeV2) associated with PSD plants impose the need to detect this viral complex. We developed a multiplex RT-PCR (mPCR) technique capable of detecting two viruses in a single assay from pre-flowering plant samples, which is a useful tool for early diagnosis of PSD. We also determined the limit of detection (LOD) using asymmetric plasmid dilutions of both PMeV and PMeV2, which revealed that a higher titer of one virus prevents detection of the other. Thus, this technique is an alternative method for detecting PMeV and PMeV2 in a single reaction.
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Affiliation(s)
- Marlonni Maurastoni
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Tathiana F Sá-Antunes
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Scarlett A Oliveira
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Alexandre M C Santos
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - José A Ventura
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
- Instituto Capixaba de Pesquisa, Assistência Técnica e Extensão Rural, Vitória, Epírito Santo, Brazil
| | - Patricia M B Fernandes
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil.
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16
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Diaz-Lara A, Mollov D, Golino D, Al Rwahnih M. Complete genome sequence of rose virus A, the first carlavirus identified in rose. Arch Virol 2019; 165:241-244. [PMID: 31701224 DOI: 10.1007/s00705-019-04460-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 10/05/2019] [Indexed: 11/29/2022]
Abstract
A novel virus was discovered in a Rosa wichuraiana Crep. by high-throughput sequencing and tentatively named "rose virus A" (RVA). Based on sequence identity and phylogenetic analysis, RVA represents a new member of the genus Carlavirus (family Betaflexiviridae). The genome of RVA is 8,849 nucleotides long excluding the poly(A) tail and contains six open reading frames (ORFs). The predicted ORFs code for a replicase, triple gene block (TGB), coat protein, and nucleic acid binding protein, as in a typical carlavirus. RVA is the first carlavirus identified in rose and has the highest nucleotide sequence similarity to poplar mosaic virus. Reverse transcription-PCR-based assays were developed to confirm the presence of RVA in the original source and to screen additional rose plants.
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Affiliation(s)
- Alfredo Diaz-Lara
- Department of Plant Pathology, University of California-Davis, Davis, CA, 95616, USA
| | - Dimitre Mollov
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD, 20705, USA
| | - Deborah Golino
- Department of Plant Pathology, University of California-Davis, Davis, CA, 95616, USA
| | - Maher Al Rwahnih
- Department of Plant Pathology, University of California-Davis, Davis, CA, 95616, USA.
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17
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Alvarez-Díaz JC, Ortiz-Echeverry BA, Velásquez N. Duplex RT-PCR assay for simultaneous detection of TSWV and CSVd in chrysanthemum. J Virol Methods 2018; 266:41-48. [PMID: 30578896 DOI: 10.1016/j.jviromet.2018.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/16/2018] [Accepted: 12/17/2018] [Indexed: 02/06/2023]
Abstract
A novel duplex RT-PCR assay for simultaneous detection of TSWV and CSVd in chrysanthemums was developed. Previous reported primers for amplification of TSWV and CSVd were used and a novel pair of primers for CSVd was designed to improve duplex amplification compatibility. Sensitivity and efficiency of the previous reported and novel primers for CSVd were assessed. Then, the sensitivity of the combined primers to amplify both TSWV and CSVd cDNA were also evaluated. Both TSWV and CSVd were detected in preparations diluted up to 10-4 and 10-5 respectively, from total RNA extracts. This duplex RT-PCR method showed an estimated diagnostic sensitivity (DSe) of 97% and diagnostic specificity (DSp) of 99%. For combination of the primers TSWV L1/ L2 and CSVd UCO-1 F/ UCO-1R, the protocol could detect pathogen RNA from naturally infected plants until 0.1 ng and 1 ng respectively. This novel protocol for detection of TSWV/CSVd represents a useful diagnostic tool without the need of expensive probes and less extensive laboratory work. This method could be helpful to assist the selection and further propagation of healthy chrysanthemums on the field as well as to understand the dynamics and the interaction of this virus and viroid within farms.
