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Pfrieme AK, Will T, Pillen K, Stahl A. The Past, Present, and Future of Wheat Dwarf Virus Management-A Review. PLANTS (BASEL, SWITZERLAND) 2023; 12:3633. [PMID: 37896096 PMCID: PMC10609771 DOI: 10.3390/plants12203633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023]
Abstract
Wheat dwarf disease (WDD) is an important disease of monocotyledonous species, including economically important cereals. The causative pathogen, wheat dwarf virus (WDV), is persistently transmitted mainly by the leafhopper Psammotettix alienus and can lead to high yield losses. Due to climate change, the periods of vector activity increased, and the vectors have spread to new habitats, leading to an increased importance of WDV in large parts of Europe. In the light of integrated pest management, cultivation practices and the use of resistant/tolerant host plants are currently the only effective methods to control WDV. However, knowledge of the pathosystem and epidemiology of WDD is limited, and the few known sources of genetic tolerance indicate that further research is needed. Considering the economic importance of WDD and its likely increasing relevance in the coming decades, this study provides a comprehensive compilation of knowledge on the most important aspects with information on the causal virus, its vector, symptoms, host range, and control strategies. In addition, the current status of genetic and breeding efforts to control and manage this disease in wheat will be discussed, as this is crucial to effectively manage the disease under changing environmental conditions and minimize impending yield losses.
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Affiliation(s)
- Anne-Kathrin Pfrieme
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, 06484 Quedlinburg, Germany; (T.W.); (A.S.)
| | - Torsten Will
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, 06484 Quedlinburg, Germany; (T.W.); (A.S.)
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Science, Plant Breeding, Martin-Luther-University Halle-Wittenberg, 06108 Halle (Saale), Germany;
| | - Andreas Stahl
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, 06484 Quedlinburg, Germany; (T.W.); (A.S.)
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Bragard C, Baptista P, Chatzivassiliou E, Di Serio F, Gonthier P, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Milonas P, Navas‐Cortes JA, Parnell S, Potting R, Stefani E, Thulke H, Van der Werf W, Vicent Civera A, Yuen J, Zappalà L, Migheli Q, Vloutoglou I, Czwienczek E, Streissl F, Carluccio AV, Chiumenti M, Di Serio F, Rubino L, Reignault PL. Pest categorisation of chickpea chlorotic dwarf virus. EFSA J 2022; 20:e07625. [PMID: 36398295 PMCID: PMC9664252 DOI: 10.2903/j.efsa.2022.7625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The EFSA Panel on Plant Health conducted a pest categorisation of chickpea chlorotic dwarf virus (CpCDV) for the EU territory. The identity of CpCDV, a member of the genus Mastrevirus (family Geminiviridae) is established. Reliable detection and identification methods are available. The pathogen is not included in the EU Commission Implementing Regulation 2019/2072. CpCDV has been reported in Africa, Asia and Oceania. It has not been reported in the EU. CpCDV infects plant species in the family Fabaceae and several species of other families (Amaranthaceae, Brassicaceae, Caricaceae, Cucurbitaceae, Malvaceae and Solanaceae), including weeds. It may induce symptoms on its hosts, causing severe yield reduction. The virus is transmitted in a persistent, circulative and non-propagative manner by the leafhopper species Orosius orientalis and O. albicinctus, which are not regulated. O. orientalis is known to be present in some EU member states. Plants for planting (other than seeds), parts of plants and cut flowers of CpCDV hosts and viruliferous leafhoppers were identified as the most relevant pathways for the entry of CpCDV into the EU. Cultivated and wild hosts of CpCDV are distributed across the EU. Would the pest enter and establish in the EU territory, impact on the production of cultivated hosts is expected. Phytosanitary measures are available to prevent entry and spread of the virus in the EU. CpCDV fulfils the criteria that are within the remit of EFSA to assess for it to be regarded as a potential Union quarantine pest.
