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Shingote PR, Wasule DL, Parma VS, Holkar SK, Karkute SG, Parlawar ND, Senanayake DMJB. An Overview of Chili Leaf Curl Disease: Molecular Mechanisms, Impact, Challenges, and Disease Management Strategies in Indian Subcontinent. Front Microbiol 2022; 13:899512. [PMID: 35847087 PMCID: PMC9277185 DOI: 10.3389/fmicb.2022.899512] [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] [Received: 03/18/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Leaf curl disease in a chili plant is caused mainly by Chili leaf curl virus (ChiLCV) (Family: Geminiviridae, Genus: Begomovirus). ChiLCV shows a widespread occurrence in most of the chili (Capsicum spp.) growing regions. ChiLCV has a limited host range and infects tomatoes (Solanum lycopersicum), potatoes (S. tuberosum), and amaranth (Amaranthus tricolor). The virus genome is a monopartite circular single-stranded DNA molecule of 2.7 kb and associated with α and β-satellites of 1.3 and 1.4 kb, respectively. The virus genome is encapsulated in distinct twinned icosahedral particles of around 18-30 nm in size and transmitted by Bemisia tabaci (Family: Aleyrodidae, Order: Hemiptera). Recently, bipartite begomovirus has been found to be associated with leaf curl disease. The leaf curl disease has a widespread distribution in the major equatorial regions viz., Australia, Asia, Africa, Europe, and America. Besides the PCR, qPCR, and LAMP-based detection systems, recently, localized surface-plasmon-resonance (LPSR) based optical platform is used for ChiLCV detection in a 20-40 μl of sample volume using aluminum nanoparticles. Management of ChiLCV is more challenging due to the vector-borne nature of the virus, therefore integrated disease management strategies need to be followed to contain the spread and heavy crop loss. CRISPR/Cas-mediated virus resistance has gained importance in disease management of DNA and RNA viruses due to certain advantages over the conventional approaches. Therefore, CRISPR/Cas system-mediated resistance needs to be explored in chili against ChiLCV.
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Affiliation(s)
- Prashant Raghunath Shingote
- Department of Agricultural Biotechnology, Dr. Panjabrao Deshmukh Krishi Veedyapeeth, Akola, India.,Department of Agricultural Biotechnology, Vasantrao Naik College of Agricultural Biotechnology, Yavatmal, India
| | - Dhiraj Lalji Wasule
- Department of Agricultural Biotechnology, Dr. Panjabrao Deshmukh Krishi Veedyapeeth, Akola, India
| | - Vaishnavi Sanjay Parma
- Department of Agricultural Biotechnology, Dr. Panjabrao Deshmukh Krishi Veedyapeeth, Akola, India
| | - Somnath Kadappa Holkar
- Indian Council of Agricultural Research (ICAR)-National Research Centre for Grapes, Pune, India
| | - Suhas Gorakh Karkute
- Division of Vegetable Improvement, Indian Council of Agricultural Research (ICAR)-Indian Institute of Vegetable Research, Varanasi, India
| | - Narsing Devanna Parlawar
- Department of Agricultural Biotechnology, Dr. Panjabrao Deshmukh Krishi Veedyapeeth, Akola, India
| | - D M J B Senanayake
- Deparment of Agriculture, Rice Research and Development Institute, Bathalagoda, Sri Lanka
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2
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Nawaz-Ul-Rehman MS, Liaqat I, Nahid N, Saleem F, Alkahtani S, Al Qahtani A, Ye J, Mubin M. Alternanthera yellow vein virus (AYVV); a betasatellite independent begomovirus infecting Sonchus palustris in Pakistan. BRAZ J BIOL 2022; 82:e262248. [PMID: 35703634 DOI: 10.1590/1519-6984.262248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/13/2022] [Indexed: 11/22/2022] Open
Abstract
Satellites associated begomoviruses are the most diverse group of plant viruses in tropical and subtropical regions. In Pakistan, during field surveys in 2019-2020, Sonchus palustris (a weed plant) was observed showing begomovirus symptoms i.e., vein yellowing and mosaic patterns on leaves. Rolling circle amplification from total isolated DNA of symptomatic leaves was performed to amplify circular viral genomes. Subsequent cloning and sequencing showed that a new strain of Alternanthera yellow vein virus (AlYVV) is associated with vein yellowing disease of S. palustris. The identity percentage analysis through BLAST search and SDT analysis showed that the new strain is 94-98% identical to AlYVV isolates reported from Pakistan, India and China. In phylogenetic tree, it clustered with AlYVV-[PK:E prostrata:15-KX710155], AlYVV-[PK:E prostrata:13]-KX906697] and AlYVV-[PK:E prostrata:11]-KX906694] previously reported from Pakistan. There was no detectable level of betasatellite or any other satellite molecule in the samples studied here. Phylogenetic analysis of Rep and CP genes of AlYVV with corresponding genes of closely related viruses circulating in Southeast Asia showed intra-specific recombination involving both complementary and virion sense region of virus. Relaxed clock and Bayesian Skyline Plot analysis based on CP gene sequences indicated slight higher substitution rates (4.75 x 10-3 substitutions/nucleotide/year). In the Indian subcontinent satellite-associated monopartite begomoviruses predominately infect crops and non-crop plants. But AlYVV is found infecting mostly non-crop plants independent of satellite molecules. We hypothesize here that AlYVV evolved as a true monopartite begomovirus in the Indian sub-continent and could be a great threat to introduced crops under suitable conditions. Such studies are crucial to understand probable future epidemics of begomoviruses in the region.
