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Yang Z, Chen Z, Bakht F, Li S, Zi S, Li X, Zhao X, Wen G, Zhao M. Complete genome sequence of a novel badnavirus infecting Fatsia japonica in China. Arch Virol 2024; 169:97. [PMID: 38619640 DOI: 10.1007/s00705-024-06023-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 03/11/2024] [Indexed: 04/16/2024]
Abstract
The complete genome sequence of a novel badnavirus, tentatively named "fatsia badnavirus 1" (FaBV1, OM540428), was identified in Fatsia japonica. The infected plant displayed virus-like symptoms on leaves, including yellowing and chlorosis. The genome of FaBV1 is 7313 bp in length and similar in size and organization to other members of the genus Badnavirus (family Caulimoviridae), containing four open reading frames (ORFs), three of which are found in all known badnaviruses, and the other of which is only present in some badnaviruses. The virus has the genome characteristics of badnaviruses, including a tRNAMet binding site (5'-TCTGAATTTATAGCGCTA-3') and two cysteine-rich domains (C-X-C-2X-C-4X-H-4X-C and C-2X-C-11X-C-2X-C-4X-C-2X-C). Pairwise sequence comparisons of the RT+RNase H region indicated that FaBV1 shares 61.4-71.2% nucleotide (nt) sequence identity with other known badnaviruses, which is below the threshold (80% nt sequence identity in the RT+RNase H region) used for species demarcation in the genus Badnavirus. Phylogenetic analysis revealed that FaBV1, ivy ringspot-associated virus (IRSaV, MN850490.1), and cacao mild mosaic virus (CMMV, KX276640.1) together form a separate clade within the genus Badnavirus, suggesting that FaBV1 is a new member of the genus Badnavirus in the family Caulimoviridae. To our knowledge, this is the first report of a badnavirus infecting F. japonica.
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Affiliation(s)
- Zefen Yang
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Zeli Chen
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
- Quality Standard and Testing Technology Research Institute, Yunnan Academy of Agricultural Sciences, No. 2238, Beijing Road, Kunming, 650205, Yunnan, China
| | - Faryal Bakht
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Pakistan
| | - Shangyun Li
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Shaomei Zi
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Xin Li
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Xiyan Zhao
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Guosong Wen
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Mingfu Zhao
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.
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Adhab M, Zhang Y, Schoelz J. Transient expression of cauliflower mosaic virus (CaMV) P6-GFP complements a defective CaMV replicon to facilitate viral gene expression, replication and virion formation. Virology 2023; 587:109854. [PMID: 37556874 DOI: 10.1016/j.virol.2023.109854] [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: 06/20/2023] [Accepted: 07/25/2023] [Indexed: 08/11/2023]
Abstract
Over the past decades, several studies have examined the subcellular localization of the cauliflower mosaic virus (CaMV) P6 protein by tagging it with GFP (P6-GFP). These investigations have been essential in the development of models for inclusion body formation, nuclear transport, and microfilament-associated intracellular movement of P6 inclusion bodies for delivery of virions to plasmodesmata. Although it was shown early on that the translational transactivation function of P6-GFP was comparable to wild type P6, it has not been possible to incorporate a P6-GFP gene into an infectious clone of CaMV. Consequently, it has not been possible to formally prove that a P6-GFP fusion is comparable in function to the unmodified P6 protein. Here we show that transient expression of P6-GFP can complement a defective CaMV replicon through gene expression, replication and encapsidation, which validates the relevance of P6-GFP subcellular localization studies for understanding the development of CaMV infections.
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Affiliation(s)
- Mustafa Adhab
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, 65211, USA.
| | - Yu Zhang
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, 65211, USA.
| | - James Schoelz
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, 65211, USA.
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Adhab M, Zhang Y, Schoelz J. Transient expression of cauliflower mosaic virus (CaMV) P6-GFP complements a defective CaMV replicon to facilitate viral gene expression, replication and virion formation. Virology 2023; 587:109854. [DOI: https:/doi.org/10.1016/j.virol.2023.109854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
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Vinogradova S, Porotikova E, Navrotskaya E, Galbacs ZN, Massart S, Varallyay E. The First Virome of a Russian Vineyard. PLANTS (BASEL, SWITZERLAND) 2023; 12:3292. [PMID: 37765456 PMCID: PMC10534617 DOI: 10.3390/plants12183292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023]
Abstract
Among other pathogens, more than 80 viruses infect grapevine. The aim of this work was to study the virome diversity of grapevine viruses and mycoviruses of a vineyard using high-throughput sequencing technologies. The grapevine virome was studied in symptomatic vines of the Rkatsiteli cultivar (V. vinifera) collected at the vineyards of the Krasnodar Krai in Russia. Ribosomal-depleted total RNA and isolated small RNAs were used for library preparation and high-throughput sequencing. Six grapevine-infecting viruses and two viroids were validated by RT-PCR and analyzed phylogenetically. We identified the presence of grapevine leafroll-associated virus 3, grapevine Pinot gris virus, grapevine virus T, grapevine rupestris stem-pitting-associated virus, grapevine fleck virus, and grapevine rupestris vein feathering virus, as well as two viroids, grapevine yellow speckle viroid 1 and hop stunt viroid. We also studied the mycovirome of the vineyard and identified nine viruses with single-stranded positive-sense RNA genomes: alternaria arborescens mitovirus 1, botrytis cinerea mitovirus 1, botrytis cinerea mitovirus 2, botrytis cinerea mitovirus 3, botrytis cinerea mitovirus 4, sclerotinia sclerotiorum mitovirus 3, botrytis cinerea hypovirus 1, grapevine-associated narnavirus 1, and botrytis virus F. In addition, we identified botrytis cinerea hypovirus 1 satellite-like RNA and two single-stranded negative-sense RNA viruses. This is the first study of grapevine mycoviruses in Russia. The obtained result will contribute to the development of biocontrol strategies in the future.
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Affiliation(s)
- Svetlana Vinogradova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Elena Porotikova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Emiliya Navrotskaya
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Zsuzsanna Nagyne Galbacs
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, H-2100 Godollo, Hungary
| | - Sébastien Massart
- Laboratory of Integrated and Urban Phytopathology, TERRA, Gembloux Agro-Bio Tech, Liège University, 5030 Gembloux, Belgium
| | - Eva Varallyay
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, H-2100 Godollo, Hungary
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Javaran VJ, Poursalavati A, Lemoyne P, Ste-Croix DT, Moffett P, Fall ML. NanoViromics: long-read sequencing of dsRNA for plant virus and viroid rapid detection. Front Microbiol 2023; 14:1192781. [PMID: 37415816 PMCID: PMC10320856 DOI: 10.3389/fmicb.2023.1192781] [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: 03/23/2023] [Accepted: 06/06/2023] [Indexed: 07/08/2023] Open
Abstract
There is a global need for identifying viral pathogens, as well as for providing certified clean plant materials, in order to limit the spread of viral diseases. A key component of management programs for viral-like diseases is having a diagnostic tool that is quick, reliable, inexpensive, and easy to use. We have developed and validated a dsRNA-based nanopore sequencing protocol as a reliable method for detecting viruses and viroids in grapevines. We compared our method, which we term direct-cDNA sequencing from dsRNA (dsRNAcD), to direct RNA sequencing from rRNA-depleted total RNA (rdTotalRNA), and found that it provided more viral reads from infected samples. Indeed, dsRNAcD was able to detect all of the viruses and viroids detected using Illumina MiSeq sequencing (dsRNA-MiSeq). Furthermore, dsRNAcD sequencing was also able to detect low-abundance viruses that rdTotalRNA sequencing failed to detect. Additionally, rdTotalRNA sequencing resulted in a false-positive viroid identification due to the misannotation of a host-driven read. Two taxonomic classification workflows, DIAMOND & MEGAN (DIA & MEG) and Centrifuge & Recentrifuge (Cent & Rec), were also evaluated for quick and accurate read classification. Although the results from both workflows were similar, we identified pros and cons for both workflows. Our study shows that dsRNAcD sequencing and the proposed data analysis workflows are suitable for consistent detection of viruses and viroids, particularly in grapevines where mixed viral infections are common.
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Affiliation(s)
- Vahid J. Javaran
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada
- Centre SÈVE, Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Abdonaser Poursalavati
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada
- Centre SÈVE, Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Pierre Lemoyne
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada
| | - Dave T. Ste-Croix
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada
- Département de phytologie, Faculté des Sciences de l’Agriculture et de l’Alimentation, Université Laval, Québec, QC, Canada
| | - Peter Moffett
- Centre SÈVE, Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Mamadou L. Fall
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada
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Tarquini G, Dall'Ara M, Ermacora P, Ratti C. Traditional Approaches and Emerging Biotechnologies in Grapevine Virology. Viruses 2023; 15:v15040826. [PMID: 37112807 PMCID: PMC10142720 DOI: 10.3390/v15040826] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 04/29/2023] Open
Abstract
Environmental changes and global warming may promote the emergence of unknown viruses, whose spread is favored by the trade in plant products. Viruses represent a major threat to viticulture and the wine industry. Their management is challenging and mostly relies on prophylactic measures that are intended to prevent the introduction of viruses into vineyards. Besides the use of virus-free planting material, the employment of agrochemicals is a major strategy to prevent the spread of insect vectors in vineyards. According to the goal of the European Green Deal, a 50% decrease in the use of agrochemicals is expected before 2030. Thus, the development of alternative strategies that allow the sustainable control of viral diseases in vineyards is strongly needed. Here, we present a set of innovative biotechnological tools that have been developed to induce virus resistance in plants. From transgenesis to the still-debated genome editing technologies and RNAi-based strategies, this review discusses numerous illustrative studies that highlight the effectiveness of these promising tools for the management of viral infections in grapevine. Finally, the development of viral vectors from grapevine viruses is described, revealing their positive and unconventional roles, from targets to tools, in emerging biotechnologies.
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Affiliation(s)
- Giulia Tarquini
- Department of Agricultural, Environmental, Food and Animal Sciences (Di4A), University of Udine, 33100 Udine, Italy
| | - Mattia Dall'Ara
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, 40127 Bologna, Italy
| | - Paolo Ermacora
- Department of Agricultural, Environmental, Food and Animal Sciences (Di4A), University of Udine, 33100 Udine, Italy
| | - Claudio Ratti
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, 40127 Bologna, Italy
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Kishan G, Kumar R, Sharma SK, Srivastava N, Gupta N, Kumar A, Baranwal VK. Development and application of crude sap-based recombinase polymerase amplification assay for the detection and occurrence of grapevine geminivirus A in Indian grapevine cultivars. FRONTIERS IN PLANT SCIENCE 2023; 14:1151471. [PMID: 36968414 PMCID: PMC10034316 DOI: 10.3389/fpls.2023.1151471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Geminiviruses are known to infect several fields and horticultural crops around the globe. Grapevine geminivirus A (GGVA) was reported in the United States in 2017, and since then, it has been reported in several countries. The complete genome recovered through high-throughput sequencing (HTS)-based virome analysis in Indian grapevine cultivars had all of the six open reading frames (ORFs) and a conserved nonanucleotide sequence 5'-TAATATTAC-3' similar to all other geminiviruses. Recombinase polymerase amplification (RPA), an isothermal amplification technique, was developed for the detection of GGVA in grapevine samples employing crude sap lysed in 0.5 M NaOH solution and compared with purified DNA/cDNA as a template. One of the key advantages of this assay is that it does not require any purification or isolation of the viral DNA and can be performed in a wide range of temperatures (18°C-46°C) and periods (10-40 min), which makes it a rapid and cost-effective method for the detection of GGVA in grapevine. The developed assay has a sensitivity up to 0.1 fg μl-1 using crude plant sap as a template and detected GGVA in several grapevine cultivars of a major grapevine-growing area. Because of its simplicity and rapidity, it can be replicated for other DNA viruses infecting grapevine and will be a very useful technique for certification and surveillance in different grapevine-growing regions of the country.