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3
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Identification of New Chickpea Virus and Control of Chickpea Virus Disease. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:6465505. [PMID: 35668786 PMCID: PMC9167091 DOI: 10.1155/2022/6465505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 03/28/2022] [Accepted: 05/02/2022] [Indexed: 11/18/2022]
Abstract
Objective. The objective of the study was to discuss the classification, virus characteristics, detection methods, and control measures of chickpea virus, with an aim to provide a theoretical basis for identification of new chickpea virus and control of chickpea virus disease. Methods. The domestic and foreign studies were reviewed, and the virus coat protein or nucleic acid sequence was identified by immunological and molecular diagnostic techniques. Results. There were 14 main types of chickpea viruses attacking, and seven Luteoviridae viruses were reported, namely, chickpea chlorotic stunt virus (CpCSV), bean leafroll virus (BLRV), beet western yellows virus (BWYV), soybean dwarf virus (SbDV), cotton leafroll dwarf virus (CLRDV), cucurbit aphid-borne yellows virus (CABYV), and phasey bean mild yellows virus (PhBMYV). The family Geminiviridae includes chickpea chlorotic dwarf virus (CpCDV), chickpea chlorosis virus (CpCV), chickpea redleaf virus (CpRLV), chickpea yellows virus (CpYV), and mastrevirus. The family Nanoviridae is dominated by the faba bean necrotic yellows virus (FBNYV). The family Bromoviridae includes cucumber mosaic virus (CMV) and alfalfa mosaic virus (AMV). Conclusion. At present, there are mainly 12 types of viruses infecting chickpeas, which are transmitted by leafhoppers or aphids and are associated with symptoms such as yellowing, chlorosis, and stunted pod development, resulting in serious yield loss. Correct use of various molecular diagnostic tools to detect and identify chickpea virus can accurately assess chickpea virus infection and provide a basis for the prevention and treatment of chickpea virus disease.
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Chatzivassiliou EK. An Annotated List of Legume-Infecting Viruses in the Light of Metagenomics. PLANTS 2021; 10:plants10071413. [PMID: 34371616 PMCID: PMC8309371 DOI: 10.3390/plants10071413] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 11/16/2022]
Abstract
Legumes, one of the most important sources of human food and animal feed, are known to be susceptible to a plethora of plant viruses. Many of these viruses cause diseases which severely impact legume production worldwide. The causal agents of some important virus-like diseases remain unknown. In recent years, high-throughput sequencing technologies have enabled us to identify many new viruses in various crops, including legumes. This review aims to present an updated list of legume-infecting viruses. Until 2020, a total of 168 plant viruses belonging to 39 genera and 16 families, officially recognized by the International Committee on Taxonomy of Viruses (ICTV), were reported to naturally infect common bean, cowpea, chickpea, faba-bean, groundnut, lentil, peas, alfalfa, clovers, and/or annual medics. Several novel legume viruses are still pending approval by ICTV. The epidemiology of many of the legume viruses are of specific interest due to their seed-transmission and their dynamic spread by insect-vectors. In this review, major aspects of legume virus epidemiology and integrated control approaches are also summarized.
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Affiliation(s)
- Elisavet K Chatzivassiliou
- Plant Pathology Laboratory, Department of Crop Science, School of Plant Sciences, Agricultural University of Athens, 11855 Athens, Greece
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Complete Genome Sequence of a New Chickpea Chlorotic Dwarf Virus Strain Isolated from Tomato in Kenya, Obtained from Illumina Sequencing. Microbiol Resour Announc 2020; 9:9/5/e01344-19. [PMID: 32001561 PMCID: PMC6992865 DOI: 10.1128/mra.01344-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
High-throughput sequence analysis revealed the complete genome sequence of a novel, hitherto uncharacterized strain of Chickpea chlorotic dwarf virus (CpCDV) from tomato plants in Kenya. The sequence shared its highest nucleotide similarity (88.7%) with two CpCDV isolates from Burkina Faso. High-throughput sequence analysis revealed the complete genome sequence of a novel, hitherto uncharacterized strain of Chickpea chlorotic dwarf virus (CpCDV) from tomato plants in Kenya. The sequence shared its highest nucleotide similarity (88.7%) with two CpCDV isolates from Burkina Faso.
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6
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Hameed U, Zia-Ur-Rehman M, Ali SA, Haider MS, Brown JK. Invasion of previously unreported dicot plant hosts by chickpea chlorotic dwarf virus in Pakistan. Virusdisease 2019; 30:95-100. [DOI: 10.1007/s13337-018-0454-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 04/18/2018] [Indexed: 10/16/2022] Open
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Kanakala S, Kuria P. Chickpea chlorotic dwarf virus: An Emerging Monopartite Dicot Infecting Mastrevirus. Viruses 2018; 11:E5. [PMID: 30577666 PMCID: PMC6357115 DOI: 10.3390/v11010005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 11/26/2018] [Accepted: 12/04/2018] [Indexed: 12/25/2022] Open
Abstract
Chickpea stunt disease (CSD), caused by Chickpea chlorotic dwarf virus (CpCDV) is a threat to chickpea production leading to yield losses of 75⁻95%. Chickpea chlorotic dwarf virus is a monopartite, single-stranded circular DNA virus in the genus Mastrevirus and family Geminiviridae. It is transmitted by Orosius albicinctus in a circulative (persistent) and nonpropagative manner. Symptoms of CSD include very small leaves, intense discoloration (yellowing (kabuli type) and reddening (desi type)), and bushy stunted appearance of the plant. Presently, CpCDVs occurs in Africa, Asia, Australia, and the Middle East, causing extensive losses on economically important crops in in the families Fabaceae, Asteraceae, Amaranthaceae, Brassicaceae, Cucurbitaceae, Caricaceae, Chenopodiaceae, Leguminosae, Malvaceae, Pedaliaceae, and Solanaceae. High frequency of recombinations has played a significant role in the wide host range, diversification, and rapid evolution of CpCDVs. This review highlights the extensive research on the CpCDV genome diversity, host range, plant⁻virus⁻insect interactions, and RNA interference-based resistance of CpCDV, providing new insights into the host adaptation and virus evolution.