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Affiliation(s)
- Juan C Alvarez-Díaz
- Departamento de Investigación y desarrollo, Universidad Católica de Oriente, Sector 3, cra. 46 No. 40B 50, Rionegro, Colombia.
| | - Bianor A Ortiz-Echeverry
- Departamento de Investigación y desarrollo, Universidad Católica de Oriente, Sector 3, cra. 46 No. 40B 50, Rionegro, Colombia
| | - Nubia Velásquez
- Departamento de Investigación y desarrollo, Universidad Católica de Oriente, Sector 3, cra. 46 No. 40B 50, Rionegro, Colombia
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18
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Pallás V, Sánchez-Navarro JA, James D. Recent Advances on the Multiplex Molecular Detection of Plant Viruses and Viroids. Front Microbiol 2018; 9:2087. [PMID: 30250456 PMCID: PMC6139301 DOI: 10.3389/fmicb.2018.02087] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/15/2018] [Indexed: 12/14/2022] Open
Abstract
Plant viruses are still one of the main contributors to economic losses in agriculture. It has been estimated that plant viruses can cause as much as 50 billion euros loss worldwide, per year. This situation may be worsened by recent climate change events and the associated changes in disease epidemiology. Reliable and early detection methods are still one of the main and most effective actions to develop control strategies for plant viral diseases. During the last years, considerable progress has been made to develop tools with high specificity and low detection limits for use in the detection of these plant pathogens. Time and cost reductions have been some of the main objectives pursued during the last few years as these increase their feasibility for routine use. Among other strategies, these objectives can be achieved by the simultaneous detection and (or) identification of several viruses in a single assay. Nucleic acid-based detection techniques are especially suitable for this purpose. Polyvalent detection has allowed the detection of multiple plant viruses at the genus level. Multiplexing RT polymerase chain reaction (PCR) has been optimized for the simultaneous detection of more than 10 plant viruses/viroids. In this short review, we provide an update on the progress made during the last decade on techniques such as multiplex PCR, polyvalent PCR, non-isotopic molecular hybridization techniques, real-time PCR, and array technologies to allow simultaneous detection of multiple plant viruses. Also, the potential and benefits of the powerful new technique of deep sequencing/next-generation sequencing are described.
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Affiliation(s)
- Vicente Pallás
- Instituto de Biología Molecular y Celular de Plantas, IBMCP, Universitat Politècnica de València – Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Jesus A. Sánchez-Navarro
- Instituto de Biología Molecular y Celular de Plantas, IBMCP, Universitat Politècnica de València – Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Delano James
- Sidney Laboratory, Canadian Food Inspection Agency, Sidney, BC, Canada
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19
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Wang R, Dong J, Wang Z, Zhou T, Li Y, Ding W. Complete nucleotide sequence of a new carlavirus in chrysanthemums in China. Arch Virol 2018. [PMID: 29525974 DOI: 10.1007/s00705-018-3791-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A new virus causing a serious stunt disease of chrysanthemum was identified in China by high-throughput sequencing (HTS) and named chrysanthemum virus R (CVR). The complete sequence of CVR was determined by reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE). The genomic RNA of CVR consists of 8,874 nucleotides (nt), excluding the poly(A) tail, contains six putative open reading frames (ORFs), and has a genomic organization typical of members of the genus Carlavirus. BLAST analysis of the full genome sequence showed low similarity (38%-56% sequence identity) to other members of the genus Carlavirus. BLAST analysis and phylogenetic analysis based on the amino acid (aa) sequences of the CVR replicase and coat protein (CP) confirmed that CVR is a distinct member of the genus Carlavirus.
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Affiliation(s)
- Rong Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151 Malianwa North Road, Beijing, 100193, China.
| | - Jiali Dong
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151 Malianwa North Road, Beijing, 100193, China
| | - Zhen Wang
- Shandong Agricultural University, Tai'an, 271018, China
| | - Tao Zhou
- State Key Laboratory for Agro-Biotechnology and Department for Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Yong Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151 Malianwa North Road, Beijing, 100193, China
| | - Wanlong Ding
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151 Malianwa North Road, Beijing, 100193, China.