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Affiliation(s)
- Gopi Kishan
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
- ICAR-Indian Institute of Seed Science, Kushmaur, Mau, Uttar Pradesh, India
| | - Rakesh Kumar
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Susheel Kumar Sharma
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Nishant Srivastava
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Nitika Gupta
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ashwini Kumar
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Virendra Kumar Baranwal
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Zhang B, Zhang M, Jia X, Hu G, Ren F, Fan X, Dong Y. Integrated Transcriptome and Metabolome Dissecting Interaction between Vitis vinifera L. and Grapevine Fabavirus. Int J Mol Sci 2023; 24:ijms24043247. [PMID: 36834661 PMCID: PMC9961852 DOI: 10.3390/ijms24043247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/22/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
Grapevine fabavirus (GFabV) is a novel member of the Fabavirus genus associated with chlorotic mottling and deformation symptoms in grapevines. To gain insights into the interaction between GFabV and grapevines, V. vinifera cv. 'Summer Black' infected with GFabV was investigated under field conditions through physiological, agronomic, and multi-omics approaches. GFabV induced significant symptoms on 'Summer Black', and caused a moderate decrease in physiological efficiency. In GFabV-infected plants, alterations in carbohydrate- and photosynthesis-related genes might trigger some defense responses. In addition, secondary metabolism involved in plant defense was progressively induced by GFabV. Jasmonic acid and ethylene signaling were down-regulated in GFabV-infected leaves and berries along with the expression of proteins related to LRR and protein kinases, suggesting that GFabV can block the defense in healthy leaves and berries. Furthermore, this study provided biomarkers for early monitoring of GFabV infection in grapevines, and contributed to a better understanding of the complex grapevine-virus interaction.
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Affiliation(s)
| | | | | | | | | | - Xudong Fan
- Correspondence: (X.F.); (Y.D.); Tel.: +86-139-4292-9163 (X.F.); +86-138-9829-5984 (Y.D.)
| | - Yafeng Dong
- Correspondence: (X.F.); (Y.D.); Tel.: +86-139-4292-9163 (X.F.); +86-138-9829-5984 (Y.D.)
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Ishwara Bhat A, Selvarajan R, Balasubramanian V. Emerging and Re-Emerging Diseases Caused by Badnaviruses. Pathogens 2023; 12:pathogens12020245. [PMID: 36839517 PMCID: PMC9963457 DOI: 10.3390/pathogens12020245] [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: 12/23/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
New and emerging plant diseases are caused by different pathogens including viruses that often cause significant crop losses. Badnaviruses are pararetroviruses that contain a single molecule of ds DNA genome of 7 to 9 kb in size and infect a large number of economically important crops such as banana and plantains, black pepper, cacao, citrus, grapevine, pineapple, sugarcane, sweet potato, taro, and yam, causing significant yield losses. Many of the species in the genus have a restricted host range and several of them are known to infect a single crop. Combined infections of different virus species and strains offer conditions that favor the development of new strains via recombination, especially in vegetatively propagated crops. The primary spread of badnaviruses is through vegetative propagating materials while for the secondary spread, they depend on insects such as mealybugs and aphids. Disease emerges as a consequence of the interactions between host and pathogens under favorable environmental conditions. The viral genome of the pararetroviruses is known to be integrated into the chromosome of the host and a few plants with integrants when subjected to different kinds of abiotic stress will give rise to episomal forms of the virus and cause disease. Attempts have been made to develop management strategies for badnaviruses both conventionally and using precision breeding techniques such as genome editing. Until 2016 only 32 badnavirus species infecting different crops were known, but in a span of six years, this number has gone up to 68. The current review highlights the emerging disease problems and management options for badnaviruses infecting economically important crops.
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Affiliation(s)
- Alangar Ishwara Bhat
- Division of Crop Protection, ICAR-Indian Institute of Spices Research, Kozhikode 673012, Kerala, India
| | - Ramasamy Selvarajan
- Division of Crop Protection, ICAR-National Research Centre for Banana, Trichy 620102, Tamil Nadu, India
| | - Velusamy Balasubramanian
- Division of Crop Protection, ICAR-National Research Centre for Banana, Trichy 620102, Tamil Nadu, India
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Biology and Ultrastructural Characterization of Grapevine Badnavirus 1 and Grapevine Virus G. Viruses 2022; 14:v14122695. [PMID: 36560699 PMCID: PMC9787950 DOI: 10.3390/v14122695] [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: 11/03/2022] [Revised: 11/21/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
The biological characteristics of grapevine viruses, such as their transmission and host range, are important for the adoption of successful prophylaxis strategies. The aim of this study was to investigate the traits of two newly described grapevine viruses widely distributed in Croatia, grapevine badnavirus 1 (GBV-1) and grapevine virus G (GVG). The vine mealybug (Planoccocus ficus) proved to be a vector of GBV-1 and GVG capable of vine-to-vine transmission with overall experimental transmission rates of 61% and 14.6%, respectively. Transmission was also demonstrated by grafting, with an overall transmission rate of 53.8% for GBV-1 and 100% for GVG, as well as by green grafting using the T-budding technique. Symptoms of GBV-1 and GVG were not observed on the woody cylinders of the indicators LN 33, Kober 5BB, 110 Richter and cvs. Chardonnay and Cabernet Sauvignon. Seed transmission and mechanical transmission were not confirmed. Electron microscopy revealed accumulation of GBV-1 particles and viroplasms in the cytoplasm, but no alternations of the cell structure. Infection with GVG revealed the proliferation of tonoplast-associated vesicles inside phloem cells and cell wall thickening.
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Grapevine Badnavirus 1: Detection, Genetic Diversity, and Distribution in Croatia. PLANTS 2022; 11:plants11162135. [PMID: 36015438 PMCID: PMC9416389 DOI: 10.3390/plants11162135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022]
Abstract
Grapevine badnavirus 1 (GBV-1) was recently discovered in grapevine using high throughput sequencing. In order to carry out large-scale testing that will allow for better insights into virus distribution, conventional and real-time PCR assays were developed using sequences both from previously known, and four newly characterized isolates. Throughout the growing season and dormancy, GBV-1 can be detected by real-time PCR using available tissue, with the possibility of false-negative results early in vegetation growth. GBV-1 real-time PCR analysis of 4302 grapevine samples from the Croatian continental and coastal wine-growing regions revealed 576 (~13.4%) positive vines. In the continental wine-growing region, virus incidence was confirmed in only two collection plantations, whereas in the coastal region, infection was confirmed in 30 commercial vineyards and one collection plantation. Infection rates ranged from 1.9 to 96% at the different sites, with predominantly autochthonous grapevine cultivars infected. Conventional PCR products obtained from 50 newly discovered GBV-1 isolates, containing the 375 nucleotides long portion of the reverse transcriptase gene, showed nucleotide and amino acid identities ranging from 94.1 to 100% and from 92.8 to 100%, respectively. The reconstructed phylogenetic tree positioned the GBV-1 isolates taken from the same vineyard close to each other indicating a possible local infection event, although the tree nodes were generally not well supported.
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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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13
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Navrotskaya E, Porotikova E, Yurchenko E, Galbacs ZN, Varallyay E, Vinogradova S. High-Throughput Sequencing of Small RNAs for Diagnostics of Grapevine Viruses and Viroids in Russia. Viruses 2021; 13:2432. [PMID: 34960701 PMCID: PMC8709451 DOI: 10.3390/v13122432] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 11/16/2022] Open
Abstract
The use of high-throughput sequencing (HTS) technology has led to significant progress in the identification of many viruses and their genetic variants. In this study, we used the HTS platform to sequence small RNAs (sRNAs) of grapevine to study the virome. Isolation of RNA was performed using symptomatic grapevines collected from commercial vineyards in Krasnodar Krai in 2017-2018. To determine the viromes of vineyards, we used an integrated approach that included a bioinformatic analysis of the results of sRNA HTS and the molecular method RT-PCR, which made it possible to identify 13 viruses and 4 viroids. Grapevine leafroll-associated virus 4 (GLRaV-4), Grapevine Syrah Virus-1 (GSyV-1), Raspberry bushy dwarf virus (RBDV), Australian grapevine viroid (AGVd), and Grapevine yellow speckle viroid 2 (GYSVd-2) were identified for the first time in Russia. Out of 38 samples analyzed, 37 had mixed infections with 4-11 viruses, indicating a high viral load. Analysis of the obtained sequences of fragments of virus genomes made it possible to identify recombination events in GLRaV-1, GLRaV-2, GLRaV-3, GLRaV-4, GVT, GPGV, GRSPaV, GVA, and GFLV. The obtained results indicate a wide spread of the viruses and a high genetic diversity in the vineyards of Krasnodar Krai and emphasize the urgent need to develop and implement long-term strategies for the control of viral grapevine diseases.
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Affiliation(s)
- Emiliya Navrotskaya
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia; (E.N.); (E.P.)
| | - Elena Porotikova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia; (E.N.); (E.P.)
| | - Eugeniya Yurchenko
- Federal State Budgetary Scientific Institution ‘North Caucasian Federal Scientific Horticulture and Viticulture Center’, Protection and Plant Biotechnology Scientific Center, Head, 40 Years of Victory Street 39, 350072 Krasnodar, Russia;
| | - Zsuzsanna Nagyne Galbacs
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, H-2100 Godollo, Hungary; (Z.N.G.); (E.V.)
| | - Eva Varallyay
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, H-2100 Godollo, Hungary; (Z.N.G.); (E.V.)
| | - Svetlana Vinogradova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia; (E.N.); (E.P.)
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14
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Javaran VJ, Moffett P, Lemoyne P, Xu D, Adkar-Purushothama CR, Fall ML. Grapevine Virology in the Third-Generation Sequencing Era: From Virus Detection to Viral Epitranscriptomics. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112355. [PMID: 34834718 PMCID: PMC8623739 DOI: 10.3390/plants10112355] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/16/2021] [Accepted: 10/29/2021] [Indexed: 05/30/2023]
Abstract
Among all economically important plant species in the world, grapevine (Vitis vinifera L.) is the most cultivated fruit plant. It has a significant impact on the economies of many countries through wine and fresh and dried fruit production. In recent years, the grape and wine industry has been facing outbreaks of known and emerging viral diseases across the world. Although high-throughput sequencing (HTS) has been used extensively in grapevine virology, the application and potential of third-generation sequencing have not been explored in understanding grapevine viruses and their impact on the grapevine. Nanopore sequencing, a third-generation technology, can be used for the direct sequencing of both RNA and DNA with minimal infrastructure. Compared to other HTS methods, the MinION nanopore platform is faster and more cost-effective and allows for long-read sequencing. Due to the size of the MinION device, it can be easily carried for field viral disease surveillance. This review article discusses grapevine viruses, the principle of third-generation sequencing platforms, and the application of nanopore sequencing technology in grapevine virus detection, virus-plant interactions, as well as the characterization of viral RNA modifications.
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Affiliation(s)
- Vahid Jalali Javaran
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada; (V.J.J.); (P.L.); (D.X.)
- Département de Biologie, Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada;
| | - Peter Moffett
- Département de Biologie, Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada;
| | - Pierre Lemoyne
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada; (V.J.J.); (P.L.); (D.X.)
| | - Dong Xu
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada; (V.J.J.); (P.L.); (D.X.)
| | - Charith Raj Adkar-Purushothama
- Département de Biochimie, Faculté de Médecine des Sciences de la Santé, 3201 rue Jean-Mignault, Sherbrooke, QC J1E 4K8, Canada;
| | - Mamadou Lamine Fall
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada; (V.J.J.); (P.L.); (D.X.)