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Affiliation(s)
- Surapathrudu Kanakala
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50010, USA.
| | - Paul Kuria
- Kenya Agricultural and Livestock Research Organization, Nairobi 00200, Kenya.
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Leonetti P, Accotto GP, Hanafy MS, Pantaleo V. Viruses and Phytoparasitic Nematodes of Cicer arietinum L.: Biotechnological Approaches in Interaction Studies and for Sustainable Control. FRONTIERS IN PLANT SCIENCE 2018; 9:319. [PMID: 29599788 PMCID: PMC5862823 DOI: 10.3389/fpls.2018.00319] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 02/27/2018] [Indexed: 05/31/2023]
Abstract
Cicer arietinum L. (chickpea) is the world's fourth most widely grown pulse. Chickpea seeds are a primary source of dietary protein for humans, and chickpea cultivation contributes to biological nitrogen fixation in the soil, given its symbiotic relationship with rhizobia. Therefore, chickpea cultivation plays a pivotal role in innovative sustainable models of agro-ecosystems inserted in crop rotation in arid and semi-arid environments for soil improvement and the reduction of chemical inputs. Indeed, the arid and semi-arid tropical zones of Africa and Asia have been primary areas of cultivation and diversification. Yet, nowadays, chickpea is gaining prominence in Canada, Australia, and South America where it constitutes a main ingredient in vegetarian and vegan diets. Viruses and plant parasitic nematodes (PPNs) have been considered to be of minor and local impact in primary areas of cultivation. However, the introduction of chickpea in new environments exposes the crop to these biotic stresses, compromising its yields. The adoption of high-throughput genomic technologies, including genome and transcriptome sequencing projects by the chickpea research community, has provided major insights into genome evolution as well as genomic architecture and domestication. This review summarizes the major viruses and PPNs that affect chickpea cultivation worldwide. We also present an overview of the current state of chickpea genomics. Accordingly, we explore the opportunities that genomics, post-genomics and novel editing biotechnologies are offering in order to understand chickpea diseases and stress tolerance and to design innovative control strategies.
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Affiliation(s)
- Paola Leonetti
- Institute for Sustainable Plant Protection, Research Unit of Bari, National Research Council, Bari, Italy
| | - Gian Paolo Accotto
- Institute for Sustainable Plant Protection, Research Unit of Turin, National Research Council, Turin, Italy
| | - Moemen S. Hanafy
- Department of Plant Biotechnology, National Research Centre, Cairo, Egypt
| | - Vitantonio Pantaleo
- Institute for Sustainable Plant Protection, Research Unit of Bari, National Research Council, Bari, Italy
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9
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Zaagueri T, Miozzi L, Mnari-Hattab M, Noris E, Accotto GP, Vaira AM. Deep Sequencing Data and Infectivity Assays Indicate that Chickpea Chlorotic Dwarf Virus is the Etiological Agent of the "Hard Fruit Syndrome" of Watermelon. Viruses 2017; 9:E311. [PMID: 29068372 PMCID: PMC5707518 DOI: 10.3390/v9110311] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/13/2017] [Accepted: 10/21/2017] [Indexed: 11/25/2022] Open
Abstract
Chickpea chlorotic dwarf virus (CpCDV), a polyphagous mastrevirus, family Geminiviridae, has been recently linked to the onset of the "hard fruit syndrome" of watermelon, first described in Tunisia, that makes fruits unmarketable due to the presence of white hard portions in the flesh, chlorotic mottling on the rind, and an unpleasant taste. To investigate the etiological agent of this disease, total RNA extracted from symptomatic watermelon fruits was subjected to small RNA sequencing through next generation sequencing (NGS) techniques. Data obtained showed the presence of CpCDV and two other viral species. However, following validation through polymerase chain reaction (PCR), CpCDV was the only viral species consistently detected in all samples. Watermelon seedlings were then challenged by an agroinfectious CpCDV clone; several plants proved to be CpCDV-infected, and were able to produce fruits. CpCDV infected and replicated in watermelon fruits and leaves, leading to abnormality in fruits and in seed production, similar to those described in field. These results indicate that CpCDV is the etiological agent of the "hard fruit syndrome" of watermelon.