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20
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Park M, Baek E, Yoon JY, Palukaitis P. The Use of a Tobacco mosaic virus-Based Expression Vector System in Chrysanthemum. THE PLANT PATHOLOGY JOURNAL 2017; 33:429-433. [PMID: 28811760 PMCID: PMC5538447 DOI: 10.5423/ppj.nt.04.2017.0083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 04/28/2017] [Accepted: 05/04/2017] [Indexed: 06/07/2023]
Abstract
Chrysanthemums (Chrysanthemum morifolium) are susceptible to tobacco mosaic virus (TMV). TMV-based expression vectors have been used in high-throughput experiments for production of foreign protein in plants and also expressing green fluorescent protein (GFP) to allow visualization of TMV movement. Here, we used TMV expressing the GFP to examine the infection of chrysanthemum by a TMV-based expression vector. Viral replication, movement and GFP expression by TMV-GFP were verified in upper leaves of chrysanthemums up to 73 days post inoculation (dpi) by RT-PCR. Neither wild-type TMV nor TMV-GFP induced symptoms. GFP fluorescence was seen in the larger veins of the inoculated leaf, in the stem above the inoculation site and in petioles of upper leaves, although there was no consistent detection of GFP fluorescence in the lamina of upper leaves under UV. Thus, a TMV-based expression vector can infect chrysanthemum and can be used for the in vivo study of gene functions.
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Affiliation(s)
- Minju Park
- Department of Horticulture Sciences, Seoul Women’s University, Seoul 01797,
Korea
| | - Eseul Baek
- Department of Horticulture Sciences, Seoul Women’s University, Seoul 01797,
Korea
| | - Ju-Yeon Yoon
- National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365,
Korea
| | - Peter Palukaitis
- Department of Horticulture Sciences, Seoul Women’s University, Seoul 01797,
Korea
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21
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Guan Z, Wu D, Song A, Chen F, Chen S, Fang W. A highly sensitive method for the detection of Chrysanthemum virus B. ELECTRON J BIOTECHN 2017. [DOI: 10.1016/j.ejbt.2017.01.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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22
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Zhang X, Peng Y, Wang Y, Zhang Z, Li D, Yu J, Han C. Simultaneous detection and differentiation of three genotypes of Brassica yellows virus by multiplex reverse transcription-polymerase chain reaction. Virol J 2016; 13:189. [PMID: 27876078 PMCID: PMC5120529 DOI: 10.1186/s12985-016-0647-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 11/10/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Brassica yellows virus (BrYV), proposed to be a new polerovirus species, three distinct genotypes (BrYV-A, BrYV-B and BrYV-C) have been described. This study was to develop a simple, rapid, sensitive, cost-effective method for simultaneous detection and differentiation of three genotypes of BrYV. RESULTS In this study, a multiplex reverse transcription-polymerase chain reaction (mRT-PCR) was developed for simultaneous detection and differentiation of the three genotypes of BrYV. The three genotypes of BrYV and Tunip yellows virus (TuYV) could be differentiated simultaneously using six optimized specific oligonucleotide primers, including one universal primer for detecting BrYV, three BrYV genotype-specific primers, and a pair of primers for specific detection of TuYV. Primers were designed from conserved regions of each virus and their specificity was confirmed by sequencing PCR products. The mRT-PCR products were 278 bp for BrYV-A, 674 bp for BrYV-B, 505 bp for BrYV-C, and 205 bp for TuYV. Amplification of three target genotypes was optimized by increasing the PCR annealing temperatures to 62 °C. One to three fragments specific for the virus genotypes were simultaneously amplified from infected samples and identified by their specific molecular sizes in agarose gel electrophoresis. No specific products could be amplified from cDNAs of other viruses which could infect crucifer crops. Detection limits of the plasmids for multiplex PCR were 100 fg for BrYV-A and BrYV-B, 10 pg for BrYV-C, and 1 pg for TuYV, respectively. The mRT-PCR was applied successfully for detection of three BrYV genotypes from field samples collected in China. CONCLUSIONS The simple, rapid, sensitive, and cost-effective mRT-PCR was developed successfully for detection and differentiation of the three genotypes of BrYV.
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Affiliation(s)
- Xiaoyan Zhang
- State Key Laboratory for Agrobiotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, China
| | - Yanmei Peng
- State Key Laboratory for Agrobiotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, China
| | - Ying Wang
- State Key Laboratory for Agrobiotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, China
| | - Zongying Zhang
- State Key Laboratory for Agrobiotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, China
| | - Dawei Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jialin Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chenggui Han
- State Key Laboratory for Agrobiotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, China
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