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15
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Mushtaq M, Dar AA, Basu U, Bhat BA, Mir RA, Vats S, Dar MS, Tyagi A, Ali S, Bansal M, Rai GK, Wani SH. Integrating CRISPR-Cas and Next Generation Sequencing in Plant Virology. Front Genet 2021; 12:735489. [PMID: 34759957 PMCID: PMC8572880 DOI: 10.3389/fgene.2021.735489] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/16/2021] [Indexed: 12/26/2022] Open
Abstract
Plant pathology has been revolutionized by the emergence and intervention of next-generation sequencing technologies (NGS) which provide a fast, cost-effective, and reliable diagnostic for any class of pathogens. NGS has made tremendous advancements in the area of research and diagnostics of plant infecting viromes and has bridged plant virology with other advanced research fields like genome editing technologies. NGS in a broader perspective holds the potential for plant health improvement by diagnosing and mitigating the new or unusual symptoms caused by novel/unidentified viruses. CRISPR-based genome editing technologies can enable rapid engineering of efficient viral/viroid resistance by directly targeting specific nucleotide sites of plant viruses and viroids. Critical genes such as eIf (iso) 4E or eIF4E have been targeted via the CRISPR platform to produce plants resistant to single-stranded RNA (ssRNA) viruses. CRISPR/Cas-based multi-target DNA or RNA tests can be used for rapid and accurate diagnostic assays for plant viruses and viroids. Integrating NGS with CRISPR-based genome editing technologies may lead to a paradigm shift in combating deadly disease-causing plant viruses/viroids at the genomic level. Furthermore, the newly discovered CRISPR/Cas13 system has unprecedented potential in plant viroid diagnostics and interference. In this review, we have highlighted the application and importance of sequencing technologies on covering the viral genomes for precise modulations. This review also provides a snapshot vision of emerging developments in NGS technologies for the characterization of plant viruses and their potential utilities, advantages, and limitations in plant viral diagnostics. Furthermore, some of the notable advances like novel virus-inducible CRISPR/Cas9 system that confers virus resistance with no off-target effects have been discussed.
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Affiliation(s)
- Muntazir Mushtaq
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Aejaz Ahmad Dar
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Umer Basu
- Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | | | - Rakeeb Ahmad Mir
- Department of Biotechnology, School of Biosciences and Biotechnology, BGSB University, Rajouri, India
| | - Sanskriti Vats
- Department of Agricultural Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - M. S. Dar
- Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Anshika Tyagi
- Department of Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Sajad Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Monika Bansal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Gyanendra Kumar Rai
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
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16
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Fan X, Zhang Z, Li C, Ren F, Hu G, Zhang B, Dong Y. High-Throughput Sequencing Indicates a Novel Marafivirus in Grapevine Showing Vein-Clearing Symptoms. PLANTS 2021; 10:plants10071487. [PMID: 34371690 PMCID: PMC8309299 DOI: 10.3390/plants10071487] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/16/2021] [Accepted: 07/17/2021] [Indexed: 11/18/2022]
Abstract
A putative new marafivirus was identified in a ‘Jumeigui’ grapevine exhibitting obvious vein-clearing symptoms by high-throughput sequencing, which tentatively named grapevine-associated marafivirus (GaMV). The nearly complete genomic sequence of GaMV was amplified by reverse transcription PCR, and the terminal sequences were determined using the rapid amplification of cDNA ends method. The nearly complete genome of GaMV is 6346 bp long, excluding the poly(A) tail, and shows 51.2–62.3% nucleotide identity with other members of the genera Marafivirus, Maculavirus and Tymovirus in the family Tymoviridae. Additionally, it includes five functional domains homologous to those found in members of these genera. A phylogenetic analysis showed that GaMV clustered with other species-related marafiviruses. These data support GaMV being a representative member of a novel species in the genus Marafivirus. Furthermore, GaMV was graft-transmissible and 26 of 516 (5.04%) grapevine samples from five provinces in China tested positive by reverse transcription PCR. The coat protein of GaMV isolates shared 91.7–100% and 96.7–100% identities at the nt and aa levels, respectively. The coat protein-based phylogenetic trees revealed three well-defined clusters.
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17
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Uhls A, Petersen S, Keith C, Howard S, Bao X, Qiu W. Grapevine vein clearing virus Is Prevalent and Genetically Variable in Grape Aphid ( Aphis illinoisensis Shimer) Populations. PLANT DISEASE 2021; 105:1531-1538. [PMID: 33174799 DOI: 10.1094/pdis-10-20-2176-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Grapevine vein clearing virus (GVCV) causes severe stunting and death of cultivated grapevines and is prevalent in native Vitis spp. and Ampelopsis cordata in the Midwest region of the United States. GVCV can be transmitted from wild A. cordata to Vitis spp. by grape aphid (Aphis illinoisensis) under greenhouse conditions, but its prevalence, genetic composition, and genome number in native grape aphids are unknown. In this study, we collected grape aphids from native Vitaceae across the state of Missouri in 2018 and 2019, and conducted diagnostic, genetic, and quantitative analyses. GVCV was detected in 91 of the 105 randomly sampled communities on 71 Vitaceae plants (87%). It was present in 211 of 525 single grape aphids (40%). Diverse GVCV variants from aphids were present on both GVCV-negative and GVCV-positive plants. Identical GVCV variants were found in grape aphids sampled from wild and cultivated Vitaceae, indicating that viruliferous aphids likely migrate and disperse GVCV variants among wild and cultivated Vitaceae. In addition, we found that the number of GVCV genomes varies largely in the stylet and body of individual aphids. Our study provides a snapshot of GVCV epidemics and genetic structure in its mobile vector and sessile hosts. This presents a good model for studying the epidemiology, ecology, and evolution of a plant virus.
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Affiliation(s)
- Adam Uhls
- Center for Grapevine Biotechnology, W. H. Darr College of Agriculture, Missouri State University, Springfield, MO 65897
| | - Sylvia Petersen
- Center for Grapevine Biotechnology, W. H. Darr College of Agriculture, Missouri State University, Springfield, MO 65897
| | - Cory Keith
- Center for Grapevine Biotechnology, W. H. Darr College of Agriculture, Missouri State University, Springfield, MO 65897
| | - Susanne Howard
- Center for Grapevine Biotechnology, W. H. Darr College of Agriculture, Missouri State University, Springfield, MO 65897
| | - Xiaokai Bao
- Center for Grapevine Biotechnology, W. H. Darr College of Agriculture, Missouri State University, Springfield, MO 65897
| | - Wenping Qiu
- Center for Grapevine Biotechnology, W. H. Darr College of Agriculture, Missouri State University, Springfield, MO 65897
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18
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Sun S, Hu Y, Jiang G, Tian Y, Ding M, Yu C, Zhou X, Qian Y. Molecular Characterization and Genomic Function of Grapevine Geminivirus A. Front Microbiol 2020; 11:555194. [PMID: 32983075 PMCID: PMC7493466 DOI: 10.3389/fmicb.2020.555194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/12/2020] [Indexed: 11/20/2022] Open
Abstract
A new grapevine geminivirus A (GGVA) isolate (named as GGVA-17YM1) and its associated defective genome (GGVA-D) were identified from a grapevine sample collected in Yuanmou, Yunnan Province, using sRNA high throughput sequencing and traditional Sanger sequencing. To explore the pathogenicity of GGVA and GGVA-D, infectious clones of GGVA-17YM1 and GGVA-D-17YM1 were constructed. Infection assays indicated that Nicotiana benthamiana plants inoculated with GGVA alone or a combination of GGVA and GGVA-D exhibited upward curled apical leaves and dwarfism. Southern blotting and quantitative real-time polymerase chain reaction analysis revealed that GGVA-D increased the accumulation level of GGVA DNA. Transient expression using a PVX-derived recombinant vector indicated that C2 and C4 encoded by GGVA are involved in symptom induction in N. benthamiana. Furthermore, the V2 protein inhibited local RNA silencing in co-infiltration assays in GFP transgenic N. benthamiana plants. Subsequently, full-length genome sequencing resulted in the identification of 11 different isolates of GGVA and 9 associated defective DNA molecules. Phylogenetic analysis based on whole genome sequences showed that all GGVA isolates, including our sequences, clustered into two distinct branches with no geographical grouping. Analyses of molecular variation indicated single nucleotide polymorphisms (SNPs) with more transitions (55.97%) than transversions (44.03%). Furthermore, the main variants for ORF C1, C3, or V1 were synonymous mutations, and non-synonymous mutations for ORF C2, C4, and V2. Genetic selection analysis indicated that negative selection acted on four ORFs (V1, C1, C2, and C3), while V2 and C4 were under positive selection. Our results contribute to the characterization of the genetic diversity of GGVA and provide insights into its pathogenicity.
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Affiliation(s)
- Suwei Sun
- Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Ya Hu
- Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | | | - Yimin Tian
- Technical Center for Animal, Plant and Food Inspection and Quarantine, Shanghai Customs District, Shanghai, China
| | - Ming Ding
- Institute of Biotechnology and Germplasm Resources, Yunnan Academy of Agricultural Science, Kunming, China
| | - Cui Yu
- Technical Center for Animal, Plant and Food Inspection and Quarantine, Shanghai Customs District, Shanghai, China
| | - Xueping Zhou
- Institute of Biotechnology, Zhejiang University, Hangzhou, China.,Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yajuan Qian
- Institute of Biotechnology, Zhejiang University, Hangzhou, China
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19
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Qiu W, Petersen SM, Howard S. North American Grape 'Norton' is Resistant to Grapevine Vein Clearing Virus. PLANT DISEASE 2020; 104:2051-2053. [PMID: 32520650 DOI: 10.1094/pdis-10-19-2161-sc] [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: 06/11/2023]
Abstract
Grapevines (Vitis spp.) host viruses belonging to 17 families. Virus-associated diseases are a constant challenge to grape production. Genetic resources for breeding virus-resistant grape cultivars are scarce. 'Norton' is a hybrid grape of North American Vitis aestivalis and is resistant to powdery mildew and downy mildew. In this study, we assessed resistance of 'Norton' to grapevine vein clearing virus (GVCV), which is prevalent in native, wild Vitaceae and in vineyards in the Midwest region of the U.S. We did not detect GVCV in 'Norton' as either the scion or the rootstock up to 3 years after it was grafted with a GVCV-infected 'Chardonel' grapevine. Upon sequencing of small RNAs, we were able to assemble the GVCV genome from virus small RNAs in GVCV-infected 'Chardonel' scion or rootstock, but not from grafted 'Norton' scion and rootstock. This study unveils a new trait of 'Norton' that can be used in breeding GVCV-resistant grape cultivars, and to investigate genetic mechanisms of 'Norton' resistance to GVCV.
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Affiliation(s)
- Wenping Qiu
- Center for Grapevine Biotechnology, The Darr College of Agriculture, Missouri State University, Springfield, MO 65897, U.S.A
| | - Sylvia M Petersen
- Center for Grapevine Biotechnology, The Darr College of Agriculture, Missouri State University, Springfield, MO 65897, U.S.A
| | - Susanne Howard
- Center for Grapevine Biotechnology, The Darr College of Agriculture, Missouri State University, Springfield, MO 65897, U.S.A
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20
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Bragard C, Dehnen-Schmutz K, Gonthier P, Jacques MA, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Milonas P, Navas-Cortes JA, Parnell S, Potting R, Reignault PL, Thulke HH, Van der Werf W, Vicent Civera A, Yuen J, Zappalà L, Candresse T, Chatzivassiliou E, Finelli F, Martelli GP, Winter S, Bosco D, Chiumenti M, Di Serio F, Kaluski T, Minafra A, Rubino L. Pest categorisation of non-EU viruses and viroids of Vitis L. EFSA J 2019; 17:e05669. [PMID: 32626420 PMCID: PMC7009087 DOI: 10.2903/j.efsa.2019.5669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Following a request from the EU Commission, the Panel on Plant Health addressed the pest categorisation of the viruses and viroids of Vitis L. determined as being either non-EU or of undetermined standing in a previous EFSA opinion. These infectious agents belong to different genera and are heterogeneous in their biology. With the exclusion of grapevine virus 101-14.N.23.9.1/South Africa/2009 for which very limited information exists, the pest categorisation was completed for 30 viruses or viroids having acknowledged identities and available detection methods. All these viruses are efficiently transmitted by vegetative propagation techniques, with plants for planting representing the major pathway for long-distance dispersal and thus considered as the major pathway for potential entry. Depending on the virus, additional pathway(s) can also be seeds, pollen and/or vector(s). Most of the viruses categorised here are known to infect only one or few plant genera, but some of them have a wide host range, thus extending the possible entry pathways. Grapevine yellow speckle viroid 2, blueberry leaf mottle virus, grapevine Ajinashika virus, grapevine Anatolian ringspot virus, grapevine berry inner necrosis virus, grapevine deformation virus, grapevine fabavirus, grapevine red blotch virus, grapevine stunt virus, grapevine Tunisian ringspot virus, grapevine vein-clearing virus, temperate fruit decay-associated virus, peach rosette mosaic virus, tobacco ringspot virus, tomato ringspot virus meet all the criteria evaluated by EFSA to qualify as potential Union quarantine pests (QPs). With the exception of impact for the EU territory, on which the Panel was unable to conclude, blackberry virus S, grapevine geminivirus A, grapevine leafroll-associated virus 7, grapevine leafroll-associated virus 13, grapevine satellite virus, grapevine virus E, grapevine virus I, grapevine virus J, grapevine virus S, summer grape enamovirus, summer grape latent virus satisfy all the other criteria to be considered as potential Union QPs. Australian grapevine viroid, grapevine cryptic virus 1, grapevine endophyte endornavirus and wild vitis virus 1 do not meet all the criteria evaluated by EFSA to be regarded as potential Union QPs because they are not known to cause an impact on Vitis. For several viruses, especially those recently discovered, the categorisation is associated with high uncertainties mainly because of the absence of data on their biology, distribution and impact. Since this opinion addresses specifically non-EU viruses, in general these viruses do not meet the criteria assessed by EFSA to qualify as a potential Union regulated non-quarantine pests.