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Affiliation(s)
- Takoua Zaagueri
- Laboratoire de Biotechnologie Appliquée à l'Agriculture, Institut National de la Recherche Agronomique de Tunisie (INRAT), Université de Carthage, El Rue Hedi Karray Menzah, 1004 Tunis, Tunisia.
- Institute for Sustainable Plant Protection (IPSP), CNR, 10135 Turin, Italy.
| | - Laura Miozzi
- Institute for Sustainable Plant Protection (IPSP), CNR, 10135 Turin, Italy.
| | - Monia Mnari-Hattab
- Laboratoire de Biotechnologie Appliquée à l'Agriculture, Institut National de la Recherche Agronomique de Tunisie (INRAT), Université de Carthage, El Rue Hedi Karray Menzah, 1004 Tunis, Tunisia.
| | - Emanuela Noris
- Institute for Sustainable Plant Protection (IPSP), CNR, 10135 Turin, Italy.
| | - Gian Paolo Accotto
- Institute for Sustainable Plant Protection (IPSP), CNR, 10135 Turin, Italy.
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection (IPSP), CNR, 10135 Turin, Italy.
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10
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Fontenele RS, Alves-Freitas DMT, Silva PIT, Foresti J, Silva PR, Godinho MT, Varsani A, Ribeiro SG. Discovery of the first maize-infecting mastrevirus in the Americas using a vector-enabled metagenomics approach. Arch Virol 2017; 163:263-267. [PMID: 28956174 DOI: 10.1007/s00705-017-3571-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 09/04/2017] [Indexed: 01/18/2023]
Abstract
The genus Mastrevirus (family Geminiviridae) is composed of single-stranded DNA viruses that infect mono- and dicotyledonous plants and are transmitted by leafhoppers. In South America, there have been only two previous reports of mastreviruses, both identified in sweet potatoes (from Peru and Uruguay). As part of a general viral surveillance program, we used a vector-enabled metagenomics (VEM) approach and sampled leafhoppers (Dalbulus maidis) in Itumbiara (State of Goiás), Brazil. High-throughput sequencing of viral DNA purified from the leafhopper sample revealed mastrevirus-like contigs. Using a set of abutting primers, a 2746-nt circular genome was recovered. The circular genome has a typical mastrevirus genome organization and shares <63% pairwise identity with other mastrevirus isolates from around the world. Therefore, the new mastrevirus was tentatively named "maize striate mosaic virus". Seventeen maize leaf samples were collected in the same field as the leafhoppers, and ten samples were found to be positive for this mastrevirus. Furthermore, the ten genomes recovered from the maize samples share >99% pairwise identity with the one from the leafhopper. This is the first report of a maize-infecting mastrevirus in the Americas, the first identified in a non-vegetatively propagated mastrevirus host in South America, and the first mastrevirus to be identified in Brazil.
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Affiliation(s)
- Rafaela S Fontenele
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil.,The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine School of Life Sciences, Arizona State University, Tempe, AZ, USA, 85287
| | | | - Pedro I T Silva
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
| | - Josemar Foresti
- Faculdade de Agronomia e Medicina Veterinária, Campus Darcy Ribeiro, Universidade de Brasília, Brasília, DF, Brasil
| | - Paulo R Silva
- Faculdade de Agronomia e Medicina Veterinária, Campus Darcy Ribeiro, Universidade de Brasília, Brasília, DF, Brasil
| | | | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine School of Life Sciences, Arizona State University, Tempe, AZ, USA, 85287. .,Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South Africa.
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11
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New strains of chickpea chlorotic dwarf virus discovered on diseased papaya and tomato plants in Burkina Faso. Arch Virol 2017; 162:1791-1794. [DOI: 10.1007/s00705-017-3262-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 01/11/2017] [Indexed: 11/27/2022]
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12
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Hema M, Sreenivasulu P, Patil BL, Kumar PL, Reddy DVR. Tropical food legumes: virus diseases of economic importance and their control. Adv Virus Res 2015; 90:431-505. [PMID: 25410108 DOI: 10.1016/b978-0-12-801246-8.00009-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Diverse array of food legume crops (Fabaceae: Papilionoideae) have been adopted worldwide for their protein-rich seed. Choice of legumes and their importance vary in different parts of the world. The economically important legumes are severely affected by a range of virus diseases causing significant economic losses due to reduction in grain production, poor quality seed, and costs incurred in phytosanitation and disease control. The majority of the viruses infecting legumes are vectored by insects, and several of them are also seed transmitted, thus assuming importance in the quarantine and in the epidemiology. This review is focused on the economically important viruses of soybean, groundnut, common bean, cowpea, pigeonpea, mungbean, urdbean, chickpea, pea, faba bean, and lentil and begomovirus diseases of three minor tropical food legumes (hyacinth bean, horse gram, and lima bean). Aspects included are geographic distribution, impact on crop growth and yields, virus characteristics, diagnosis of causal viruses, disease epidemiology, and options for control. Effectiveness of selection and planting with virus-free seed, phytosanitation, manipulation of crop cultural and agronomic practices, control of virus vectors and host plant resistance, and potential of transgenic resistance for legume virus disease control are discussed.