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Affiliation(s)
- M S Nawaz-Ul-Rehman
- University of Agriculture, Centre of Agricultural Biochemistry and Biotechnology, Faisalabad, Pakistan
| | - I Liaqat
- GC University Lahore, Department of Zoology, Lahore, Pakistan
| | - N Nahid
- GC University Faisalabad, Department of Bioinformatics and Biotechnology, Faisalabad, Pakistan
| | - F Saleem
- University of Agriculture, Centre of Agricultural Biochemistry and Biotechnology, Faisalabad, Pakistan
| | - S Alkahtani
- King Saud University, College of Science, Department of Zoology, Riyadh, Saudi Arabia
| | - A Al Qahtani
- King Faisal Specialist Hospital and Research Center, Research Center, Department of Infection and Immunity, Riyadh, Saudi Arabia
| | - J Ye
- Chinese Academy of Sciences, Institute of Microbiology, Laboratory of Vector-Borne Diseases, State Key Laboratory of Plant Genomics, Beijing, PR China
| | - M Mubin
- University of Agriculture, Centre of Agricultural Biochemistry and Biotechnology, Faisalabad, Pakistan.,Chinese Academy of Sciences, Institute of Microbiology, Laboratory of Vector-Borne Diseases, State Key Laboratory of Plant Genomics, Beijing, PR China
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3
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Incidence and Molecular Identification of Begomoviruses Infecting Tomato and Pepper in Myanmar. PLANTS 2022; 11:plants11081031. [PMID: 35448759 PMCID: PMC9030778 DOI: 10.3390/plants11081031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 11/17/2022]
Abstract
In Myanmar, yellow mosaic and leaf curl diseases caused by whitefly-transmitted begomoviruses are serious problems for vegetables such as tomatoes and peppers. To investigate the incidence of begomoviruses in Myanmar between 2017 and 2019, a field survey of tomato and pepper plants with virus-like symptoms was conducted in the Naypyitaw, Tatkon, and Mohnyin areas of Myanmar. Among the 59 samples subjected to begomovirus detection using polymerase chain reaction, 59.3% were infected with begomoviruses. Complete genome sequences using rolling circle amplification identified five begomovirus species: tomato yellow leaf curl Thailand virus (TYLCTHV), tomato yellow leaf curl Kanchanaburi virus (TYLCKaV), tobacco leaf curl Yunnan virus (TbLCYnV), chili leaf curl Pakistan virus (ChiLCV/PK), and tobacco curly shoot Myanmar virus (TbCSV-[Myanmar]). Excluding the previously reported TYLCTHV, three begomoviruses (ChiLCV/PK, TYLCKaV, and TbLCYnV) were identified in Myanmar for the first time. Based on the 91% demarcation threshold of begomovirus species, TbCSV-[Myanmar] was identified as a new species in this study. Among these, ChiLCV/PK and TbCSV-[Myanmar] were the most predominant in tomato and pepper fields in Myanmar. Identification of begomovirus species may be helpful for predicting the origin of viruses and preventing their spread.
