1
|
Rodríguez-Verástegui LL, Ramírez-Zavaleta CY, Capilla-Hernández MF, Gregorio-Jorge J. Viruses Infecting Trees and Herbs That Produce Edible Fleshy Fruits with a Prominent Value in the Global Market: An Evolutionary Perspective. PLANTS (BASEL, SWITZERLAND) 2022; 11:203. [PMID: 35050091 PMCID: PMC8778216 DOI: 10.3390/plants11020203] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 05/12/2023]
Abstract
Trees and herbs that produce fruits represent the most valuable agricultural food commodities in the world. However, the yield of these crops is not fully achieved due to biotic factors such as bacteria, fungi, and viruses. Viruses are capable of causing alterations in plant growth and development, thereby impacting the yield of their hosts significantly. In this work, we first compiled the world's most comprehensive list of known edible fruits that fits our definition. Then, plant viruses infecting those trees and herbs that produce fruits with commercial importance in the global market were identified. The identified plant viruses belong to 30 families, most of them containing single-stranded RNA genomes. Importantly, we show the overall picture of the host range for some virus families following an evolutionary approach. Further, the current knowledge about plant-virus interactions, focusing on the main disorders they cause, as well as yield losses, is summarized. Additionally, since accurate diagnosis methods are of pivotal importance for viral diseases control, the current and emerging technologies for the detection of these plant pathogens are described. Finally, the most promising strategies employed to control viral diseases in the field are presented, focusing on solutions that are long-lasting.
Collapse
Affiliation(s)
| | - Candy Yuriria Ramírez-Zavaleta
- Cuerpo Académico Procesos Biotecnológicos, Universidad Politécnica de Tlaxcala, Av. Universidad Politécnica 1, San Pedro Xalcaltzinco 90180, Mexico; (C.Y.R.-Z.); (M.F.C.-H.)
| | - María Fernanda Capilla-Hernández
- Cuerpo Académico Procesos Biotecnológicos, Universidad Politécnica de Tlaxcala, Av. Universidad Politécnica 1, San Pedro Xalcaltzinco 90180, Mexico; (C.Y.R.-Z.); (M.F.C.-H.)
| | - Josefat Gregorio-Jorge
- Consejo Nacional de Ciencia y Tecnología, Universidad Politécnica de Tlaxcala, Av. Insurgentes Sur 1582, Col. Crédito Constructor, Ciudad de Mexico 03940, Mexico
| |
Collapse
|
2
|
Cao X, Zhao R, Wang H, Zhang H, Zhao X, Khan LU, Huang X. Genomic diversity of Areca Palm Velarivirus 1 (APV1) in Areca palm (Areca catechu) plantations in Hainan, China. BMC Genomics 2021; 22:725. [PMID: 34620080 PMCID: PMC8499421 DOI: 10.1186/s12864-021-07976-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 08/30/2021] [Indexed: 11/16/2022] Open
Abstract
Background Areca palm (Areca catechu L.) is an important commercial crop in southeast Asia, but its cultivation is threatened by yellowing leaf disease (YLD). Areca palm velarivirus 1 (APV1) was recently associated with YLD, but little is known regarding its population and genetic diversity. To assess the diversity of YLD, the APV1 genome was sequenced in YLD samples collected from different sites in Hainan. Results Twenty new and complete APV1 genomes were identified. The APV1 isolates had highly conserved sequences in seven open reading frames (ORFs; > 95% nucleotide [nt] identity) at the 3′ terminal, but there was diversity (81–87% nt identity) in three ORFs at the 5′ terminal. Phylogenetic analysis divided the APV1 isolates into three phylogroups, with 16 isolates (> 70%) in phylogroup A. Mixed infections with different genotypes in the same tree were identified; this was closely correlated with higher levels of genetic recombination. Conclusions Phylogroup A is the most prevalent APV1 genotype in areca palm plantations in Hainan, China. Mixed infection with different genotypes can lead to genomic recombination of APV1. Our data provide a foundation for accurate diagnostics, characterization of etiology, and elucidation of the evolutionary relationships of APV1 populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07976-6.
Collapse
Affiliation(s)
- Xianmei Cao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Ruibai Zhao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Hongxing Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Huaiwen Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Xue Zhao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Latif Ullah Khan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Xi Huang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China.
| |
Collapse
|
3
|
Vondras AM, Lerno L, Massonnet M, Minio A, Rowhani A, Liang D, Garcia J, Quiroz D, Figueroa‐Balderas R, Golino DA, Ebeler SE, Al Rwahnih M, Cantu D. Rootstock influences the effect of grapevine leafroll-associated viruses on berry development and metabolism via abscisic acid signalling. MOLECULAR PLANT PATHOLOGY 2021; 22:984-1005. [PMID: 34075700 PMCID: PMC8295520 DOI: 10.1111/mpp.13077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/17/2021] [Accepted: 04/19/2021] [Indexed: 05/14/2023]
Abstract
Grapevine leafroll-associated virus (GLRaV) infections are accompanied by symptoms influenced by host genotype, rootstock, environment, and which individual or combination of GLRaVs is present. Using a dedicated experimental vineyard, we studied the responses to GLRaVs in ripening berries from Cabernet Franc grapevines grafted to different rootstocks and with zero, one, or pairs of leafroll infection(s). RNA sequencing data were mapped to a high-quality Cabernet Franc genome reference assembled to carry out this study and integrated with hormone and metabolite abundance data. This study characterized conserved and condition-dependent responses to GLRaV infection(s). Common responses to GLRaVs were reproduced in two consecutive years and occurred in plants grafted to different rootstocks in more than one infection condition. Though different infections were inconsistently distinguishable from one another, the effects of infections in plants grafted to different rootstocks were distinct at each developmental stage. Conserved responses included the modulation of genes related to pathogen detection, abscisic acid (ABA) signalling, phenylpropanoid biosynthesis, and cytoskeleton remodelling. ABA, ABA glucose ester, ABA and hormone signalling-related gene expression, and the expression of genes in several transcription factor families differentiated the effects of GLRaVs in berries from Cabernet Franc grapevines grafted to different rootstocks. These results support that ABA participates in the shared responses to GLRaV infection and differentiates the responses observed in grapevines grafted to different rootstocks.