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Affiliation(s)
- Masarapu Hema
- Department of Virology, Sri Venkateswara University, Tirupati, India
| | - Pothur Sreenivasulu
- Formerly Professor of Virology, Sri Venkateswara University, Tirupati, India
| | - Basavaprabhu L Patil
- National Research Centre on Plant Biotechnology, IARI, Pusa Campus, New Delhi, India
| | - P Lava Kumar
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Dodla V R Reddy
- Formerly Principal Virologist, ICRISAT, Patancheru, Hyderabad, India.
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13
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Fahmy IF, Taha O, El-Ashry AN. First genome analysis and molecular characterization of Chickpea chlorotic dwarf virus Egyptian isolate infecting squash. Virusdisease 2015; 26:33-41. [PMID: 26436119 PMCID: PMC4585055 DOI: 10.1007/s13337-014-0246-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/29/2014] [Indexed: 10/24/2022] Open
Abstract
This study aims to identifying and characterizing some molecular properties of geminiviruses co-infection in squash field crop cultivated in Egypt. Squash crops observed to be heavily infected with several insect vectors, also severe chlorosis and stunting was observed. Electron microscopic analysis has revealed geminate capsid particles which indicate the infection of Geminiviruses, especially SqLCV which represent an economic problem to squash filed crop in Egypt. We have investigated possible mixed infections with different plant viruses associated with chlorotic stunt diseases and or other genus groups of geminiviruses. The main objective of this study is to investigate the recombination events, possible recombinants and variants among these genera in the same family differing in vector transmission. This is the first report of the molecular characterization, phylogenetic analysis and putative recombination events of the full length genome of the Chickpea Chlorotic Dwarf Mastrevirus in Egypt. And the first report of co-infection with another begomovirus infecting squash plants. A full length clone of both viruses were isolated and characterized at the molecular level. The complete nucleotide sequence of DNA-A was determined (2,572 bp) and submitted to the genbank under accession no. KF692356. The isolate from Egypt has about 97.8 % homology with the Chickpea chlorotic dwarf virus (CpCDV) isolate from Syria DNA-A isolate FR687959, a 83.2 % homology with the Sudan isolate AM933134 and a 82.7 % homology with Pakistan isolate FR687960. To best of our knowledge this is the first report of complete genome of CpCDV that infect squash plants in Egypt and worldwide.
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Affiliation(s)
- Inas Farouk Fahmy
- />Phytopathogen Vector Interaction Lab, Department of Microbiology, Agricultural Research Center (ARC), Agricultural Genetic Engineering Research Institute, Giza, Egypt
| | - Omnia Taha
- />Phytopathogen Vector Interaction Lab, Department of Microbiology, Agricultural Research Center (ARC), Agricultural Genetic Engineering Research Institute, Giza, Egypt
| | - Abdel Nasser El-Ashry
- />Department of Plant Pathology, Faculty of Agriculture, Institute fuer Nutzpflanzenwissenschaften und Ressourcen Schutz, University of Bonn, Bonn, Germany
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14
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Identification of an Australian-like dicot-infecting mastrevirus in Pakistan. Arch Virol 2014; 160:825-30. [DOI: 10.1007/s00705-014-2299-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Accepted: 11/28/2014] [Indexed: 10/24/2022]
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15
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Kraberger S, Kumari SG, Hamed AA, Gronenborn B, Thomas JE, Sharman M, Harkins GW, Muhire BM, Martin DP, Varsani A. Molecular diversity of Chickpea chlorotic dwarf virus in Sudan: high rates of intra-species recombination - a driving force in the emergence of new strains. INFECTION GENETICS AND EVOLUTION 2014; 29:203-15. [PMID: 25444941 DOI: 10.1016/j.meegid.2014.11.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 11/17/2014] [Accepted: 11/21/2014] [Indexed: 10/24/2022]
Abstract
In Sudan Chickpea chlorotic dwarf virus (CpCDV, genus Mastrevirus, family Geminiviridae) is an important pathogen of pulses that are grown both for local consumption, and for export. Although a few studies have characterised CpCDV genomes from countries in the Middle East, Africa and the Indian subcontinent, little is known about CpCDV diversity in any of the major chickpea production areas in these regions. Here we analyse the diversity of 146 CpCDV isolates characterised from pulses collected across the chickpea growing regions of Sudan. Although we find that seven of the twelve known CpCDV strains are present within the country, strain CpCDV-H alone accounted for ∼73% of the infections analysed. Additionally we identified four new strains (CpCDV-M, -N, -O and -P) and show that recombination has played a significant role in the diversification of CpCDV, at least in this region. Accounting for observed recombination events, we use the large amounts of data generated here to compare patterns of natural selection within protein coding regions of CpCDV and other dicot-infecting mastrevirus species.