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21
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Xiao H, Li C, Al Rwahnih M, Dolja V, Meng B. Metagenomic Analysis of Riesling Grapevine Reveals a Complex Virome Including Two New and Divergent Variants of Grapevine leafroll-associated virus 3. PLANT DISEASE 2019; 103:1275-1285. [PMID: 30932733 DOI: 10.1094/pdis-09-18-1503-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The virome of a major white wine grape of cultivar Riesling showing decline and leafroll disease symptoms was analyzed through high-throughput sequencing (HTS) using total RNAs as templates and the Illumina HiSeq 2500 platform. Analysis of HTS data revealed the presence of five viruses and three viroids in the infected vine. These viruses are Grapevine leafroll-associated virus 1 (GLRaV-1) and GLRaV-3 (genus Ampelovirus, family Closteroviridae) and three viruses of the family Betaflexiviridae (namely, Grapevine virus A [GVA], Grapevine virus B, and Grapevine rupestris stem pitting-associated virus [GRSPaV]). We also show that multiple distinct strains of three viruses (GLRaV-3, GVA, and GRSPaV) were present in this diseased grapevine. The complete genomes of two novel and highly divergent isolates of GLRaV-3 were determined using the draft genomes derived from HTS data and two independent rapid amplification of cDNA ends (RACE) strategies to obtain sequences at both the 5' and the 3' termini of the viral genomes. Questionable genome regions of both isolates were also verified through cloning of reverse transcription polymerase chain reaction products and Sanger sequencing. These two isolates are vastly divergent from all other isolates of GLRaV-3 whose genome sequences are available in GenBank. Isolate ON8415A has up to 76% nucleotide sequence identities to other isolates representing existing variant groups. We also revealed high degrees of variation in both length and sequence in the terminal untranslated regions (UTRs) of GLRaV-3 variants. The 5'-UTR of most GLRaV-3 isolates whose complete genomes have been sequenced contain tandem repeats of 65 nucleotides, a highly unusual feature rarely observed in (+)single-stranded RNA viruses. Mechanisms for the biogenesis of these tandem repeats and their function in virus replication and pathogenesis require investigation. Findings of this research add to the genetic diversity, evolutionary biology, and diagnostics of GLRaV-3 that afflicts the global grape wine industry.
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Affiliation(s)
- Huogen Xiao
- 1 Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Caihong Li
- 1 Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Maher Al Rwahnih
- 2 Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A.; and
| | - Valerian Dolja
- 3 Department of Botany and Plant Pathology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, U.S.A
| | - Baozhong Meng
- 1 Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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22
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Villamor DEV, Ho T, Al Rwahnih M, Martin RR, Tzanetakis IE. High Throughput Sequencing For Plant Virus Detection and Discovery. PHYTOPATHOLOGY 2019; 109:716-725. [PMID: 30801236 DOI: 10.1094/phyto-07-18-0257-rvw] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Over the last decade, virologists have discovered an unprecedented number of viruses using high throughput sequencing (HTS), which led to the advancement of our knowledge on the diversity of viruses in nature, particularly unraveling the virome of many agricultural crops. However, these new virus discoveries have often widened the gaps in our understanding of virus biology; the forefront of which is the actual role of a new virus in disease, if any. Yet, when used critically in etiological studies, HTS is a powerful tool to establish disease causality between the virus and its host. Conversely, with globalization, movement of plant material is increasingly more common and often a point of dispute between countries. HTS could potentially resolve these issues given its capacity to detect and discover. Although many pipelines are available for plant virus discovery, all share a common backbone. A description of the process of plant virus detection and discovery from HTS data are presented, providing a summary of the different pipelines available for scientists' utility in their research.
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Affiliation(s)
- D E V Villamor
- 1 Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - T Ho
- 1 Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - M Al Rwahnih
- 2 Department of Plant Pathology, University of California, Davis 95616; and
| | - R R Martin
- 3 Horticulture Crops Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330
| | - I E Tzanetakis
- 1 Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
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23
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Petersen SM, Keith C, Austin K, Howard S, Su L, Qiu W. A Natural Reservoir and Transmission Vector of Grapevine Vein Clearing Virus. PLANT DISEASE 2019; 103:571-577. [PMID: 30484754 DOI: 10.1094/pdis-06-18-1073-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Grapevine vein clearing virus (GVCV) is associated with a vein-clearing and vine-decline disease. In this study, we surveyed wild Ampelopsis cordata from the Vitaceae family and found that 31% (35 of 113) of native A. cordata plants are infected with GVCV. The full-length genome sequence of one GVCV isolate from A. cordata shared 99.8% identical nucleotides with an isolate from a nearby cultivated 'Chardonel' grapevine, suggesting the occurrence of an insect vector. To identify a vector, we collected Aphis illinoisensis (common name: grape aphids) from wild A. cordata plants and detected GVCV in the aphid populations. We found that A. illinoisensis is capable of transmitting GVCV from infected A. cordata to Chardonel grapevines in the greenhouse. Upon transmission, GVCV caused severe symptoms on the infected Chardonel 45 days post transmission. We conclude that wild GVCV isolates from A. cordata are capable of inducing a severe disease on cultivated grapevines once they spread from native A. cordata to vineyards via grape aphids. The discovery of a natural reservoir and an insect vector of GVCV provides timely knowledge for disease management in vineyards and critical clues on viral evolution and epidemiology.
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Affiliation(s)
- Sylvia M Petersen
- Center for Grapevine Biotechnology, William H. Darr College of Agriculture, Missouri State University, Mountain Grove, MO 65711
| | - Cory Keith
- Center for Grapevine Biotechnology, William H. Darr College of Agriculture, Missouri State University, Mountain Grove, MO 65711
| | - Kaylie Austin
- Center for Grapevine Biotechnology, William H. Darr College of Agriculture, Missouri State University, Mountain Grove, MO 65711
| | - Susanne Howard
- Center for Grapevine Biotechnology, William H. Darr College of Agriculture, Missouri State University, Mountain Grove, MO 65711
| | - Li Su
- Center for Grapevine Biotechnology, William H. Darr College of Agriculture, Missouri State University, Mountain Grove, MO 65711
| | - Wenping Qiu
- Center for Grapevine Biotechnology, William H. Darr College of Agriculture, Missouri State University, Mountain Grove, MO 65711
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Pooggin MM. Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization. Front Microbiol 2018; 9:2779. [PMID: 30524398 PMCID: PMC6256188 DOI: 10.3389/fmicb.2018.02779] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/30/2018] [Indexed: 11/13/2022] Open
Abstract
RNA interference (RNAi)-based antiviral defense generates small interfering RNAs that represent the entire genome sequences of both RNA and DNA viruses as well as viroids and viral satellites. Therefore, deep sequencing and bioinformatics analysis of small RNA population (small RNA-ome) allows not only for universal virus detection and genome reconstruction but also for complete virome reconstruction in mixed infections. Viral infections (like other stress factors) can also perturb the RNAi and gene silencing pathways regulating endogenous gene expression and repressing transposons and host genome-integrated endogenous viral elements which can potentially be released from the genome and contribute to disease. This review describes the application of small RNA-omics for virus detection, virome reconstruction and antiviral defense characterization in cultivated and non-cultivated plants. Reviewing available evidence from a large and ever growing number of studies of naturally or experimentally infected hosts revealed that all families of land plant viruses, their satellites and viroids spawn characteristic small RNAs which can be assembled into contigs of sufficient length for virus, satellite or viroid identification and for exhaustive reconstruction of complex viromes. Moreover, the small RNA size, polarity and hotspot profiles reflect virome interactions with the plant RNAi machinery and allow to distinguish between silent endogenous viral elements and their replicating episomal counterparts. Models for the biogenesis and functions of small interfering RNAs derived from all types of RNA and DNA viruses, satellites and viroids as well as endogenous viral elements are presented and discussed.
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Affiliation(s)
- Mikhail M. Pooggin
- Institut National de la Recherche Agronomique, UMR BGPI, Montpellier, France
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25
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Setiono FJ, Chatterjee D, Fuchs M, Perry KL, Thompson JR. The Distribution and Detection of Grapevine red blotch virus in its Host Depend on Time of Sampling and Tissue Type. PLANT DISEASE 2018; 102:2187-2193. [PMID: 30226420 DOI: 10.1094/pdis-03-18-0450-re] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Grapevine red blotch virus (GRBV) is the causal agent of grapevine red blotch, an emerging disease that affects cultivated grapevine such as Vitis vinifera. The ability to detect viruses in grapevine is often hindered by low virus titers compounded by a variable distribution in the plant and seasonal variations. In order to examine these two variables in relation to GRBV, we developed a quantitative polymerase chain reaction (qPCR) method that incorporates both internal and external references to enhance assay robustness. In greenhouse-grown vines infected with GRBV, qPCR identified highest virus titers in the petioles of fully expanded leaves and significantly reduced levels of virus in the shoot extremities. In vineyard-grown vines infected with GRBV, the virus titer in July and October 2016 followed a pattern similar to that found for the greenhouse-grown plants but, most strikingly, close to half (44%) of the samples analyzed in June 2015 tested negative for infection. The technique presented and results obtained highlight the variability of virus distribution in its host and provide a useful guide for selecting the best tissues for optimal GRBV diagnosis.
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Affiliation(s)
- Felicia J Setiono
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Debotri Chatterjee
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Marc Fuchs
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva 14456, USA
| | - Keith L Perry
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University
| | - Jeremy R Thompson
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University
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26
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Hily JM, Candresse T, Garcia S, Vigne E, Tannière M, Komar V, Barnabé G, Alliaume A, Gilg S, Hommay G, Beuve M, Marais A, Lemaire O. High-Throughput Sequencing and the Viromic Study of Grapevine Leaves: From the Detection of Grapevine-Infecting Viruses to the Description of a New Environmental Tymovirales Member. Front Microbiol 2018; 9:1782. [PMID: 30210456 PMCID: PMC6123372 DOI: 10.3389/fmicb.2018.01782] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/16/2018] [Indexed: 12/20/2022] Open
Abstract
In the past decade, high-throughput sequencing (HTS) has had a major impact on virus diversity studies as well as on diagnosis, providing an unbiased and more comprehensive view of the virome of a wide range of organisms. Rather than the serological and molecular-based methods, with their more "reductionist" view focusing on one or a few known agents, HTS-based approaches are able to give a "holistic snapshot" of the complex phytobiome of a sample of interest. In grapevine for example, HTS is powerful enough to allow for the assembly of complete genomes of the various viral species or variants infecting a sample of known or novel virus species. In the present study, a total RNAseq-based approach was used to determine the full genome sequences of various grapevine fanleaf virus (GFLV) isolates and to analyze the eventual presence of other viral agents. From four RNAseq datasets, a few complete grapevine-infecting virus and viroid genomes were de-novo assembled: (a) three GFLV genomes, 11 grapevine rupestris stem-pitting associated virus (GRSPaV) and six viroids. In addition, a novel viral genome was detected in all four datasets, consisting of a single-stranded, positive-sense RNA molecule of 6033 nucleotides. This genome displays an organization similar to Tymoviridae family members in the Tymovirales order. Nonetheless, the new virus shows enough differences to be considered as a new species defining a new genus. Detection of this new agent in the original grapevines proved very erratic and was only consistent at the end of the growing season. This virus was never detected in the spring period, raising the possibility that it might not be a grapevine-infecting virus, but rather a virus infecting a grapevine-associated organism that may be transiently present on grapevine samples at some periods of the year. Indeed, the Tymoviridae family comprises isometric viruses infecting a wide range of hosts in different kingdoms (Plantae, Fungi, and Animalia). The present work highlights the fact that even though HTS technologies produce invaluable data for the description of the sanitary status of a plant, in-depth biological studies are necessary before assigning a new virus to a particular host in such metagenomic approaches.