Collapse
Affiliation(s)
- Amanda M. Vondras
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Larry Lerno
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Mélanie Massonnet
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Andrea Minio
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Adib Rowhani
- Department of Plant PathologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Dingren Liang
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Jadran Garcia
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Daniela Quiroz
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCaliforniaUSA
| | | | - Deborah A. Golino
- Department of Plant PathologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Susan E. Ebeler
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Maher Al Rwahnih
- Department of Plant PathologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Dario Cantu
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCaliforniaUSA
| |
Collapse
|
4
|
Katsiani A, Maliogka VI, Katis N, Svanella-Dumas L, Olmos A, Ruiz-García AB, Marais A, Faure C, Theil S, Lotos L, Candresse T. High-Throughput Sequencing Reveals Further Diversity of Little Cherry Virus 1 with Implications for Diagnostics. Viruses 2018; 10:E385. [PMID: 30037079 PMCID: PMC6070981 DOI: 10.3390/v10070385] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/11/2018] [Accepted: 07/19/2018] [Indexed: 12/21/2022] Open
Abstract
Little cherry virus 1 (LChV1, Velarivirus, Closteroviridae) is a widespread pathogen of sweet or sour cherry and other Prunus species, which exhibits high genetic diversity and lacks a putative efficient transmission vector. Thus far, four distinct phylogenetic clusters of LChV1 have been described, including isolates from different Prunus species. The recent application of high throughput sequencing (HTS) technologies in fruit tree virology has facilitated the acquisition of new viral genomes and the study of virus diversity. In the present work, several new LChV1 isolates from different countries were fully sequenced using different HTS approaches. Our results reveal the presence of further genetic diversity within the LChV1 species. Interestingly, mixed infections of the same sweet cherry tree with different LChV1 variants were identified for the first time. Taken together, the high intra-host and intra-species diversities of LChV1 might affect its pathogenicity and have clear implications for its accurate diagnostics.
Collapse
Affiliation(s)
- Asimina Katsiani
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Varvara I Maliogka
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Nikolaos Katis
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Laurence Svanella-Dumas
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, CS20032, Villenave d'Ornon CEDEX, F-33882 Bordeaux, France.
| | - Antonio Olmos
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Naquera km 4.5, Moncada, 46113 Valencia, Spain.
| | - Ana B Ruiz-García
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Naquera km 4.5, Moncada, 46113 Valencia, Spain.
| | - Armelle Marais
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, CS20032, Villenave d'Ornon CEDEX, F-33882 Bordeaux, France.
| | - Chantal Faure
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, CS20032, Villenave d'Ornon CEDEX, F-33882 Bordeaux, France.
| | - Sébastien Theil
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, CS20032, Villenave d'Ornon CEDEX, F-33882 Bordeaux, France.
| | - Leonidas Lotos
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, CS20032, Villenave d'Ornon CEDEX, F-33882 Bordeaux, France.
| |
Collapse
|
5
|
Serrano A, Espinoza C, Armijo G, Inostroza-Blancheteau C, Poblete E, Meyer-Regueiro C, Arce A, Parada F, Santibáñez C, Arce-Johnson P. Omics Approaches for Understanding Grapevine Berry Development: Regulatory Networks Associated with Endogenous Processes and Environmental Responses. FRONTIERS IN PLANT SCIENCE 2017; 8:1486. [PMID: 28936215 PMCID: PMC5594091 DOI: 10.3389/fpls.2017.01486] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/10/2017] [Indexed: 05/21/2023]
Abstract
Grapevine fruit development is a dynamic process that can be divided into three stages: formation (I), lag (II), and ripening (III), in which physiological and biochemical changes occur, leading to cell differentiation and accumulation of different solutes. These stages can be positively or negatively affected by multiple environmental factors. During the last decade, efforts have been made to understand berry development from a global perspective. Special attention has been paid to transcriptional and metabolic networks associated with the control of grape berry development, and how external factors affect the ripening process. In this review, we focus on the integration of global approaches, including proteomics, metabolomics, and especially transcriptomics, to understand grape berry development. Several aspects will be considered, including seed development and the production of seedless fruits; veraison, at which anthocyanin accumulation begins in the berry skin of colored varieties; and hormonal regulation of berry development and signaling throughout ripening, focusing on the transcriptional regulation of hormone receptors, protein kinases, and genes related to secondary messenger sensing. Finally, berry responses to different environmental factors, including abiotic (temperature, water-related stress and UV-B radiation) and biotic (fungi and viruses) stresses, and how they can significantly modify both, development and composition of vine fruit, will be discussed. Until now, advances have been made due to the application of Omics tools at different molecular levels. However, the potential of these technologies should not be limited to the study of single-level questions; instead, data obtained by these platforms should be integrated to unravel the molecular aspects of grapevine development. Therefore, the current challenge is the generation of new tools that integrate large-scale data to assess new questions in this field, and to support agronomical practices.
Collapse
Affiliation(s)
- Alejandra Serrano
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Carmen Espinoza
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Grace Armijo
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Claudio Inostroza-Blancheteau
- Núcleo de Investigación en Producción Alimentaría, Facultad de Recursos Naturales, Escuela de Agronomía, Universidad Católica de TemucoTemuco, Chile
| | - Evelyn Poblete
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Carlos Meyer-Regueiro
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Anibal Arce
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Francisca Parada
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Claudia Santibáñez
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de ChileSantiago, Chile
- Ecophysiology and Functional Genomic of Grapevine, Institut des Sciences de la Vigne et du Vin, Institut National de la Recherche Agronomique, Université de BordeauxBordeaux, France
| | - Patricio Arce-Johnson
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de ChileSantiago, Chile
- *Correspondence: Patricio Arce-Johnson,
| |
Collapse
|
6
|
Mascia T, Gallitelli D. Synergies and antagonisms in virus interactions. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 252:176-192. [PMID: 27717453 DOI: 10.1016/j.plantsci.2016.07.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 07/22/2016] [Accepted: 07/27/2016] [Indexed: 05/25/2023]
Abstract
Metagenomic surveys and data from next generation sequencing revealed that mixed infections among plant viruses are probably a rule rather than an exception in natural pathosystems. The documented cases may range from synergism to antagonism, which may depend from the spatiotemporal order of arrival of the viruses on the host and upon the host itself. In synergistic interactions, the measurable differences in replication, phenotypic and cytopathological changes, cellular tropism, within host movement, and transmission rate of one of the two viruses or both are increased. Conversely, a decrease in replication, or inhibition of one or more of the above functions by one virus against the other, leads to an antagonistic interaction. Viruses may interact directly and by transcomplementation of defective functions or indirectly, through responses mediated by the host like the defense mechanism based on RNA silencing. Outcomes of these interactions can be applied to the risk assessment of transgenic crops expressing viral proteins, or cross-protected crops for the identification of potential hazards. Prior to experimental evidence, mathematical models may help in forecasting challenges deriving from the great variety of pathways of synergistic and antagonistic interactions. Actually, it seems that such predictions do not receive sufficient credit in the framework of agriculture.