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Lavanya R, Arun V. Detection of Begomovirus in chilli and tomato plants using functionalized gold nanoparticles. Sci Rep 2021; 11:14203. [PMID: 34244585 PMCID: PMC8271019 DOI: 10.1038/s41598-021-93615-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023] Open
Abstract
Begomoviruses are a major class of Geminiviruses that affects most dicotyledonous plants and causes heavy economic losses to farmers. Early detection of begomovirus is essential to control the spread of the disease and prevent loss. Many available detection methods like ELISA, immunosorbent electron microscopy, PCR or qPCR require expertise in handling sophisticated instruments, complex data interpretation and costlier chemicals, enzymes or antibodies. Hence there is a need for a simpler detection method, here we report the development of a visual detection method based on functionalized gold nanoparticles (AuNP assay). The assay was able to detect up to 500 ag/µl of begomoviral DNA (pTZCCPp3, a clone carrying partial coat protein gene) suspended in MilliQ water. Screening of chilli plants for begomoviral infection by PCR (Deng primers) and AuNP assay showed that AuNP assay (77.7%) was better than PCR (49.4%). The AuNP assay with clccpi1 probe was able to detect begomoviral infection in chilli, tomato, common bean, green gram and black gram plants which proved the utility and versatility of the AuNP assay. The specificity of the assay was demonstrated by testing with total DNA from different plants that are not affected by begomoviruses.
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Affiliation(s)
- R. Lavanya
- grid.412734.70000 0001 1863 5125Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research, Chennai, Tamil Nadu India
| | - V. Arun
- grid.412734.70000 0001 1863 5125Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research, Chennai, Tamil Nadu India
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Devendran R, Kumar M, Ghosh D, Yogindran S, Karim MJ, Chakraborty S. Capsicum-infecting begomoviruses as global pathogens: host-virus interplay, pathogenesis, and management. Trends Microbiol 2021; 30:170-184. [PMID: 34215487 DOI: 10.1016/j.tim.2021.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 01/28/2023]
Abstract
Whitefly-transmitted begomoviruses are among the major threats to the cultivation of Capsicum spp. (Family: Solanaceae) worldwide. Capsicum-infecting begomoviruses (CIBs) have a broad host range and are commonly found in mixed infections, which, in turn, fuels the emergence of better-adapted species through intraspecies and interspecies recombination. Virus-encoded proteins hijack host factors to breach the well-coordinated antiviral response of plants. Epigenetic modifications of histones associated with viral minichromosomes play a critical role in this molecular arms race. Moreover, the association of DNA satellites further enhances the virulence of CIBs as the subviral agents aid the helper viruses to circumvent plant antiviral defense and facilitate expansion of their host range and disease development. The objective of this review is to provide a comprehensive overview on various aspects of CIBs such as their emergence, epidemiology, mechanism of pathogenesis, and the management protocols being employed for combating them.
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Affiliation(s)
- Ragunathan Devendran
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Manish Kumar
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Dibyendu Ghosh
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sneha Yogindran
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Mir Jishan Karim
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Supriya Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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6
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Molecular and biological characterization of Chilli leaf curl virus and associated betasatellite infecting Cucurbita maxima in Oman. Virusdisease 2020; 31:378-382. [PMID: 32904994 DOI: 10.1007/s13337-020-00601-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 05/20/2020] [Indexed: 10/24/2022] Open
Abstract
During a survey in February 2016, leaf curl disease symptoms were witnessed in Cucurbita maxima plants in Al-Batina commercial farm in Oman. Symptoms exhibited were characteristic of begomovirus infection as leaf curling, yellowing, and color breaking followed by mosaic pattern. The transmission electron microscopy confirmed the presence of typical twinned geminate typical of Geminate virus particles. Rolling circle amplification (RCA) was employed to characterize the unknown causal agent of C. maxima disease. In molecular identification RCA produced nearly 2.8 and 1.4 kb DNA molecules corresponding to begomovirus and satellite molecules, cloned and sequenced them. In Blast, species demarcation tool and phylogenetic analysis revealed the begomovirus and satellite isolates were determined as Chilli leaf curl virus (ChLCV) and tomato leaf curl betasatellite (ToLCB). In biological analysis by agrobacterium mediated inoculation, ChLCV displayed upward leaf curling and vein swelling symptoms in Nicotiana benthamiana plants; however, in presence of ToLCB enhanced downward leaf curling and crumpling symptoms were revealed. This study provides the first evidence that ChLCV and ToLCB caused leaf curl disease of C. maxima in Oman.