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Affiliation(s)
- Jean-Michel Hily
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Villenave d'Ornon, Bordeaux, France
| | - Shahinez Garcia
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Emmanuelle Vigne
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Mélanie Tannière
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Véronique Komar
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Guillaume Barnabé
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Antoine Alliaume
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Sophie Gilg
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Gérard Hommay
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Monique Beuve
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Armelle Marais
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Villenave d'Ornon, Bordeaux, France
| | - Olivier Lemaire
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
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27
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Vončina D, Almeida RPP. Screening of some Croatian autochthonous grapevine varieties reveals a multitude of viruses, including novel ones. Arch Virol 2018; 163:2239-2243. [PMID: 29680925 DOI: 10.1007/s00705-018-3850-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 04/06/2018] [Indexed: 11/24/2022]
Abstract
Next-generation sequencing of total RNA samples from four Croatian autochthonous grapevine varieties revealed the presence of a novel virus in two grapevine accessions. The complete genome sequence of a novel virus, tentatively named "grapevine badnavirus 1" (GBV-1), was reconstructed from a de novo-assembled contig. GBV-1 has a genome of 7,145 nucleotides containing three ORFs with sequence similarity to other badnaviruses. In addition, several other viruses and viroids, including grapevine virus G, grapevine virus K/D, grapevine virus T, grapevine Roditis leaf discoloration-associated virus, grapevine yellow speckle viroids 1 and 2, and hop stunt viroid were detected and identified for the first time in Croatian grapevines in the course of this study.
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Affiliation(s)
- Darko Vončina
- Department of Plant Pathology, University of Zagreb Faculty of Agriculture, 10 000, Zagreb, Croatia.
| | - Rodrigo P P Almeida
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, 94720, USA
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28
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Rumbou A, Candresse T, Marais A, Theil S, Langer J, Jalkanen R, Büttner C. A novel badnavirus discovered from Betula sp. affected by birch leaf-roll disease. PLoS One 2018; 13:e0193888. [PMID: 29494687 PMCID: PMC5833271 DOI: 10.1371/journal.pone.0193888] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 02/20/2018] [Indexed: 01/26/2023] Open
Abstract
In declining birches (Betula sp.) from different European stands affected by the “birch leaf-roll disease” (BLRD) a novel virus is identified by means of RNA-Seq virome analysis. The virus represents a new member in the genus Badnavirus, family Caulimoviridae, tentatively named Birch leaf roll-associated virus (BLRaV) and it is the first badnavirus found to infect birch. Complete genome sequences (7,862–7,864 nucleotides) of three viral isolates of Finnish and German origin have been determined. The virus sequences show a typical badnavirus organization with three major open reading frames (ORFs) and a fourth potential ORF overlapping with the end of ORF3. ORFs 1-2-3 show low level of amino acid identity to the corresponding proteins encoded by other badnaviruses, reaching a maximum of 44% identity (ORF3). Grapevine vein-clearing virus appears as the closest badnavirus when considering the polymerase region. So far, we can exclude evidence for presence of endogenous BLRaV elements in the birch genome, while evidence for the episomal activity of BLRaV is provided. The viral population holds significant haplotype diversity, while co-infection by different BLRaV variants are observed in single hosts. BLRaV presence is associated with the BLRD in both silver (B. pendula) and downy birch (B. pubescens). These results challenge the earlier hypothesis of a causal role of Cherry leaf roll virus in BLRD. Further work is now needed to finally prove that BLRaV is the causal agent for the BLRD.
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Affiliation(s)
- Artemis Rumbou
- Division Phytomedicine, Albrecht Daniel Thaer-Institute, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
- * E-mail:
| | - Thierry Candresse
- Equipe Virologie, UMR 1332 BFP, French National Institute for Agricultural Research (INRA), Villenave d'Ornon Cedex, France
| | - Armelle Marais
- Equipe Virologie, UMR 1332 BFP, French National Institute for Agricultural Research (INRA), Villenave d'Ornon Cedex, France
| | - Sebastien Theil
- Equipe Virologie, UMR 1332 BFP, French National Institute for Agricultural Research (INRA), Villenave d'Ornon Cedex, France
| | - Juliane Langer
- Division Phytomedicine, Albrecht Daniel Thaer-Institute, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Risto Jalkanen
- Rovaniemi Unit, Finnish Forest Research Institute (Metla), Natural Resources Institute, Luke, Rovaniemi, Finland
| | - Carmen Büttner
- Division Phytomedicine, Albrecht Daniel Thaer-Institute, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
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29
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Viral small RNAs reveal the genomic variations of three grapevine vein clearing virus quasispecies populations. Virus Res 2017; 229:24-27. [PMID: 28012998 DOI: 10.1016/j.virusres.2016.12.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 11/23/2022]
Abstract
Viral small RNAs (vsRNAs) include viral small interfering RNAs (vsiRNAs) that are initiators and products of RNA silencing, and small RNAs that are derived from viral RNAs with function still unknown. Sequencing of vsRNAs allows assembling of viral genomes and revelation of viral population variations at genomic levels. Grapevine vein clearing virus (GVCV) is a new member of the family Caulimoviridae whose DNA genome is replicated by reverse transcription of pre-genomic RNA molecules. In this short report, three genomic sequences of GVCV were assembled from vsRNAs that were isolated and sequenced from three individual grapevines in commercial vineyards and compared to the GVCV-CHA reference genome. Profiles of single nucleotide polymorphism among three viral populations indicated a closer relatedness between two populations in different grape cultivars at the same location than those in the same grape cultivar at different locations, suggesting the spread of GVCV populations among vineyards of close proximity. Classic types of vsiRNAs (21-nt, 22-nt, and 24-nt) were found in the three GVCV vsiRNA populations, but these did not produce alignment hotspots on the GVCV-CHA reference genome. The number of 36-nt reads is the highest among vsRNAs, the role of these vsRNAs remains unclear. The analysis of vsRNAs provides a first holistic picture of genomic variations among GVCV viral quasispecies populations that help monitor epidemics and evolution of GVCV populations, an emerging virus that is becoming a threat to grape production in the Midwest region of the USA.
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30
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Perrone I, Chitarra W, Boccacci P, Gambino G. Grapevine-virus-environment interactions: an intriguing puzzle to solve. THE NEW PHYTOLOGIST 2017; 213:983-987. [PMID: 27748957 DOI: 10.1111/nph.14271] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Affiliation(s)
- Irene Perrone
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135, Torino, Italy
| | - Walter Chitarra
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135, Torino, Italy
| | - Paolo Boccacci
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135, Torino, Italy
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135, Torino, Italy
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31
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Al Rwahnih M, Alabi OJ, Westrick NM, Golino D, Rowhani A. Description of a Novel Monopartite Geminivirus and Its Defective Subviral Genome in Grapevine. PHYTOPATHOLOGY 2017; 107:240-251. [PMID: 27670772 DOI: 10.1094/phyto-07-16-0282-r] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A novel virus was detected in grapevines by Illumina sequencing during the screening of two table grape (Vitis vinifera) accessions, cultivars Black Beet and Nagano Purple, from South Korea. The monopartite circular ssDNA genome sequence was subsequently confirmed by rolling cycle amplification, cloning and Sanger sequencing. The complete viral genomic sequence from both accessions ranged from 2,903 to 2,907 nucleotides in length and contained the conserved nonanucleotide sequence TAATATT↓AC and other sequence features typical of the family Geminiviridae, including two predicted sense and four complementary-sense open reading frames. Phylogenetic analysis placed the novel virus in a unique taxon within the family Geminiviridae. A naturally occurring defective subviral DNA was also discovered. This defective DNA molecule carried a deletion of approximately 46% of the full-length genome. Both the genomic and defective DNA molecules were graft-transmissible although no disease is yet correlated with their occurrence in Vitis spp. The tentative names Grapevine geminivirus A (GGVA) and GGVA defective DNA (GGVA D-DNA) are proposed. PCR assays developed using primers designed in the coat protein gene led to the detection of GGVA in 1.74% of 1,262 vines derived from 15 grapevine cultivars from six countries across three continents.
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Affiliation(s)
- Maher Al Rwahnih
- First, third, fourth, and fifth authors: Department of Plant Pathology, University of California, Davis, 95616; and second author: Department of Plant Pathology & Microbiology, Texas A&M AgriLife Research and Extension Center, Weslaco 78596
| | - Olufemi J Alabi
- First, third, fourth, and fifth authors: Department of Plant Pathology, University of California, Davis, 95616; and second author: Department of Plant Pathology & Microbiology, Texas A&M AgriLife Research and Extension Center, Weslaco 78596
| | - Nathaniel M Westrick
- First, third, fourth, and fifth authors: Department of Plant Pathology, University of California, Davis, 95616; and second author: Department of Plant Pathology & Microbiology, Texas A&M AgriLife Research and Extension Center, Weslaco 78596
| | - Deborah Golino
- First, third, fourth, and fifth authors: Department of Plant Pathology, University of California, Davis, 95616; and second author: Department of Plant Pathology & Microbiology, Texas A&M AgriLife Research and Extension Center, Weslaco 78596
| | - Adib Rowhani
- First, third, fourth, and fifth authors: Department of Plant Pathology, University of California, Davis, 95616; and second author: Department of Plant Pathology & Microbiology, Texas A&M AgriLife Research and Extension Center, Weslaco 78596
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32
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Beach S, Kovens M, Hubbert L, Honesty S, Guo Q, Pap D, Dai R, Kovacs L, Qiu W. Genetic and Phenotypic Characterization of Grapevine vein clearing virus from Wild Vitis rupestris. PHYTOPATHOLOGY 2017; 107:138-144. [PMID: 27577962 DOI: 10.1094/phyto-04-16-0173-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Grapevine vein clearing virus (GVCV), a new member of the genus Badnavirus in the family Caulimoviridae, is associated with a vein clearing and vine decline disease that severely affects grape production and berry quality in commercial vineyards in the Midwest region of the United States. In this paper, the genetic and phenotypic characteristics of GVCV-VRU1 and GVCV-VRU2, two isolates from wild Vitis rupestris grapevines in their native habitat, are described. The GVCV-VRU1 genome is 7,755 bp long while the GVCV-VRU2 genome consists of 7,725 bp, both of which are different from the genome of the GVCV-CHA isolate (7,753 bp), which was originally discovered in the grape cultivar 'Chardonel'. The nucleotide sequence identity among GVCV-VRU1, GVCV-VRU2, and GVCV-CHA ranges from 91.6 to 93.4%, and open reading frame (ORF) II is the most divergent ORF with only 83.3 to 88.5% identity. Sequence analysis of the ORF II indicated that GVCV isolates genetically similar to GVCV-VRU1 and GVCV-VRU2 also are present in commercial vineyards. Symptoms of GVCV-VRU1- or GVCV-VRU2-infected wild V. rupestris grapevine appeared initially as translucent vein clearing on young leaves and progressed to vein necrosis on mature leaves. Inoculation of GVCV-VRU1 or GVCV-VRU2 by grafting onto grape cultivar Chardonel resulted in mild mottle and leaf distortion. The natural range of wild V. rupestris grapevines overlaps with commercial vineyards in the Midwestern United States. Therefore, the discovery of GVCV isolates in wild V. rupestris grapevines has important implications for epidemics and management of the GVCV-associated disease.