Collapse
Affiliation(s)
- Tiziana Mascia
- Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; Istituto del CNR per la Protezione sostenibile delle Piante, Unità Operativa di Supporto di Bari, Via Amendola 165/A, 70126 Bari, Italy
| | - Donato Gallitelli
- Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; Istituto del CNR per la Protezione sostenibile delle Piante, Unità Operativa di Supporto di Bari, Via Amendola 165/A, 70126 Bari, Italy.
| |
Collapse
|
7
|
Armijo G, Schlechter R, Agurto M, Muñoz D, Nuñez C, Arce-Johnson P. Grapevine Pathogenic Microorganisms: Understanding Infection Strategies and Host Response Scenarios. FRONTIERS IN PLANT SCIENCE 2016; 7:382. [PMID: 27066032 PMCID: PMC4811896 DOI: 10.3389/fpls.2016.00382] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/13/2016] [Indexed: 05/18/2023]
Abstract
Grapevine (Vitis vinifera L.) is one of the most important fruit crop worldwide. Commercial cultivars are greatly affected by a large number of pathogenic microorganisms that cause diseases during pre- and/or post-harvest periods, affecting production, processing and export, along with fruit quality. Among the potential threats, we can find bacteria, fungi, oomycete, or viruses with different life cycles, infection mechanisms and evasion strategies. While plant-pathogen interactions are cycles of resistance and susceptibility, resistance traits from natural resources are selected and may be used for breeding purposes and for a sustainable agriculture. In this context, here we summarize some of the most important diseases affecting V. vinifera together with their causal agents. The aim of this work is to bring a comprehensive review of the infection strategies deployed by significant types of pathogens while understanding the host response in both resistance and susceptibility scenarios. New approaches being used to uncover grapevine status during biotic stresses and scientific-based procedures needed to control plant diseases and crop protection are also addressed.
Collapse
Affiliation(s)
| | | | | | | | | | - Patricio Arce-Johnson
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de ChileSantiago, Chile
| |
Collapse
|
8
|
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: 17] [Impact Index Per Article: 1.9] [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.
Collapse
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.
| |
Collapse
|
9
|
Reynard JS, Schneeberger PHH, Frey JE, Schaerer S. Biological, Serological, and Molecular Characterization of a Highly Divergent Strain of Grapevine leafroll-associated virus 4 Causing Grapevine Leafroll Disease. PHYTOPATHOLOGY 2015; 105:1262-1269. [PMID: 25822183 DOI: 10.1094/phyto-12-14-0386-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The complete genome sequence of a highly divergent strain of Grapevine leafroll-associated virus 4 (GLRaV-4) was determined using 454 pyrosequencing technology. This virus, designated GLRaV-4 Ob, was detected in Vitis vinifera 'Otcha bala' from our grapevine virus collection at Agroscope. The GLRaV-4 Ob genome length and organization share similarities with members of subgroup II in the genus Ampelovirus (family Closteroviridae). Otcha bala was graft-inoculated onto indicator plants of cultivar Gamay to evaluate the biological properties of this new strain, and typical leafroll symptoms were induced. A monoclonal antibody for the rapid detection of GLRaV-4 Ob by enzyme-linked immunosorbent assay is available, thus facilitating large-scale diagnostics of this virus. Based on the relatively small size of the coat protein, the reduced amino acid identity and the distinct serological properties, our study clearly shows that GLRaV-4 Ob is a divergent strain of GLRaV-4. Furthermore, molecular and serological data revealed that the AA42 accession from which GLRaV-7 was originally reported is in fact co-infected with GLRaV-4 Ob and GLRaV-7. This finding challenges the idea that GLRaV-7 is a leafroll-causing agent.
Collapse
Affiliation(s)
- Jean-Sébastien Reynard
- First and fourth authors: Agroscope-Virology and Phytoplasmology, Nyon, Switzerland; second author: Swiss Tropical and Public Health Institute-Virology, Basel, Switzerland; and third author: Agroscope-Molecular Diagnostics, Genomics and Bioinformatics, Waedenswil, Switzerland
| | - Pierre H H Schneeberger
- First and fourth authors: Agroscope-Virology and Phytoplasmology, Nyon, Switzerland; second author: Swiss Tropical and Public Health Institute-Virology, Basel, Switzerland; and third author: Agroscope-Molecular Diagnostics, Genomics and Bioinformatics, Waedenswil, Switzerland
| | - Jürg Ernst Frey
- First and fourth authors: Agroscope-Virology and Phytoplasmology, Nyon, Switzerland; second author: Swiss Tropical and Public Health Institute-Virology, Basel, Switzerland; and third author: Agroscope-Molecular Diagnostics, Genomics and Bioinformatics, Waedenswil, Switzerland
| | - Santiago Schaerer
- First and fourth authors: Agroscope-Virology and Phytoplasmology, Nyon, Switzerland; second author: Swiss Tropical and Public Health Institute-Virology, Basel, Switzerland; and third author: Agroscope-Molecular Diagnostics, Genomics and Bioinformatics, Waedenswil, Switzerland
| |
Collapse
|
10
|
An assemblage of divergent variants of a novel putative closterovirus from American persimmon. Virus Genes 2015; 51:105-11. [PMID: 25921465 DOI: 10.1007/s11262-015-1202-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 04/17/2015] [Indexed: 10/23/2022]
Abstract
Deep-sequencing analysis of nucleic acids extracted from leaf tissue of an American persimmon (Diospyros virginiana L.) and subsequent-sequencing analyses uncovered at least four distinct closterovirus-like molecules. Two complete genomes of 18,569 and 18,030 nucleotides (nt) and partial genomes of 4,899 and 9,019 nt were determined. The two complete genomes encoded 11 potential open reading frames and the characteristic organization of closteroviruses. Among the four genomes, the putative heat shock protein 70 homolog (HSP70h), RNA-dependent RNA polymerase, and coat protein showed 82-85, 72-91, and 84-87 % amino acid sequence identities, respectively. These results suggested that the four identified viruses could be divergent variants in a single host plant. The phylogenetic tree based on HSP70h showed that their closest relative, although distant, is Olive leaf yellowing-associated virus, a putative unassigned member of the family Closteroviridae. The name Persimmon virus B was proposed for this new virus, representing another unassigned member of the family.