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Affiliation(s)
- Simona Kraberger
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand
| | - Safaa G Kumari
- Virology Laboratory, International Centre for Agricultural Research in the Dry Areas (ICARDA), Tunis, Tunisia.
| | - Abdelmagid A Hamed
- Plant Pathology Research Program, Agricultural Research Corporation, P.O. Box 126, Wadmedani, Sudan
| | - Bruno Gronenborn
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France
| | - John E Thomas
- Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, GPO Box 267, Brisbane, QLD 4001, Australia
| | - Murray Sharman
- Department of Agriculture, Fisheries and Forestry, Ecoscience Precinct, GPO Box 267, Brisbane, QLD 4001, Australia
| | - Gordon W Harkins
- South African National Bioinformatics Institute, SA Medical Research Unit for Bioinformatics Capacity Development, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa
| | - Brejnev M Muhire
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Darren P Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Arvind Varsani
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand; Electron Microscope Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, 7700, South Africa; Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA.
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Abstract
Cool-season grain legume crops become infected with a wide range of viruses, many of which cause serious diseases and major yield losses. This review starts by discussing which viruses are important in the principal cool-season grain legume crops in different parts of the world, the losses they cause and their economic impacts in relation to control. It then describes the main types of control measures available: host resistance, phytosanitary measures, cultural measures, chemical control, and biological control. Examples are provided of successful deployment of the different types of measures to control virus epidemics in cool-season grain legume crops. Next it emphasizes the need for integrated approaches to control because single control measures used alone rarely suffice to adequately reduce virus-induced yield losses in these crops. Development of effective integrated disease management (IDM) strategies depends on an interdisciplinary team approach to (i) understand the ecological and climatic factors which lead to damaging virus epidemics and (ii) evaluate the effectiveness of individual control measures. In addition to using virus-resistant cultivars, other IDM components include sowing virus-tested seed stocks, selecting cultivars with low seed transmission rates, using diverse phytosanitary or cultural practices that minimize the virus source or reduce its spread, and using selective pesticides in an environmentally responsible way. The review finishes by briefly discussing the implications of climate change in increasing problems associated with control and the opportunities to control virus diseases more effectively through new technologies.
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Al Rwahnih M, Dave A, Anderson MM, Rowhani A, Uyemoto JK, Sudarshana MR. Association of a DNA virus with grapevines affected by red blotch disease in California. PHYTOPATHOLOGY 2013; 103:1069-1076. [PMID: 23656312 DOI: 10.1094/phyto-10-12-0253-r] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
In the Napa Valley of California, vineyards of 'Cabernet Franc' (CF) clone 214, 'Cabernet Sauvignon' clone 337, and 'Zinfandel' clone 1A (Z1A) with grapevines exhibiting foliar symptoms of red blotches, marginal reddening, and red veins that were accompanied by reduced sugar accumulation in fruit at harvest were initially suspected to be infected with leafroll-associated viruses. However, reverse-transcription polymerase chain reaction (PCR) tests were negative for all known leafroll-associated viruses, with the exception of Grapevine leafroll-associated virus 2 in Z1A. Metagenomic analysis of cDNA libraries obtained from double-stranded RNA enriched nucleic acid (NA) preparations from bark scrapings of dormant canes on an Illumina platform revealed sequences having a distant relationship with members of the family Geminiviridae. Sequencing of products obtained by PCR assays using overlapping primers and rolling circle amplification (RCA) confirmed the presence of a single circular genome of 3,206 nucleotides which was nearly identical to the genome of a recently reported Grapevine cabernet franc-associated virus found in declining grapevines in New York. We propose to call this virus "Grapevine red blotch-associated virus" (GRBaV) to describe its association with grapevine red blotch disease. Primers specific to GRBaV amplified a product of expected size (557 bp) from NA preparations obtained from petioles of several diseased source vines. Chip bud inoculations successfully transmitted GRBaV to test plants of CF, as confirmed by PCR analysis. This is the first report of a DNA virus associated with red blotch disease of grapevines in California.