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Affiliation(s)
- Steven Beach
- First, second, third, fourth, fifth, sixth, seventh, and ninth authors: Center for Grapevine Biotechnology, Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711; and eighth author: Department of Biology, Missouri State University, Springfield, MO 65897
| | - Michael Kovens
- First, second, third, fourth, fifth, sixth, seventh, and ninth authors: Center for Grapevine Biotechnology, Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711; and eighth author: Department of Biology, Missouri State University, Springfield, MO 65897
| | - LeAnn Hubbert
- First, second, third, fourth, fifth, sixth, seventh, and ninth authors: Center for Grapevine Biotechnology, Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711; and eighth author: Department of Biology, Missouri State University, Springfield, MO 65897
| | - Shae Honesty
- First, second, third, fourth, fifth, sixth, seventh, and ninth authors: Center for Grapevine Biotechnology, Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711; and eighth author: Department of Biology, Missouri State University, Springfield, MO 65897
| | - Qiang Guo
- First, second, third, fourth, fifth, sixth, seventh, and ninth authors: Center for Grapevine Biotechnology, Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711; and eighth author: Department of Biology, Missouri State University, Springfield, MO 65897
| | - Daniel Pap
- First, second, third, fourth, fifth, sixth, seventh, and ninth authors: Center for Grapevine Biotechnology, Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711; and eighth author: Department of Biology, Missouri State University, Springfield, MO 65897
| | - Ru Dai
- First, second, third, fourth, fifth, sixth, seventh, and ninth authors: Center for Grapevine Biotechnology, Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711; and eighth author: Department of Biology, Missouri State University, Springfield, MO 65897
| | - Laszlo Kovacs
- First, second, third, fourth, fifth, sixth, seventh, and ninth authors: Center for Grapevine Biotechnology, Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711; and eighth author: Department of Biology, Missouri State University, Springfield, MO 65897
| | - Wenping Qiu
- First, second, third, fourth, fifth, sixth, seventh, and ninth authors: Center for Grapevine Biotechnology, Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711; and eighth author: Department of Biology, Missouri State University, Springfield, MO 65897
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Hadidi A, Flores R, Candresse T, Barba M. Next-Generation Sequencing and Genome Editing in Plant Virology. Front Microbiol 2016; 7:1325. [PMID: 27617007 PMCID: PMC4999435 DOI: 10.3389/fmicb.2016.01325] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 08/11/2016] [Indexed: 01/18/2023] Open
Abstract
Next-generation sequencing (NGS) has been applied to plant virology since 2009. NGS provides highly efficient, rapid, low cost DNA, or RNA high-throughput sequencing of the genomes of plant viruses and viroids and of the specific small RNAs generated during the infection process. These small RNAs, which cover frequently the whole genome of the infectious agent, are 21-24 nt long and are known as vsRNAs for viruses and vd-sRNAs for viroids. NGS has been used in a number of studies in plant virology including, but not limited to, discovery of novel viruses and viroids as well as detection and identification of those pathogens already known, analysis of genome diversity and evolution, and study of pathogen epidemiology. The genome engineering editing method, clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system has been successfully used recently to engineer resistance to DNA geminiviruses (family, Geminiviridae) by targeting different viral genome sequences in infected Nicotiana benthamiana or Arabidopsis plants. The DNA viruses targeted include tomato yellow leaf curl virus and merremia mosaic virus (begomovirus); beet curly top virus and beet severe curly top virus (curtovirus); and bean yellow dwarf virus (mastrevirus). The technique has also been used against the RNA viruses zucchini yellow mosaic virus, papaya ringspot virus and turnip mosaic virus (potyvirus) and cucumber vein yellowing virus (ipomovirus, family, Potyviridae) by targeting the translation initiation genes eIF4E in cucumber or Arabidopsis plants. From these recent advances of major importance, it is expected that NGS and CRISPR-Cas technologies will play a significant role in the very near future in advancing the field of plant virology and connecting it with other related fields of biology.
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Affiliation(s)
- Ahmed Hadidi
- United States Department of Agriculture – Agricultural Research ServiceBeltsville, MD, USA
| | - Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia–Consejo Superior de Investigaciones CientíficasValencia, Spain
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Université de BordeauxBordeaux, France
| | - Marina Barba
- Consiglio per la Ricerca in Agricoltura e l’analisi dell’Economia Agraria, Centro di Ricerca per la Patologia VegetaleRome, Italy
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Bhat AI, Hohn T, Selvarajan R. Badnaviruses: The Current Global Scenario. Viruses 2016; 8:E177. [PMID: 27338451 PMCID: PMC4926197 DOI: 10.3390/v8060177] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/18/2016] [Accepted: 05/25/2016] [Indexed: 12/16/2022] Open
Abstract
Badnaviruses (Family: Caulimoviridae; Genus: Badnavirus) are non-enveloped bacilliform DNA viruses with a monopartite genome containing about 7.2 to 9.2 kb of dsDNA with three to seven open reading frames. They are transmitted by mealybugs and a few species by aphids in a semi-persistent manner. They are one of the most important plant virus groups and have emerged as serious pathogens affecting the cultivation of several horticultural crops in the tropics, especially banana, black pepper, cocoa, citrus, sugarcane, taro, and yam. Some badnaviruses are also known as endogenous viruses integrated into their host genomes and a few such endogenous viruses can be awakened, e.g., through abiotic stress, giving rise to infective episomal forms. The presence of endogenous badnaviruses poses a new challenge for the fool-proof diagnosis, taxonomy, and management of the diseases. The present review aims to highlight emerging disease problems, virus characteristics, transmission, and diagnosis of badnaviruses.
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Affiliation(s)
| | - Thomas Hohn
- UNIBAS, Botanical Institute, 4056 Basel, Switzerland.
| | - Ramasamy Selvarajan
- ICAR-National Research Centre for Banana, Tiruchirapalli 620102, Tamil Nadu, India.
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Chiumenti M, Giampetruzzi A, Morelli M, Savino VN, Martelli GP, La Notte P, Palmisano F, Saldarelli P. Detection and molecular characterization of a Grapevine Roditis leaf discoloration-associated virus (GRLDaV) variant in an autochthonous grape from Apulia (Italy). Virus Genes 2016; 52:428-31. [PMID: 26924587 DOI: 10.1007/s11262-016-1305-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/16/2016] [Indexed: 11/26/2022]
Abstract
The complete nucleotide sequence and genome organization of a new Badnavirus isolated from the autochthonous grapevine variety "Bombino nero" from Apulia (Italy) was determined. The genome of this virus consists of 7097 nt and has four open reading frames (ORFs). Analysis of putative proteins encoded by each ORF revealed greatest sequence similarity to Grapevine Roditis leaf discoloration-associated virus w4 (GRLDaV; NC_027131). In a pairwise alignment with GLRDaV w4 genome sequence, the "Bombino Nero" sequence was 109 nt longer with a major 57 nt insertion between positions 2405 and 2413. Furthermore, its putative ORF4 is located after the ORF3, while in the GLRDaV w4 sequence, the putative ORF4 completely overlapped ORF3. Nucleotide analysis classifies this new Badnavirus as a GLRDaV strain, which was named GRLDaV-BN. Multi-year field observations showed that the GLRDaV-BN-infected vine was symptomless.
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Affiliation(s)
- Michela Chiumenti
- CNR-Istituto per la Protezione Sostenibile delle Piante (IPSP), UOS Bari, Via Amendola 122/D, 70126, Bari, Italy.
| | - Annalisa Giampetruzzi
- CNR-Istituto per la Protezione Sostenibile delle Piante (IPSP), UOS Bari, Via Amendola 122/D, 70126, Bari, Italy
| | - Massimiliano Morelli
- CNR-Istituto per la Protezione Sostenibile delle Piante (IPSP), UOS Bari, Via Amendola 122/D, 70126, Bari, Italy
| | - Vito Nicola Savino
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti (DiSSPA), Università degli Studi di Bari Aldo Moro, 70126, Bari, Italy
- Centro di Ricerca, Sperimentazione e Formazione in Agricoltura (CRSFA) "Basile Caramia", Locorotondo, 70010, Bari, Italy
| | - Giovanni Paolo Martelli
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti (DiSSPA), Università degli Studi di Bari Aldo Moro, 70126, Bari, Italy
| | - Pierfederico La Notte
- CNR-Istituto per la Protezione Sostenibile delle Piante (IPSP), UOS Bari, Via Amendola 122/D, 70126, Bari, Italy
- Centro di Ricerca, Sperimentazione e Formazione in Agricoltura (CRSFA) "Basile Caramia", Locorotondo, 70010, Bari, Italy
| | - Francesco Palmisano
- Centro di Ricerca, Sperimentazione e Formazione in Agricoltura (CRSFA) "Basile Caramia", Locorotondo, 70010, Bari, Italy
| | - Pasquale Saldarelli
- CNR-Istituto per la Protezione Sostenibile delle Piante (IPSP), UOS Bari, Via Amendola 122/D, 70126, Bari, Italy
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Xiao H, Kim WS, Meng B. A highly effective and versatile technology for the isolation of RNAs from grapevines and other woody perennials for use in virus diagnostics. Virol J 2015; 12:171. [PMID: 26482551 PMCID: PMC4615883 DOI: 10.1186/s12985-015-0376-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/05/2015] [Indexed: 10/31/2022] Open
Abstract
BACKGROUND Isolation of pure RNA from woody perennials, especially fruit crops such as grapevine rich in complex secondary metabolites, has remained very challenging. Lack of effective RNA isolation technology has resulted in difficulties in viral diagnosis and discovery as well as studies on many biological processes of these highly important woody plants. It is imperative to develop and refine methodologies with which large amounts of pure nucleic acids can be readily isolated from woody perennials. METHODS We compared five commonly used RNA isolation kits in isolating total RNA from twelve species of woody perennials. We made modifications to select RNA isolation systems to simplify and improve their efficiency in RNA isolation. The yield and quality of isolated RNAs were assessed via gel electrophoresis and spectrophotometric measurement. We also performed RT-PCR and RT-qPCR to detect several major viruses from grapevines. RESULTS Two of the kits were shown to be the best in both the yield and quality of the isolated RNA from all twelve woody species. Using disposable extraction bags for tissue homogenization not only improved the yield without affecting quality, but also made the RNA isolation technology simpler, less costly, and suitable for adoption by many potential users with facility limitations. This system was successfully applied to a wide range of woody plants, including fruit crops, ornamentals and timber trees. Inclusion of polyvinylpyrrolidone in the extraction buffer drastically improved the performance of the system in isolating total RNA from old grapevine leaves collected later in the season. This modification made our system highly effective in isolating quality RNA from grapevine leaves throughout the entire growing season. We further demonstrated that the resulting nucleic acid preparations are suitable for detection of several major grapevine viruses with RNA or DNA genomes using PCR, RT-PCR and qPCR as well as for assays on plant microRNAs. CONCLUSIONS This improved RNA isolation system would have wide applications in viral diagnostics and discovery, studies on gene expression and regulation, transcriptomics, and small RNA biology in grapevines. We believe this system will also be useful in diverse applications pertaining to research on many other woody perennials and recalcitrant plant species.
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Affiliation(s)
- Huogen Xiao
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
| | - Won-Sik Kim
- Norgen BioTek, Thorald, ON, L2V 4Y6, Canada.
| | - Baozhong Meng
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
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Sudarshana MR, Perry KL, Fuchs MF. Grapevine Red Blotch-Associated Virus, an Emerging Threat to the Grapevine Industry. PHYTOPATHOLOGY 2015; 105:1026-1032. [PMID: 25738551 DOI: 10.1094/phyto-12-14-0369-fi] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Grapevine red blotch-associated virus (GRBaV) is a newly identified virus of grapevines and a putative member of a new genus within the family Geminiviridae. This virus is associated with red blotch disease that was first reported in California in 2008. It affects the profitability of vineyards by substantially reducing fruit quality and ripening. In red-berried grapevine cultivars, foliar disease symptoms consist of red blotches early in the season that can expand and coalesce across most of the leaf blade later in the season. In white-berried grapevine cultivars, foliar disease symptoms are less conspicuous and generally involve irregular chlorotic areas that may become necrotic late in the season. Determining the GRBaV genome sequence yielded critical information for the design of primers for polymerase chain reaction-based diagnostics. To date, GRBaV has been reported in the major grape-growing areas in North America and two distinct phylogenetic clades have been described. Spread of GRBaV is suspected in certain vineyards but a vector of epidemiological significance has yet to be identified. Future research will need to focus on virus spread, the production of clean planting stocks, and the development of management options that are effective, economical, and environmentally friendly.