Collapse
|
11
|
Bester R, Pepler PT, Burger JT, Maree HJ. Relative quantitation goes viral: An RT-qPCR assay for a grapevine virus. J Virol Methods 2014; 210:67-75. [PMID: 25286180 DOI: 10.1016/j.jviromet.2014.09.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/16/2014] [Accepted: 09/24/2014] [Indexed: 10/24/2022]
Abstract
Accurate detection and quantitation of viruses can be beneficial to plant-virus interaction studies. In this study, three SYBR green real-time RT-PCR assays were developed to quantitate grapevine leafroll-associated virus 3 (GLRaV-3) in infected vines. Three genomic regions (ORF1a, coat protein and 3'UTR) were targeted to quantitate GLRaV-3 relative to three stably expressed reference genes (actin, GAPDH and α-tubulin). These assays were able to detect all known variant groups of GLRaV-3, including the divergent group VI, with equal efficiency. No link could be established between the concentration ratios of the different genomic regions and subgenomic RNA (sgRNA) expression. However, a significant lower virus concentration ratio for plants infected with variant group VI compared to variant group II was observed for the ORF1a, coat protein and the 3'UTR. Significant higher accumulation of the virus in the growth tip was also detected for both variant groups. The quantitation of viral genomic regions under different conditions can contribute to elucidating disease aetiology and enhance knowledge about virus ecology.
Collapse
Affiliation(s)
- R Bester
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - P T Pepler
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - J T Burger
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - H J Maree
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; ARC Infruitec-Nietvoorbij (The Fruit, Vine and Wine Institute of the Agricultural Research Council), Private Bag X5026, Stellenbosch 7599, South Africa.
| |
Collapse
|
12
|
Naidu R, Rowhani A, Fuchs M, Golino D, Martelli GP. Grapevine Leafroll: A Complex Viral Disease Affecting a High-Value Fruit Crop. PLANT DISEASE 2014; 98:1172-1185. [PMID: 30699617 DOI: 10.1094/pdis-08-13-0880-fe] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Grapevine (Vitis spp.) is one of the most widely grown fruit crops in the world. It is a deciduous woody perennial vine for which the cultivation of domesticated species began approximately 6,000 to 8,000 years ago in the Near East. Grapevines are broadly classified into red- and white-berried cultivars based on their fruit skin color, although yellow, pink, crimson, dark blue, and black-berried cultivars also exist. Grapevines can be subject to attacks by many different pests and pathogens, including graft-transmissible agents such as viruses, viroids, and phytoplasmas. Among the virus and virus-like diseases, grapevine leafroll disease (GLD) is by far the most widespread and economically damaging viral disease of grapevines in many regions around the world. The global expansion of the grape and wine industry has seen a parallel increase in the incidence and economic impact of GLD. Despite the fact that GLD was recognized as a potential threat to grape production for several decades, our knowledge of the nature of the disease is still quite limited due to a variety of challenges related to the complexity of this virus disease, the association of several distinct GLD-associated viruses, and contrasting symptoms in red- and white-berried cultivars. In view of the growing significance of GLD to wine grape production worldwide, this feature article provides an overview of the state of knowledge on the biology and epidemiology of the disease and describes management strategies currently deployed in vineyards.
Collapse
Affiliation(s)
| | | | - Marc Fuchs
- Cornell University, New York State Agricultural Experiment Station, Geneva
| | | | - Giovanni P Martelli
- Università degli Studi di Bari "Aldo Moro" and Istituto di Virologia Vegetale del CNR, UOS Bari, Bari, Italy
| |
Collapse
|
13
|
Osman F, Hodzic E, Omanska-Klusek A, Olineka T, Rowhani A. Development and validation of a multiplex quantitative PCR assay for the rapid detection of Grapevine virus A, B and D. J Virol Methods 2013; 194:138-45. [DOI: 10.1016/j.jviromet.2013.07.046] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 07/26/2013] [Accepted: 07/26/2013] [Indexed: 10/26/2022]
|
14
|
Poojari S, Alabi OJ, Fofanov VY, Naidu RA. A leafhopper-transmissible DNA virus with novel evolutionary lineage in the family geminiviridae implicated in grapevine redleaf disease by next-generation sequencing. PLoS One 2013; 8:e64194. [PMID: 23755117 PMCID: PMC3673993 DOI: 10.1371/journal.pone.0064194] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 04/10/2013] [Indexed: 01/25/2023] Open
Abstract
A graft-transmissible disease displaying red veins, red blotches and total reddening of leaves in red-berried wine grape (Vitis vinifera L.) cultivars was observed in commercial vineyards. Next-generation sequencing technology was used to identify etiological agent(s) associated with this emerging disease, designated as grapevine redleaf disease (GRD). High quality RNA extracted from leaves of grape cultivars Merlot and Cabernet Franc with and without GRD symptoms was used to prepare cDNA libraries. Assembly of highly informative sequence reads generated from Illumina sequencing of cDNA libraries, followed by bioinformatic analyses of sequence contigs resulted in specific identification of taxonomically disparate viruses and viroids in samples with and without GRD symptoms. A single-stranded DNA virus, tentatively named Grapevine redleaf-associated virus (GRLaV), and Grapevine fanleaf virus were detected only in grapevines showing GRD symptoms. In contrast, Grapevine rupestris stem pitting-associated virus, Hop stunt viroid, Grapevine yellow speckle viroid 1, Citrus exocortis viroid and Citrus exocortis Yucatan viroid were present in both symptomatic and non-symptomatic grapevines. GRLaV was transmitted by the Virginia creeper leafhopper (Erythroneura ziczac Walsh) from grapevine-to-grapevine under greenhouse conditions. Molecular and phylogenetic analyses indicated that GRLaV, almost identical to recently reported Grapevine Cabernet Franc-associated virus from New York and Grapevine red blotch-associated virus from California, represents an evolutionarily distinct lineage in the family Geminiviridae with genome characteristics distinct from other leafhopper-transmitted geminiviruses. GRD significantly reduced fruit yield and affected berry quality parameters demonstrating negative impacts of the disease. Higher quantities of carbohydrates were present in symptomatic leaves suggesting their possible role in the expression of redleaf symptoms.