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18
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Kraberger S, Harkins GW, Kumari SG, Thomas JE, Schwinghamer MW, Sharman M, Collings DA, Briddon RW, Martin DP, Varsani A. Evidence that dicot-infecting mastreviruses are particularly prone to inter-species recombination and have likely been circulating in Australia for longer than in Africa and the Middle East. Virology 2013; 444:282-91. [PMID: 23886492 DOI: 10.1016/j.virol.2013.06.024] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Revised: 06/08/2013] [Accepted: 06/24/2013] [Indexed: 11/25/2022]
Abstract
Viruses of the genus Mastrevirus (family Geminiviridae) are transmitted by leafhoppers and infect either mono- or dicotyledonous plants. Here we have determined the full length sequences of 49 dicot-infecting mastrevirus isolates sampled in Australia, Eritrea, India, Iran, Pakistan, Syria, Turkey and Yemen. Comprehensive analysis of all available dicot-infecting mastrevirus sequences showed the diversity of these viruses in Australia to be greater than in the rest of their known range, consistent with earlier studies, and that, in contrast with the situation in monocot-infecting mastreviruses, detected inter-species recombination events outnumbered intra-species recombination events. Consistent with Australia having the greatest diversity of known dicot-infecting mastreviruses phylogeographic analyses indicating the most plausible scheme for the spread of these viruses to their present locations, suggest that most recent common ancestor of these viruses is likely nearer Australia than it is to the other regions investigated.
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Affiliation(s)
- Simona Kraberger
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
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19
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A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae). Arch Virol 2013; 158:1411-24. [DOI: 10.1007/s00705-012-1601-7] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 12/01/2012] [Indexed: 10/27/2022]
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20
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Rosario K, Padilla-Rodriguez M, Kraberger S, Stainton D, Martin DP, Breitbart M, Varsani A. Discovery of a novel mastrevirus and alphasatellite-like circular DNA in dragonflies (Epiprocta) from Puerto Rico. Virus Res 2013; 171:231-7. [DOI: 10.1016/j.virusres.2012.10.017] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 10/14/2012] [Accepted: 10/18/2012] [Indexed: 11/28/2022]
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21
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Kraberger S, Thomas JE, Geering AD, Dayaram A, Stainton D, Hadfield J, Walters M, Parmenter KS, van Brunschot S, Collings DA, Martin DP, Varsani A. Australian monocot-infecting mastrevirus diversity rivals that in Africa. Virus Res 2012; 169:127-36. [DOI: 10.1016/j.virusres.2012.07.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 07/14/2012] [Accepted: 07/17/2012] [Indexed: 11/26/2022]
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22
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Hadfield J, Thomas JE, Schwinghamer MW, Kraberger S, Stainton D, Dayaram A, Parry JN, Pande D, Martin DP, Varsani A. Molecular characterisation of dicot-infecting mastreviruses from Australia. Virus Res 2012; 166:13-22. [PMID: 22406325 DOI: 10.1016/j.virusres.2012.02.024] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 02/16/2012] [Accepted: 02/20/2012] [Indexed: 11/24/2022]
Abstract
Monocotyledonous and dicotyledonous plant infecting mastreviruses threaten various agricultural systems throughout Africa, Eurasia and Australasia. In Australia three distinct mastrevirus species are known to infect dicotyledonous hosts such as chickpea, bean and tobacco. Amongst 34 new "dicot-infecting" mastrevirus full genome sequences obtained from these hosts we discovered one new species, four new strains, and various variants of previously described mastrevirus species. Besides providing additional support for the hypothesis that evolutionary processes operating during dicot-infecting mastrevirus evolution (such as patterns of pervasive homologous and non-homologous recombination, and strong purifying selection acting on all genes) have mostly mirrored those found in their monocot-infecting counterparts, we find that the Australian dicot-infecting viruses display patterns of phylogeographic clustering reminiscent of those displayed by monocot infecting mastrevirus species such as Panicum streak virus and Maize streak virus.