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7
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Laprom A, Nilthong S, Chukeatirote E. Incidence of viruses infecting pepper in Thailand. Biomol Concepts 2019; 10:184-193. [PMID: 31743101 DOI: 10.1515/bmc-2019-0021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/03/2019] [Indexed: 01/13/2023] Open
Abstract
This study was conducted to determine the incidence, diversity and distribution of viruses infecting pepper (Capsicum spp.) in the central, northern and northeastern parts of Thailand. During a survey in 2016 - 2019, a total of 2,149 leaf samples from symptomatic and asymptomatic peppers were collected randomly from farmer's fields, and preliminary tested by an enzyme-linked immunosorbent assay (ELISA) using 7 antibodies specific for cucumber mosaic virus (CMV), chilli veinal mottle virus (ChiVMV), tomato necrotic ringspot virus (TNRV), tobacco mosaic virus (TMV), potato virus Y (PVY), tomato spotted wilt virus (TSWV), and begomoviruses. Our data revealed that the incidence of the viruses infecting pepper in Thailand was high, accounting for nearly 70% (1,482 infected samples). The highest viral incidence was found in the central part (96%), followed by the north (74.4%) and the northeastern (52.8%), respectively. Begomoviruses, CMV, ChiVMV, and TNRV were detected in the samples at varying rates, whereas PVY, TMV, and TSWV were not detected. Of these, the most frequently found virus was Begomoviruses accounting for nearly 33%, with the highest rate (ca. 82%) in the central Provinces of Thailand. In addition, of the 1,482 infected samples, mixed infections among the four viruses were also found in 616 samples (ca. 42%), and CMV + ChiVMV (approximately 11%) was the most common mixed infection. This is the first report describing an occurrence of viruses in pepper of Thailand, and the results obtained have revealed that viruses infecting pepper are widespread, which may pose a threat to pepper production in Thailand.
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Affiliation(s)
- Amisa Laprom
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Chiang Rai, Thailand
| | - Somrudee Nilthong
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Chiang Rai, Thailand
| | - Ekachai Chukeatirote
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Chiang Rai, Thailand
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8
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Rodríguez-Negrete EA, Morales-Aguilar JJ, Domínguez-Duran G, Torres-Devora G, Camacho-Beltrán E, Leyva-López NE, Voloudakis AE, Bejarano ER, Méndez-Lozano J. High-Throughput Sequencing Reveals Differential Begomovirus Species Diversity in Non-Cultivated Plants in Northern-Pacific Mexico. Viruses 2019; 11:v11070594. [PMID: 31261973 PMCID: PMC6669537 DOI: 10.3390/v11070594] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/28/2019] [Accepted: 06/17/2019] [Indexed: 12/24/2022] Open
Abstract
Plant DNA viruses of the genus Begomovirus have been documented as the most genetically diverse in the family Geminiviridae and present a serious threat for global horticultural production, especially considering climate change. It is important to characterize naturally existing begomoviruses, since viral genetic diversity in non-cultivated plants could lead to future disease epidemics in crops. In this study, high-throughput sequencing (HTS) was employed to determine viral diversity of samples collected in a survey performed during 2012–2016 in seven states of Northern-Pacific Mexico, areas of diverse climatic conditions where different vegetable crops are subject to intensive farming. In total, 132 plant species, belonging to 34 families, were identified and sampled in the natural ecosystems surrounding cultivated areas (agro-ecological interface). HTS analysis and subsequent de novo assembly revealed a number of geminivirus-related DNA signatures with 80 to 100% DNA similarity with begomoviral sequences present in the genome databank. The analysis revealed DNA signatures corresponding to 52 crop-infecting and 35 non-cultivated-infecting geminiviruses that, interestingly, were present in different plant species. Such an analysis deepens our knowledge of geminiviral diversity and could help detecting emerging viruses affecting crops in different agro-climatic regions.
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Affiliation(s)
- Edgar Antonio Rodríguez-Negrete
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico
| | - Juan José Morales-Aguilar
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico
| | - Gustavo Domínguez-Duran
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico
| | - Gadiela Torres-Devora
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico
| | - Erika Camacho-Beltrán
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico
| | - Norma Elena Leyva-López
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico
| | - Andreas E Voloudakis
- Laboratory of Plant Breeding and Biometry, Agricultural University of Athens, 75 Iera Odos, Athens 11855, Greece
| | - Eduardo R Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Campus Teatinos, 29071 Málaga, Spain
| | - Jesús Méndez-Lozano
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico.