Collapse
Affiliation(s)
- Sudarsana Poojari
- Department of Plant Pathology, Washington State University, Irrigated Agriculture Research and Extension Center, Prosser, Washington, United States of America
| | | | | | | |
Collapse
|
15
|
Maree HJ, Almeida RPP, Bester R, Chooi KM, Cohen D, Dolja VV, Fuchs MF, Golino DA, Jooste AEC, Martelli GP, Naidu RA, Rowhani A, Saldarelli P, Burger JT. Grapevine leafroll-associated virus 3. Front Microbiol 2013; 4:82. [PMID: 23596440 PMCID: PMC3627144 DOI: 10.3389/fmicb.2013.00082] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 03/22/2013] [Indexed: 11/17/2022] Open
Abstract
Grapevine leafroll disease (GLD) is one of the most important grapevine viral diseases affecting grapevines worldwide. The impact on vine health, crop yield, and quality is difficult to assess due to a high number of variables, but significant economic losses are consistently reported over the lifespan of a vineyard if intervention strategies are not implemented. Several viruses from the family Closteroviridae are associated with GLD. However, Grapevine leafroll-associated virus 3 (GLRaV-3), the type species for the genus Ampelovirus, is regarded as the most important causative agent. Here we provide a general overview on various aspects of GLRaV-3, with an emphasis on the latest advances in the characterization of the genome. The full genome of several isolates have recently been sequenced and annotated, revealing the existence of several genetic variants. The classification of these variants, based on their genome sequence, will be discussed and a guideline is presented to facilitate future comparative studies. The characterization of sgRNAs produced during the infection cycle of GLRaV-3 has given some insight into the replication strategy and the putative functionality of the ORFs. The latest nucleotide sequence based molecular diagnostic techniques were shown to be more sensitive than conventional serological assays and although ELISA is not as sensitive it remains valuable for high-throughput screening and complementary to molecular diagnostics. The application of next-generation sequencing is proving to be a valuable tool to study the complexity of viral infection as well as plant pathogen interaction. Next-generation sequencing data can provide information regarding disease complexes, variants of viral species, and abundance of particular viruses. This information can be used to develop more accurate diagnostic assays. Reliable virus screening in support of robust grapevine certification programs remains the cornerstone of GLD management.
Collapse
Affiliation(s)
- Hans J. Maree
- Department of Genetics, Stellenbosch UniversityStellenbosch, South Africa
- Biotechnology Platform, Agricultural Research CouncilStellenbosch, South Africa
| | - Rodrigo P. P. Almeida
- Department of Environmental Science, Policy and Management, University of CaliforniaBerkeley, CA, USA
| | - Rachelle Bester
- Department of Genetics, Stellenbosch UniversityStellenbosch, South Africa
| | - Kar Mun Chooi
- School of Biological Sciences, University of AucklandAuckland, New Zealand
| | - Daniel Cohen
- The New Zealand Institute for Plant and Food ResearchAuckland, New Zealand
| | - Valerian V. Dolja
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA
| | - Marc F. Fuchs
- Department of Plant Pathology and Plant-Microbe Biology, Cornell UniversityGeneva, NY, USA
| | - Deborah A. Golino
- Department of Plant Pathology, University of CaliforniaDavis, CA, USA
| | - Anna E. C. Jooste
- Plant Protection Research Institute, Agricultural Research CouncilPretoria, South Africa
| | - Giovanni P. Martelli
- Department of Soil, Plant and Food Sciences, University Aldo Moro of BariBari, Italy
| | - Rayapati A. Naidu
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State UniversityProsser, WA, USA
| | - Adib Rowhani
- Department of Plant Pathology, University of CaliforniaDavis, CA, USA
| | | | - Johan T. Burger
- Department of Genetics, Stellenbosch UniversityStellenbosch, South Africa
| |
Collapse
|
16
|
Generic and sequence-variant specific molecular assays for the detection of the highly variable Grapevine leafroll-associated virus 3. J Virol Methods 2013; 189:20-9. [DOI: 10.1016/j.jviromet.2012.12.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 12/17/2012] [Accepted: 12/19/2012] [Indexed: 11/19/2022]
|
17
|
Ghanem-Sabanadzovic NA, Sabanadzovic S, Gugerli P, Rowhani A. Genome organization, serology and phylogeny of Grapevine leafroll-associated viruses 4 and 6: taxonomic implications. Virus Res 2011; 163:120-8. [PMID: 21925555 DOI: 10.1016/j.virusres.2011.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 08/31/2011] [Accepted: 09/01/2011] [Indexed: 10/17/2022]
Abstract
Complete nucleotide sequences of the type isolate of Grapevine leafroll-associated virus 4 (GLRaV-4) and of an isolate of GLRaV-6 from cv 'Estellat' (GLRaV-6Est) were generated and compared mutually and with related viruses. The genome organization of both viruses resembled that of members of Subgroup I in the genus Ampelovirus (fam. Closteroviridae). The availability of these sequences, along with previously existing data on related GLRaVs, allowed critical review of the taxonomy and nomenclature of these viruses. In phylogenetic analyses, GLRaV-4 and -6Est consistently grouped with GLRaV-5, -9, and -Pr forming a poorly resolved sub-cluster ("GLRaV-4 group") within the genus Ampelovirus. In-depth study showed that genetic distances between these viruses do not exceed the intra-species diversity observed in other closteroviruses. In Western blots, partially purified preparations of GLRaVs -4, -5, -6 and -9 reacted only with homologous monoclonal antibodies, but were all recognized by polyclonal antisera to GLRaV-5 and GLRaV-9. Serological relatedness among these viruses was further confirmed in DAS-ELISA. In immuno-electron microscopy, GLRaV-6 particles appeared uniformly decorated with homologous monoclonal antibodies, whereas GLRaV-2, used as a control, showed "bipolar" morphology of the virion. Results of this study challenge taxonomy and nomenclature of several GLRaVs suggesting that they are divergent isolates of Grapevine leafroll-associated virus 4 and not, as has been assumed, distinct species (definitive and/or putative) in the genus Ampelovirus.