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Affiliation(s)
- James Hadfield
- School of Biological Sciences, University of Canterbury, Ilam, Christchurch 8140, New Zealand
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23
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Nahid N, Amin I, Briddon RW, Mansoor S. RNA interference-based resistance against a legume mastrevirus. Virol J 2011; 8:499. [PMID: 22047503 PMCID: PMC3214926 DOI: 10.1186/1743-422x-8-499] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 11/02/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND RNA interference (RNAi) is a homology-dependant gene silencing mechanism and has been widely used to engineer resistance in plants against RNA viruses. However, its usefulness in delivering resistance against plant DNA viruses belonging to family Geminiviridae is still being debated. Although the RNAi approach has been shown, using a transient assay, to be useful in countering monocotyledonous plant-infecting geminiviruses of the genus Mastrevirus, it has yet to be investigated as a means of delivering resistance to dicot-infecting mastreviruses. Chickpea chlorotic dwarf Pakistan virus (CpCDPKV) is a legume-infecting mastrevirus that affects chickpea and other leguminous crops in Pakistan. RESULTS Here a hairpin (hp)RNAi construct containing sequences encompassing part of replication-associated protein gene, intergenic region and part of the movement protein gene of CpCDPKV under the control of the Cauliflower mosaic virus 35S promoter has been produced and stably transformed into Nicotiana benthamiana. Plants harboring the hairpin construct were challenged with CpCDPKV. All non-transgenic N. benthamiana plants developed symptoms of CpCDPKV infection within two weeks post-inoculation. In contrast, none of the inoculated transgenic plants showed symptoms of infection and no viral DNA could be detected by Southern hybridization. A real-time quantitative PCR analysis identified very low-level accumulation of viral DNA in the inoculated transgenic plants. CONCLUSIONS The results presented show that the RNAi-based resistance strategy is useful in protecting plants from a dicot-infecting mastrevirus. The very low levels of virus detected in plant tissue of transgenic plants distal to the inoculation site suggest that virus movement and/or viral replication was impaired leading to plants that showed no discernible signs of virus infection.
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Affiliation(s)
- Nazia Nahid
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), P O Box 577, Jhang Road, Faisalabad, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), P O Box 577, Jhang Road, Faisalabad, Pakistan
| | - Rob W Briddon
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), P O Box 577, Jhang Road, Faisalabad, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), P O Box 577, Jhang Road, Faisalabad, Pakistan
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Geering ADW, Thomas JE, Holton T, Hadfield J, Varsani A. Paspalum striate mosaic virus: an Australian mastrevirus from Paspalum dilatatum. Arch Virol 2011; 157:193-7. [DOI: 10.1007/s00705-011-1129-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 09/18/2011] [Indexed: 10/16/2022]
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25
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Martin DP, Briddon RW, Varsani A. Recombination patterns in dicot-infecting mastreviruses mirror those found in monocot-infecting mastreviruses. Arch Virol 2011; 156:1463-9. [PMID: 21484422 DOI: 10.1007/s00705-011-0994-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2011] [Accepted: 03/28/2011] [Indexed: 11/28/2022]
Abstract
Recombination has profoundly shaped the evolution of viruses in the family Geminiviridae and has been studied extensively in the two best characterised geminivirus lineages: the dicotyledonous plant infecting begomoviruses and the monocotyledonous plant infecting mastreviruses. Here, we demonstrate that the sizes and distributions of recombination events detectable within the members of a third major geminivirus lineage--the dicotyledonous plant infecting mastreviruses--are very similar to those of the monocot-infecting mastreviruses. This suggests that, despite host range differences, very similar biochemical, ecological and evolutionary factors must underlie recombination patterns in the dicot- and monocot-infecting mastreviruses.
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Affiliation(s)
- Darren P Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa
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Analysis of the sequence of a dicot-infecting mastrevirus (family Geminiviridae) originating from Syria. Virus Genes 2011; 42:422-8. [DOI: 10.1007/s11262-011-0586-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 02/04/2011] [Indexed: 11/25/2022]
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27
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Rybicki EP, Martin DP. Virus-derived ssDNA vectors for the expression of foreign proteins in plants. Curr Top Microbiol Immunol 2011; 375:19-45. [PMID: 22038412 DOI: 10.1007/82_2011_185] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Plant viruses with ssRNA genomes provide a unique opportunity for generating expression vehicles for biopharming in plants, as constructs containing only the replication origin, with the replication-associated protein (Rep) gene provided in cis or in trans, can be replicationally amplified in vivo by several orders of magnitude, with significant accompanying increases in transcription and expression of gene(s) of interest. Appropriate replicating vectors or replicons may be derived from several different generic geminiviruses (family Geminiviridae) or nanoviruses (family Nanoviridae), for potential expression of a wide range of single or even multiple products in a wide range of plant families. The use of vacuum or other infiltration of whole plants by Agrobacterium tumefaciens suspensions has allowed the development of a set of expression vectors that rival the deconstructed RNA virus vectors in their yield and application, with some potential advantages over the latter that still need to be explored. Several modern applications of ssDNA plant vectors and their future potential will be discussed.
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Affiliation(s)
- Edward P Rybicki
- Institute of Infectious Disease and Molecular Medicine, Cape Town, South Africa,
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