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Affiliation(s)
- Mysore R Sudarshana
- First author: United States Department of Agriculture-Agricultural Research Service, Department of Plant Pathology, University of California, Davis 95616; second author: Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, 334 Plant Science, Cornell University, Ithaca, NY 14853; and third author: Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456
| | - Keith L Perry
- First author: United States Department of Agriculture-Agricultural Research Service, Department of Plant Pathology, University of California, Davis 95616; second author: Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, 334 Plant Science, Cornell University, Ithaca, NY 14853; and third author: Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456
| | - Marc F Fuchs
- First author: United States Department of Agriculture-Agricultural Research Service, Department of Plant Pathology, University of California, Davis 95616; second author: Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, 334 Plant Science, Cornell University, Ithaca, NY 14853; and third author: Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456
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38
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Roossinck MJ, Martin DP, Roumagnac P. Plant Virus Metagenomics: Advances in Virus Discovery. PHYTOPATHOLOGY 2015; 105:716-27. [PMID: 26056847 DOI: 10.1094/phyto-12-14-0356-rvw] [Citation(s) in RCA: 205] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
In recent years plant viruses have been detected from many environments, including domestic and wild plants and interfaces between these systems-aquatic sources, feces of various animals, and insects. A variety of methods have been employed to study plant virus biodiversity, including enrichment for virus-like particles or virus-specific RNA or DNA, or the extraction of total nucleic acids, followed by next-generation deep sequencing and bioinformatic analyses. All of the methods have some shortcomings, but taken together these studies reveal our surprising lack of knowledge about plant viruses and point to the need for more comprehensive studies. In addition, many new viruses have been discovered, with most virus infections in wild plants appearing asymptomatic, suggesting that virus disease may be a byproduct of domestication. For plant pathologists these studies are providing useful tools to detect viruses, and perhaps to predict future problems that could threaten cultivated plants.
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Affiliation(s)
- Marilyn J Roossinck
- First author: Department of Plant Pathology and Environmental Microbiology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802; second author: Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, 7925 South Africa; and third author: CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | - Darren P Martin
- First author: Department of Plant Pathology and Environmental Microbiology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802; second author: Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, 7925 South Africa; and third author: CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | - Philippe Roumagnac
- First author: Department of Plant Pathology and Environmental Microbiology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802; second author: Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, 7925 South Africa; and third author: CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
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39
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Al Rwahnih M, Daubert S, Golino D, Islas C, Rowhani A. Comparison of Next-Generation Sequencing Versus Biological Indexing for the Optimal Detection of Viral Pathogens in Grapevine. PHYTOPATHOLOGY 2015; 105:758-63. [PMID: 25689518 DOI: 10.1094/phyto-06-14-0165-r] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
A bioassay is routinely used to determine the viral phytosanitary status of commercial grapevine propagation material in many countries around the world. That test is based on the symptoms developed in the field by specific indicator host plants that are graft-inoculated from the vines being tested. We compared the bioassay against next-generation sequencing (NGS) analysis of grapevine material. NGS is a laboratory procedure that catalogs the genomic sequences of the viruses and other pathogens extracted as DNA and RNA from infected vines. NGS analysis was found to be superior to the standard bioassay in detection of viruses of agronomic significance, including virus infections at low titers. NGS was also found to be superior to the bioassay in its comprehensiveness, the speed of its analysis, and for the discovery of novel, uncharacterized viruses.
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Affiliation(s)
- Maher Al Rwahnih
- Department of Plant Pathology, University of California, Davis 95616
| | - Steve Daubert
- Department of Plant Pathology, University of California, Davis 95616
| | - Deborah Golino
- Department of Plant Pathology, University of California, Davis 95616
| | - Christina Islas
- Department of Plant Pathology, University of California, Davis 95616
| | - Adib Rowhani
- Department of Plant Pathology, University of California, Davis 95616
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40
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Bag S, Al Rwahnih M, Li A, Gonzalez A, Rowhani A, Uyemoto JK, Sudarshana MR. Detection of a New Luteovirus in Imported Nectarine Trees: A Case Study to Propose Adoption of Metagenomics in Post-Entry Quarantine. PHYTOPATHOLOGY 2015; 105:840-846. [PMID: 25775105 DOI: 10.1094/phyto-09-14-0262-r] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In spring 2013, 5-year-old nectarine (Prunus persica) trees, grafted on peach rootstock Nemaguard, were found stunted in a propagation block in California. These trees had been propagated from budwood of three nectarine cultivars imported from France and cleared through the post-entry quarantine procedure. Examination of the canopy failed to reveal any obvious symptoms. However, examination of the trunks, after stripping the bark, revealed extensive pitting on the woody cylinder. To investigate the etiological agent, double-stranded RNA was extracted from bark scrapings from the scion and rootstock portions, and a cDNA library was prepared and sequenced using the Illumina platform. BLAST analysis of the contigs generated by the de novo assembly of sequence reads indicated the presence of a novel luteovirus. Complete sequence of the viral genome was determined by sequencing of three overlapping cDNA clones generated by reverse transcription-polymerase chain reaction (RT-PCR) and by rapid amplification of the 5'- and 3'-termini. The virus genome was comprised of 4,991 nucleotides with a gene organization similar to members of the genus Luteovirus (family Luteoviridae). The presence of the virus, tentatively named Nectarine stem pitting-associated virus, was confirmed in symptomatic trees by RT-PCR. Discovery of a new virus in nectarine trees after post-entry quarantine indicates the importance of including (i) metagenomic analysis by next-generation sequencing approach as an essential tool to assess the plant health status, and (ii) examination of the woody cylinders as part of the indexing process.
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Affiliation(s)
- Sudeep Bag
- First, second, and fifth authors: Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616; and third, fourth, sixth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616
| | - Maher Al Rwahnih
- First, second, and fifth authors: Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616; and third, fourth, sixth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616
| | - Ashley Li
- First, second, and fifth authors: Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616; and third, fourth, sixth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616
| | - Asaul Gonzalez
- First, second, and fifth authors: Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616; and third, fourth, sixth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616
| | - Adib Rowhani
- First, second, and fifth authors: Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616; and third, fourth, sixth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616
| | - Jerry K Uyemoto
- First, second, and fifth authors: Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616; and third, fourth, sixth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616
| | - Mysore R Sudarshana
- First, second, and fifth authors: Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616; and third, fourth, sixth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616
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41
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Glasa M, Predajňa L, Šoltys K, Sabanadzovic S, Olmos A. Detection and molecular characterisation of Grapevine Syrah virus-1 isolates from Central Europe. Virus Genes 2015; 51:112-21. [PMID: 25940164 DOI: 10.1007/s11262-015-1201-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/15/2015] [Indexed: 10/23/2022]
Abstract
Grapevine Syrah virus-1 (GSyV-1) was identified by small-RNA deep sequencing in Slovak grapevine co-infected by several other viruses. The RT-PCR assays developed in this work substantially improved the virus detection and allowed the identification of GSyV-1 in tested grapevine samples from Slovakia and the Czech Republic at an unexpectedly high rate (ca. 30 %). Subsequently, complete genome sequences of 3 GSyV-1 isolates (2 Slovak and 1 Czech) were determined by Sanger sequencing, showing a typical marafivirus genome organization. Analyses of complete genome sequences showed a higher intra-group diversity among these 3 central European GSyV-1 isolates (differences reaching 7.1 % at the nucleotide level) in comparison to 3 previously characterized North American isolates (only 1.2 % intra-group divergence). A substantially higher divergence among central European isolates and their clustering into two major phylogenetic groups was further confirmed by the partial genome analysis of additional 26 isolates. The CP-centered study did not support the geography-based clustering among central European and American isolates. Nevertheless, the sequence data of the highly variable 5'-proximal portion of the genome obtained for few additional isolates from Slovakia and Czech Republic showed the presence of both, "European-" and "north American-like", GSyV-1 isolates in the analyzed grapevine samples.
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Affiliation(s)
- Miroslav Glasa
- Department of Plant Virology, Institute of Virology, Slovak Academy of Sciences, Dúbravská cesta 9, 84505, Bratislava, Slovakia,
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Maliogka VI, Olmos A, Pappi PG, Lotos L, Efthimiou K, Grammatikaki G, Candresse T, Katis NI, Avgelis AD. A novel grapevine badnavirus is associated with the Roditis leaf discoloration disease. Virus Res 2015; 203:47-55. [PMID: 25791736 DOI: 10.1016/j.virusres.2015.03.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 03/04/2015] [Accepted: 03/08/2015] [Indexed: 01/15/2023]
Abstract
Roditis leaf discoloration (RLD), a graft-transmissible disease of grapevine, was first reported in Greece in the 1980s. Even though various native grapevine viruses were identified in the affected vines, the etiology of the disease remained unknown. In the present study, we used an NGS platform for sequencing siRNAs from a twenty-year old Roditis vine showing typical RLD symptoms. Analysis of the NGS data revealed the presence of various known grapevine viruses and viroids as well as a hitherto uncharacterized DNA virus. The circular genome of the new virus was fully reassembled. It is 6988 nts long and includes 4 open reading frames (ORFs). ORF1, ORF2 and ORF4 code for proteins with unknown functions while ORF3 encodes a polyprotein with motifs related to the replication, encapsidation and movement of the virus. Phylogenetic analysis classified the novel virus within the genus Badnavirus, with closest relationship to Fig badnavirus 1. Further studies showed that the new badnavirus is closely related with the RLD disease and the provisional name grapevine Roditis leaf discoloration-associated virus (GRLDaV) is proposed. Our findings extend the number of DNA viruses identified in grapevine, further drawing attention to the potential importance of this virus group on grapevine pathology.
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Affiliation(s)
- Varvara I Maliogka
- Lab of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, 54124 Thessaloniki, Greece.
| | - Antonio Olmos
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Plant Protection and Biotechnology Center, 46113 Moncada, Valencia, Spain
| | - Polyxeni G Pappi
- Lab of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, 54124 Thessaloniki, Greece
| | - Leonidas Lotos
- Lab of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, 54124 Thessaloniki, Greece
| | - Konstantinos Efthimiou
- Lab of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, 54124 Thessaloniki, Greece
| | - Garyfalia Grammatikaki
- Faculty of Agriculture & Food Technology, Technological Education Institute of Crete, 71 004 Heraklion, Crete, Greece
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, CS20032, F-33882 Villenave d'Ornon cedex, France; UMR 1332 Biologie du Fruit et Pathologie, Université de Bordeaux, CS20032, F-33882 Villenave d'Ornon cedex, France
| | - Nikolaos I Katis
- Lab of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, 54124 Thessaloniki, Greece
| | - Apostolos D Avgelis
- Institute of Viticulture of Heraklion, Hellenic Agricultural Organization-Demeter, 71 307 Heraklion, Crete, Greece
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Lin YT, Wang YP, Wang FD, Fung CP. Community-onset Klebsiella pneumoniae pneumonia in Taiwan: clinical features of the disease and associated microbiological characteristics of isolates from pneumonia and nasopharynx. Front Microbiol 2015. [PMID: 25741336 PMCID: PMC5808220 DOI: 10.3389/fmicb.2018.00122] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
As virus diseases cannot be controlled by traditional plant protection methods, the risk of their spread have to be minimized on vegetatively propagated plants, such as grapevine. Metagenomic approaches used for virus diagnostics offer a unique opportunity to reveal the presence of all viral pathogens in the investigated plant, which is why their application can reduce the risk of using infected material for a new plantation. Here we used a special branch, deep sequencing of virus-derived small RNAs, of this high-throughput method for virus diagnostics, and determined viromes of vineyards in Hungary. With NGS of virus-derived small RNAs we could detect not only the viruses tested routinely, but also new ones, which had never been described in Hungary before. Virus presence did not correlate with the age of the plantation, moreover phylogenetic analysis of the identified virus isolates suggests that infections are mostly caused by the use of infected propagating material. Our results, validated by other molecular methods, raised further questions to be answered before this method can be introduced as a routine, reliable test for grapevine virus diagnostics.