Collapse
|
18
|
Zhang Y, Singh K, Kaur R, Qiu W. Association of a novel DNA virus with the grapevine vein-clearing and vine decline syndrome. PHYTOPATHOLOGY 2011; 101:1081-90. [PMID: 21554183 DOI: 10.1094/phyto-02-11-0034] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
A severe vein-clearing and vine decline syndrome has emerged on grapevines (Vitis vinifera) and hybrid grape cultivars in the Midwest region of the United States. The typical symptoms are translucent vein-clearing on young leaves, short internodes and decline of vine vigor. Known viral pathogens of grapevines were not closely associated with the syndrome. To obtain a comprehensive profile of viruses in a diseased grapevine, small RNAs were enriched and two cDNA libraries were constructed from a symptomatic grapevine and a symptomless grapevine, respectively. Deep sequencing of the two cDNA libraries showed that the most abundant viral small RNAs align with the genomes of viruses in the genus Badnavirus, the family Caulimoviridae. Amplification of the viral DNA by polymerase chain reaction allowed the assembly of the whole genome sequence of a grapevine DNA virus, which shared the highest homology with the Badnavirus sequences. This is the first report of a DNA virus in grapevines. The new DNA virus is closely associated with the vein-clearing symptom, and thus has been given a provisional name Grapevine vein clearing virus (GVCV). GVCV was detected in six grapevine cultivars showing vein-clearing and vine decline syndrome in Missouri, Illinois, and Indiana, suggesting its wide distribution in the Midwest region of the United States. Discovery of DNA viruses in grapevines merits further studies on their epidemics and economic impact on grape production worldwide.
Collapse
|
19
|
Alkowni R, Zhang YP, Rowhani A, Uyemoto JK, Minafra A. Biological, molecular, and serological studies of a novel strain of grapevine leafroll-associated virus 2. Virus Genes 2011; 43:102-10. [PMID: 21487783 DOI: 10.1007/s11262-011-0607-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 03/28/2011] [Indexed: 11/26/2022]
Abstract
In California, a novel closterovirus was detected in "Redglobe" grapevine, associated with graft incompatibility and given a trivial name "Grapevine rootstock stem lesion associated virus (GRSLaV)." The biological properties of the putative virus were ascertained when asymptomatic yet infected Redglobe scion buds were graft-inoculated onto test plants of Cabernet Sauvignon propagated on 18 different rootstocks. It proved lethal on test plants growing on rootstocks 1616C, 5BB, 5C, 3309C, and 1103 P, whereas latent infections occurred on the remaining scion-rootstock combinations. In contrast, GLRaV-2 type (type strain) produced only typical leafroll symptoms. In a different experiment, GLRaV-2 type was successfully sap-transmitted to N. benthamiana, whereas sap transmission of GRSLaV was unsuccessful. Double-stranded RNA was extracted from infected Redglobe grapevines, cloned, sequenced, and determined a genome length of 16,527 nucleotides. Computer-assisted analysis of open-reading frames (ORFs) revealed a genome organization typical of monopartite viruses in the genus Closterovirus with nine ORFs (range 71-79% identity) with GLRaV-2 type, the closest similar virus species within the family Closteroviridae. Also the 3'-UTR of GRSLaV consisted of 223 nucleotides with an extended oligo(A) tract similar to that of GLRaV-2 type, Beet yellow stunt virus, and Beet yellows virus. Recombinant GRSLaV coat protein was expressed in E. coli, purified, and immunized a rabbit to produce polyclonal antiserum. Serological data matched the molecular data, whereby exposed plant tissue extracts of grapevines infected by both viruses (GRSLaV and GLRaV-2) reacted positively with homologous and heterologous viral antisera but not with healthy grapevine extracts in ELISA and Western blot tests. Based on the comparative sequence data and shared antigens, GRSLaV is now considered a strain of GLRaV-2 and redesignated as Grapevine leafroll associated virus-2 Redglobe (GLRaV-2RG). Primers specific for GLRaV-2RG were developed, which did not amplify GLRaV-2 type strain. When both sets of specific primers were used in assays of different grapevine collections, the incidence of the respective viruses varied considerably, e.g., 1.7 and 13.5%, respectively, for GLRaV-2RG and GLRaV-2 type.