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Affiliation(s)
- Yi-Tsung Lin
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital Taipei, Taiwan ; School of Medicine, National Yang-Ming University Taipei, Taiwan
| | - Yu-Ping Wang
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital Taipei, Taiwan
| | - Fu-Der Wang
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital Taipei, Taiwan ; School of Medicine, National Yang-Ming University Taipei, Taiwan
| | - Chang-Phone Fung
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital Taipei, Taiwan ; School of Medicine, National Yang-Ming University Taipei, Taiwan
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Czotter N, Molnar J, Szabó E, Demian E, Kontra L, Baksa I, Szittya G, Kocsis L, Deak T, Bisztray G, Tusnady GE, Burgyan J, Varallyay E. Community-onset Klebsiella pneumoniae pneumonia in Taiwan: clinical features of the disease and associated microbiological characteristics of isolates from pneumonia and nasopharynx. Front Microbiol 2015; 9:122. [PMID: 25741336 PMCID: PMC5808220 DOI: 10.3389/fmicb.2015.00122] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 01/30/2015] [Indexed: 12/31/2022] Open
Abstract
Klebsiella pneumoniae is an important cause of community-onset pneumonia in Asian countries and South Africa. We investigated the clinical characteristics of K. pneumoniae causing community-onset pneumonia, and the associated microbiological features between K. pneumoniae isolates from pneumonia and those from the nasopharynx in Taiwan. This study was conducted at the Taipei Veterans General Hospital during July, 2012 to February, 2014. The clinical characteristics in patients with community-onset K. pneumoniae pneumonia were analyzed. K. pneumoniae isolates from the nasopharynx of adults attending otorhinolaryngology outpatient clinics were collected to compare their microbiological features with those from pneumonia. Capsular genotypes, antimicrobial susceptibility, and multilocus sequence type (MLST) were determined among these strains. Ninety-one patients with community-onset K. pneumoniae pneumonia were enrolled. We found a high mortality (29.7%) among these patients. Capsular types K1, K2, K5, K20, K54, and K57 accounted for ∼70% of the K. pneumoniae isolates causing pneumonia, and ∼70% of all the K. pneumoniae strains isolated from the nasopharynx of patients in outpatient clinics. The MLST profiles further demonstrated the genetic relatedness between most pneumonia isolates and those from the nasopharynx. In conclusion, our results show that community-onset pneumonia caused by K. pneumoniae was associated with high mortality and could have a reservoir in the nasopharynx. To tackle this high-mortality disease, the distribution of capsular types in the nasopharynx might have implications for future vaccine development.
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Affiliation(s)
- Nikoletta Czotter
- National Agricultural Research and Innovation Center, Agricultural Biotechnology Institute, Gödöllo, Hungary
| | - Janos Molnar
- Research Center of Natural Sciences, Institute of Enzymology, HAS, Budapest, Hungary
- Department of Biotechnology, Nanophage-therapy Center, Enviroinvest Corporation, Pécs, Hungary
| | - Emese Szabó
- National Agricultural Research and Innovation Center, Agricultural Biotechnology Institute, Gödöllo, Hungary
| | - Emese Demian
- National Agricultural Research and Innovation Center, Agricultural Biotechnology Institute, Gödöllo, Hungary
| | - Levente Kontra
- National Agricultural Research and Innovation Center, Agricultural Biotechnology Institute, Gödöllo, Hungary
| | - Ivett Baksa
- National Agricultural Research and Innovation Center, Agricultural Biotechnology Institute, Gödöllo, Hungary
| | - Gyorgy Szittya
- National Agricultural Research and Innovation Center, Agricultural Biotechnology Institute, Gödöllo, Hungary
| | - Laszlo Kocsis
- Department of Horticulture, Georgikon Faculty, University of Pannonia, Keszthely, Hungary
| | - Tamas Deak
- Department of Viticulture, Institute of Viticulture and Oenology, Szent-Istvan University, Budapest, Hungary
| | - Gyorgy Bisztray
- Department of Viticulture, Institute of Viticulture and Oenology, Szent-Istvan University, Budapest, Hungary
| | - Gabor E. Tusnady
- Research Center of Natural Sciences, Institute of Enzymology, HAS, Budapest, Hungary
| | - Jozsef Burgyan
- National Agricultural Research and Innovation Center, Agricultural Biotechnology Institute, Gödöllo, Hungary
| | - Eva Varallyay
- National Agricultural Research and Innovation Center, Agricultural Biotechnology Institute, Gödöllo, Hungary
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Abstract
Production of virus-tested material of vegetatively propagated crops through national certification schemes has been implemented in many developed countries for more than 60 years and its importance for being the best virus control means is well acknowledged by growers worldwide. The two most important elements of certification schemes are the use of sensitive, reliable, and rapid detection techniques to check the health status of the material produced and effective and simple sanitation procedures for the elimination of viruses if present in candidate material before it enters the scheme. New technologies such as next-generation sequencing platforms are expected to further enhance the efficiency of certification and production of virus-tested material, through the clarification of the unknown etiology of several graft-transmissible diseases. The successful production of virus-tested material is a demanding procedure relying on the close collaboration of researchers, official services, and the private sector. Moreover, considerable efforts have been made by regional plant protection organizations such as the European and Mediterranean Plant Protection Organization (EPPO), the North American Plant Protection Organization (NAPPO), and the European Union and the USA to harmonize procedures, methodologies, and techniques in order to assure the quality, safety, and movement of the vegetatively propagated material produced around the world.
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Affiliation(s)
- Christina Varveri
- Laboratory of Virology, Benaki Phytopathological Institute, Kifissia, Greece.
| | - Varvara I Maliogka
- Faculty of agriculture, Forestry and Natural Environment, School of Agriculture, Plant Pathology Lab, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Zhang Y, Angel CA, Valdes S, Qiu W, Schoelz JE. Characterization of the promoter of Grapevine vein clearing virus. J Gen Virol 2015; 96:165-169. [PMID: 25281563 DOI: 10.1099/vir.0.069286-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Grapevine vein clearing virus (GVCV) is a recently discovered DNA virus in grapevine that is closely associated with the grapevine vein clearing syndrome observed in vineyards in Missouri and surrounding states. The genome sequence of GVCV indicates that it belongs to the genus Badnavirus in the family Caulimoviridae. To identify the GVCV promoter, we cloned portions of the GVCV large intergenic region in front of a GFP gene present in an Agrobacterium tumefaciens binary vector. GFP expression was assessed by ELISA 3 days after agroinfiltration of Nicotiana benthamiana leaves. We found that the GVCV DNA segment between nts 7332 and 7672 directed expression of GFP and this expression was stronger than expression using the Cauliflower mosaic virus 35S promoter. It was revealed by 5' and 3' RACE that transcription was initiated predominantly at nt 7571 and terminated at nt 7676.
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Affiliation(s)
- Y Zhang
- Division of Plant Sciences, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - C A Angel
- Division of Plant Sciences, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - S Valdes
- Division of Plant Sciences, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - W Qiu
- Center for Grapevine Biotechnology, William H. Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711, USA
| | - J E Schoelz
- Division of Plant Sciences, University of Missouri-Columbia, Columbia, MO 65211, USA
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Wu Q, Ding SW, Zhang Y, Zhu S. Identification of viruses and viroids by next-generation sequencing and homology-dependent and homology-independent algorithms. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:425-44. [PMID: 26047558 DOI: 10.1146/annurev-phyto-080614-120030] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
A fast, accurate, and full indexing of viruses and viroids in a sample for the inspection and quarantine services and disease management is desirable but was unrealistic until recently. This article reviews the rapid and exciting recent progress in the use of next-generation sequencing (NGS) technologies for the identification of viruses and viroids in plants. A total of four viroids/viroid-like RNAs and 49 new plant RNA and DNA viruses from 18 known or unassigned virus families have been identified from plants since 2009. A comparison of enrichment strategies reveals that full indexing of RNA and DNA viruses as well as viroids in a plant sample at single-nucleotide resolution is made possible by one NGS run of total small RNAs, followed by data mining with homology-dependent and homology-independent computational algorithms. Major challenges in the application of NGS technologies to pathogen discovery are discussed.
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Affiliation(s)
- Qingfa Wu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 China;
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48
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Abstract
Grapevine is a high value vegetatively propagated fruit crop that suffers from numerous viruses, including some that seriously affect the profitability of vineyards. Nowadays, 64 viruses belonging to different genera and families have been reported in grapevines and new virus species will likely be described in the future. Three viral diseases namely leafroll, rugose wood, and infectious degeneration are of major economic importance worldwide. The viruses associated with these diseases are transmitted by mealybugs, scale and soft scale insects, or dagger nematodes. Here, we review control measures of the major grapevine viral diseases. More specifically, emphasis is laid on (i) approaches for the production of clean stocks and propagative material through effective sanitation, robust diagnosis, as well as local and regional certification efforts, (ii) the management of vectors of viruses using cultural, biological, and chemical methods, and (iii) the production of resistant grapevines mainly through the application of genetic engineering. The benefits and limitations of the different control measures are discussed with regard to accomplishments and future research directions.
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Affiliation(s)
- Varvara I Maliogka
- Faculty of agriculture, Forestry and Natural Environment, School of Agriculture, Plant Pathology Lab, Aristotle University of Thessaloniki, Thessaloniki, Greece.
| | | | - Marc Fuchs
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, New York State Agricultural Experiment Station, Geneva, New York, USA
| | - Nikolaos I Katis
- Faculty of agriculture, Forestry and Natural Environment, School of Agriculture, Plant Pathology Lab, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Abstract
Viroids are the smallest autonomous infectious nucleic acids known so far. With a small circular RNA genome of about 250-400 nt, which apparently does not code for any protein, viroids replicate and move systemically in host plants. Since the discovery of the first viroid almost forty-five years ago, many different viroids have been isolated, characterized and, frequently, identified as the causal agents of plant diseases. The first viroid classification scheme was proposed in the early 1990s and adopted by the International Committee on Taxonomy of Viruses (ICTV) a few years later. Here, the current viroid taxonomy scheme and the criteria for viroid species demarcation are discussed, highlighting the main taxonomic questions currently under consideration by the ICTV Viroid Study Group. The impact of correct taxonomic annotation of viroid sequence variants is also addressed, taking into consideration the increasing application of next-generation sequencing and bioinformatics for known and previously unrecognized viroids.
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50
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Kutnjak D, Silvestre R, Cuellar W, Perez W, Müller G, Ravnikar M, Kreuze J. Complete genome sequences of new divergent potato virus X isolates and discrimination between strains in a mixed infection using small RNAs sequencing approach. Virus Res 2014; 191:45-50. [PMID: 25051147 DOI: 10.1016/j.virusres.2014.07.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 07/09/2014] [Accepted: 07/12/2014] [Indexed: 10/25/2022]
Abstract
Potato virus X (PVX; genus Potexvirus, family Alphaflexiviridae, order Tymovirales) is one of the most widespread and intensively studied viruses of potato. However, little is known about its diversity in its likely center of radiation, the Andean region of South America. To fill this gap, the strategy of Illumina deep sequencing of small RNAs was used to obtain complete or near complete genome sequence of PVX from 5 symptomatically infected greenhouse and 3 field samples (Solanum tuberosum) from Peru. PVX sequences determined in this study were assigned into three different phylogenetic groups of isolates. Notably, a complete genome sequence of a representative of a new PVX phylogenetic lineage was obtained, which shows a high level of sequence dissimilarity to other completely sequenced isolates (∼17%). The new PVX genotype was detected in greenhouse and field samples. One of the field samples was infected with the mixture of two PVX strains, which were efficiently discriminated using small RNA sequencing approach. The study confirms the utility of small RNAs deep sequencing for successful viral strain differentiation and discovery of new viral strains and indicates a high diversity of PVX in the Andean region of South America, a pattern which may be expected also for other potato pathogens.
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Affiliation(s)
- Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | | | | | | | | | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Jan Kreuze
- International Potato Center (CIP), Lima, Peru.
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