Collapse
Affiliation(s)
- Raed Alkowni
- Department of Biology and Biotechnology, An-Najah National University, Nablus, Palestine.
| | | | | | | | | |
Collapse
|
20
|
Quantitation of Grapevine leafroll associated virus-1 and -3, Grapevine virus A, Grapevine fanleaf virus and Grapevine fleck virus in field-collected Vitis vinifera L. ‘Nebbiolo’ by real-time reverse transcription-PCR. J Virol Methods 2011; 172:1-7. [DOI: 10.1016/j.jviromet.2010.12.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 09/30/2010] [Accepted: 12/08/2010] [Indexed: 11/18/2022]
|
21
|
Melzer MJ, Sether DM, Borth WB, Mersino EF, Hu JS. An assemblage of closteroviruses infects Hawaiian ti (Cordyline fruticosa L.). Virus Genes 2010; 42:254-60. [DOI: 10.1007/s11262-010-0537-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Accepted: 09/28/2010] [Indexed: 10/18/2022]
|
22
|
Jooste AEC, Maree HJ, Bellstedt DU, Goszczynski DE, Pietersen G, Burger JT. Three genetic grapevine leafroll-associated virus 3 variants identified from South African vineyards show high variability in their 5′UTR. Arch Virol 2010; 155:1997-2006. [DOI: 10.1007/s00705-010-0793-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Accepted: 08/27/2010] [Indexed: 11/24/2022]
|
23
|
Ghanem-Sabanadzovic NA, Sabanadzovic S, Uyemoto JK, Golino D, Rowhani A. A putative new ampelovirus associated with grapevine leafroll disease. Arch Virol 2010; 155:1871-6. [PMID: 20703503 PMCID: PMC2970810 DOI: 10.1007/s00705-010-0773-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Accepted: 07/24/2010] [Indexed: 11/30/2022]
Abstract
A putative new ampelovirus was detected in Vitis vinifera cv. Carnelian showing mild leafroll symptoms and molecularly characterized. The complete genome consisted of 13,625 nt and had a structure similar to that of members of subgroup I in the genus Ampelovirus (fam. Closteroviridae). In-depth analyses showed that the virus from cv. Carnelian is the most distinct member of the "GLRaV-4 lineage" of ampeloviruses, which comprises GLRaV-4, -5, -6, -9, and the recently characterized GLRaV-Pr, and GLRaV-De. This virus appears to be a new member of the family Closteroviridae, for which the provisional name grapevine leafroll-associated Carnelian virus is proposed.
Collapse
|
24
|
Jarugula S, Alabi OJ, Martin RR, Naidu RA. Genetic variability of natural populations of Grapevine leafroll-associated virus 2 in Pacific Northwest vineyards. PHYTOPATHOLOGY 2010; 100:698-707. [PMID: 20528188 DOI: 10.1094/phyto-100-7-0698] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Genetic variability of field populations of Grapevine leafroll-associated virus 2 (GLRaV-2) in Pacific Northwest (PNW) vineyards was characterized by sequencing the entire coat protein (CP) and a portion of the heat-shock protein-70 homolog (HSP70h) genes. Phylogenetic analysis of CP and HSP70h nucleotide sequences obtained in this study and corresponding sequences from GenBank revealed segregation of GLRaV-2 isolates into six lineages with virus isolates from PNW distributed in 'PN', 'H4', and 'RG' lineages. An estimation of the ratio of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site indicated that different selection pressures may be acting on the two genomic regions encoding proteins with distinct functions. Multiple alignments of CP amino acid sequences showed lineage-specific differences. Enzyme-linked immunosorbent assay results indicated that GLRaV-2-specific antibodies from a commercial source are unable to reliably detect GLRaV-2 isolates in the RG lineage, thereby limiting antibody-based diagnosis of all GLRaV-2 isolates currently found in PNW vineyards. A protocol based on reverse-transcription polymerase chain reaction and restriction fragment length polymorphism analysis was developed for differentiating GLRaV-2 isolates belonging to the three lineages present in the region. The taxonomic status of GLRaV-2 is discussed in light of the current knowledge of global genetic diversity of the virus.
Collapse
Affiliation(s)
- Sridhar Jarugula
- Department of Plant Pathology, Irrigated Agriculture Research and Extensive Center, Washington State University, Prosser 99350, USA
| | | | | | | |
Collapse
|
25
|
Coetzee B, Freeborough MJ, Maree HJ, Celton JM, Rees DJG, Burger JT. Deep sequencing analysis of viruses infecting grapevines: Virome of a vineyard. Virology 2010; 400:157-63. [PMID: 20172578 DOI: 10.1016/j.virol.2010.01.023] [Citation(s) in RCA: 203] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Revised: 12/02/2009] [Accepted: 01/17/2010] [Indexed: 11/26/2022]
Abstract
Double stranded RNA, isolated from 44 pooled randomly selected vines from a diseased South African vineyard, has been used in a deep sequencing analysis to build a census of the viral population. The dsRNA was sequenced in an unbiased manner using the sequencing-by-synthesis technology offered by the Illumina Genome Analyzer II and yielded 837 megabases of metagenomic sequence data. Four known viral pathogens were identified. It was found that Grapevine leafroll-associated virus 3 (GLRaV-3) is the most prevalent species, constituting 59% of the total reads, followed by Grapevine rupestris stem pitting-associated virus and Grapevine virus A. Grapevine virus E, a virus not previously reported in South African vineyards, was identified in the census. Viruses not previously identified in grapevine were also detected. The second most prevalent virus detected was a member of the Chrysoviridae family similar to Penicillium chrysogenum virus. Sequences aligning to two other mycoviruses were also detected.
Collapse
Affiliation(s)
- Beatrix Coetzee
- Department of Genetics, Stellenbosch University, Matieland, 7602, South Africa
| | | | | | | | | | | |
Collapse
|
26
|
Alabi OJ, Martin RR, Naidu RA. Sequence diversity, population genetics and potential recombination events in grapevine rupestris stem pitting-associated virus in Pacific North-West vineyards. J Gen Virol 2009; 91:265-76. [PMID: 19759241 DOI: 10.1099/vir.0.014423-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Grapevine rupestris stem pitting-associated virus (GRSPaV; genus Foveavirus, family Flexiviridae) is present in many grape-growing regions of the world. A total of 84 full-length coat protein (CP) sequences and 57 sequences representing the helicase-encoding region (HR) of the RNA-dependent RNA polymerase were obtained from wine grape cultivars grown in the Pacific North-West (PNW) of the United States and their molecular diversity was compared with corresponding sequences previously reported from other grape-growing regions. In pairwise comparisons, the CP sequences from PNW isolates showed identities between 80 and 100% at the nucleotide level and the HR sequences showed identities between 79 and 100%. A global phylogenetic analysis of the CP and HR sequences revealed segregation of GRSPaV isolates into four major lineages with isolates from PNW distributed in all four lineages, indicating a lack of clustering by geographical origin. Scion cultivars grafted onto rootstock were found to contain mixtures of more genetic variants belonging to different lineages than own-rooted cultivars. Assessment of population genetic parameters found that the CP was more variable than the HR region. The discordant gene phylogenies obtained for some CP and HR sequences and the identification of potential recombination events involving parents from different lineages provided strong evolutionary evidence for genetic diversity among GRSPaV isolates. These results underscore the highly variable nature of the virus with implications for grapevine health status and distribution of virus-tested planting materials. This study also contributes to an increased understanding of molecular population genetics of viruses infecting deciduous woody perennials.
Collapse
Affiliation(s)
- Olufemi J Alabi
- Department of Plant Pathology, Washington State University, Irrigated Agriculture Research and Extension Center, Prosser, WA 99350, USA
| | | | | |
Collapse
|
27
|
Microarray immunoassay for the detection of grapevine and tree fruit viruses. J Virol Methods 2009; 160:90-100. [DOI: 10.1016/j.jviromet.2009.04.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Revised: 04/20/2009] [Accepted: 04/23/2009] [Indexed: 11/22/2022]
|
28
|
Maliogka VI, Dovas CI, Katis NI. Generic and species-specific detection of viruses belonging to an evolutionary distinct lineage within the Ampelovirus genus. J Virol Methods 2008; 154:41-7. [PMID: 18848581 DOI: 10.1016/j.jviromet.2008.09.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Revised: 09/08/2008] [Accepted: 09/11/2008] [Indexed: 10/21/2022]
Abstract
A nested RT-PCR was developed, that allows the generic detection of a subgroup of genetically related viruses with a distinct evolutionary history within the genus Ampelovirus. Members of this lineage are Grapevine leafroll associated virus-4, -5, -6, -9 and two isolates (GLRaV-De and GLRaV-Pr) that have been recently characterized and represent new species. The method involves a one step RT-PCR for the generic detection of Closteroviridae species using degenerate primers that target the HSP70h gene followed by a nested PCR, which detects all virus-members of the lineage and differentiates them from the other grapevine closteroviruses. The 490 bp nested PCR amplicons, corresponding to a phylogenetically informative region, can be sequenced directly to obtain initial genetic information for their partial characterization and rapid classification. Additional primers were designed and successfully used for the specific detection of GLRaV-4, -5, -6, -Pr and -De on respective single or multiplex nested PCR assays. The application of a ramped annealing thermal profile in the nested PCR allowed all amplifications to run in parallel. The developed detection scheme is proposed as a tool that can be used for the enrichment of sequence information of known and uncharacterized ampeloviruses, classified within this lineage, enabling their selective amplification in mixed Closteroviridae virus infections.
Collapse
Affiliation(s)
- Varvara I Maliogka
- Plant Pathology Laboratory, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | | | | |
Collapse
|
29
|
Genome analysis and detection of a Chilean isolate of Grapevine leafroll associated virus-3. Virus Genes 2008; 37:110-8. [PMID: 18498048 DOI: 10.1007/s11262-008-0241-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2008] [Accepted: 05/05/2008] [Indexed: 11/27/2022]
Abstract
The complete genome of the Chilean isolate Cl-766 of Grapevine leafroll-associated virus-3 (GLRaV-3) has been sequenced. This is the first genome sequence obtained from a GLRaV-3 isolate of the Southern hemisphere. The genomic RNA of 17,919 nucleotides contains 13 open reading frames (ORFs) with 5' and 3' untranslated regions (UTR) of 158 and 277 nucleotides, respectively. Comparison with NY1, the only isolate with complete genomic sequence available today, shows 97.6% nucleotide identity between the two isolates. Examination of the genome variability shows that most of the genetic diversity is concentrated in ORF1a. Three additional isolates from different geographic regions of Chile were partially sequenced as well, one which showed sequence divergence with respect to the other local and foreign isolates, indicative of different evolutionary constrains. Immunodetection systems were developed using monoclonal and polyclonal antibodies produced against the recombinant major coat protein of GLRaV-3, providing sensitive and specific detection using a triple antibody sandwich-enzyme linked immunosorbent assay (TAS-ELISA) and an immunocapture-reverse transcription-polymerase chain reaction (IC-RT-PCR) assay.
Collapse
|
30
|
Evolutionary relationships of virus species belonging to a distinct lineage within the Ampelovirus genus. Virus Res 2008; 135:125-35. [PMID: 18403040 DOI: 10.1016/j.virusres.2008.02.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Revised: 02/26/2008] [Accepted: 02/26/2008] [Indexed: 11/27/2022]
Abstract
A study of the evolutionary relationships of GLRaV-4,-5,-6 and -9, and two new Ampelovirus isolates (GLRaV-Pr and -De) related to grapevine leafroll disease was conducted based on molecular variability, positive selection analysis and maximum likelihood phylogenetic reconstructions. Sequences corresponding to the N-terminal HSP70h and full CP encoding genes were determined for these viruses and datasets including homologous genomic regions from different members of the Closteroviridae were analyzed. GLRaV-Pr and -De were further characterised as distinct from the other closely related species after determination of a large genomic region (4319-4358 nts). ML phylogenetic topologies for both genes established the closer phylogenetic relationships of GLRaV-4,-5,-6,-9,-Pr and -De in regard to the other ampeloviruses, revealing very low inter-species evolutionary distances for this multitudinous lineage. The HSP70h segment phylogeny and bootstrap analysis enabled the identification of species within this lineage and provides a useful taxonomic tool for the rapid demarcation of these viruses. Estimations of d(N)/d(S) using the CP and HSP70h datasets revealed that, within the Closteroviridae, these viruses are subjected to the strongest constraints against amino acid substitutions. These estimations demonstrated a distinct evolutionary trait for this lineage probably related to its particular ecological niche that involves successful adaptation to the host, transmission through vegetative propagation and lack of vectors with high transmission efficiency.
Collapse
|