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Rojas MR, Macedo MA, Maliano MR, Soto-Aguilar M, Souza JO, Briddon RW, Kenyon L, Rivera Bustamante RF, Zerbini FM, Adkins S, Legg JP, Kvarnheden A, Wintermantel WM, Sudarshana MR, Peterschmitt M, Lapidot M, Martin DP, Moriones E, Inoue-Nagata AK, Gilbertson RL. World Management of Geminiviruses. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:637-677. [PMID: 30149794 DOI: 10.1146/annurev-phyto-080615-100327] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Management of geminiviruses is a worldwide challenge because of the widespread distribution of economically important diseases caused by these viruses. Regardless of the type of agriculture, management is most effective with an integrated pest management (IPM) approach that involves measures before, during, and after the growing season. This includes starting with resistant cultivars and virus- and vector-free transplants and propagative plants. For high value vegetables, protected culture (e.g., greenhouses and screenhouses) allows for effective management but is limited owing to high cost. Protection of young plants in open fields is provided by row covers, but other measures are typically required. Measures that are used for crops in open fields include roguing infected plants and insect vector management. Application of insecticide to manage vectors (whiteflies and leafhoppers) is the most widely used measure but can cause undesirable environmental and human health issues. For annual crops, these measures can be more effective when combined with host-free periods of two to three months. Finally, given the great diversity of the viruses, their insect vectors, and the crops affected, IPM approaches need to be based on the biology and ecology of the virus and vector and the crop production system. Here, we present the general measures that can be used in an IPM program for geminivirus diseases, specific case studies, and future challenges.
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Affiliation(s)
- Maria R Rojas
- Department of Plant Pathology, University of California, Davis, California 95616, USA; , ,
| | - Monica A Macedo
- Department of Plant Pathology, University of California, Davis, California 95616, USA; , ,
| | - Minor R Maliano
- Department of Plant Pathology, University of California, Davis, California 95616, USA; , ,
| | - Maria Soto-Aguilar
- Department of Plant Pathology, University of California, Davis, California 95616, USA; , ,
| | - Juliana O Souza
- Department of Plant Pathology, University of California, Davis, California 95616, USA; , ,
| | - Rob W Briddon
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | | | - Rafael F Rivera Bustamante
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Unidad Irapuato, Irapuato, Guanajuato, Mexico 36821
| | - F Murilo Zerbini
- Departamento de Fitopatologia/Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | - Scott Adkins
- US Department of Agriculture, Agricultural Research Service, Fort Pierce, Florida 34945, USA
| | - James P Legg
- International Institute of Tropical Agriculture, Dar-Es-Salaam, Tanzania
| | - Anders Kvarnheden
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter and Linnean Center for Plant Biology in Uppsala, 75007 Uppsala, Sweden
| | - William M Wintermantel
- US Department of Agriculture, Agricultural Research Service, Salinas, California 93905, USA
| | - Mysore R Sudarshana
- US Department of Agriculture, Agricultural Research Service, and Department of Plant Pathology, University of California, Davis, California 95616, USA
| | - Michel Peterschmitt
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France
| | - Moshe Lapidot
- Department of Vegetable Research, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel
| | - Darren P Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Enrique Moriones
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Universidad de Málaga-Consejo Superior de Investigaciones Cientficas (IHSM-UMA-CSIC), Estación Experimental "La Mayora," Algarrobo-Costa, Málaga 29750, Spain
| | | | - Robert L Gilbertson
- Department of Plant Pathology, University of California, Davis, California 95616, USA; , ,
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Tahir MA, Hameed S, Munawar A, Amin I, Mansoor S, Khan WS, Bajwa SZ. Investigating the potential of multiwalled carbon nanotubes based zinc nanocomposite as a recognition interface towards plant pathogen detection. J Virol Methods 2017; 249:130-136. [PMID: 28888402 DOI: 10.1016/j.jviromet.2017.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/27/2017] [Accepted: 09/05/2017] [Indexed: 01/09/2023]
Abstract
The emergence of nanotechnology has opened new horizons for constructing efficient recognition interfaces. This is the first report where the potential of a multiwalled carbon nanotube based zinc nanocomposite (MWCNTs-Zn NPs) investigated for the detection of an agricultural pathogen i.e. Chili leaf curl betasatellite (ChLCB). Atomic force microscope analyses revealed the presence of multiwalled carbon nanotubes (MWCNTs) having a diameter of 50-100nm with zinc nanoparticles (Zn-NPs) of 25-500nm. In this system, these bunches of Zn-NPs anchored along the whole lengths of MWCNTs were used for the immobilization of probe DNA strands. The electrochemical performance of DNA biosensor was assessed in the absence and presence of the complementary DNA during cyclic and differential pulse voltammetry scans. Target binding events occurring on the interface surface patterned with single-stranded DNA was quantitatively translated into electrochemical signals due to hybridization process. In the presence of complementary target DNA, as the result of duplex formation, there was a decrease in the peak current from 1.89×10-04 to 5.84×10-05A. The specificity of this electrochemical DNA biosensor was found to be three times as compared to non-complementary DNA. This material structuring technique can be extended to design interfaces for the recognition of the other plant viruses and biomolecules.
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Affiliation(s)
- Muhammad Ali Tahir
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Sadaf Hameed
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan; Laboratory of Advanced Theranostic Technology, College of Engineering, Peking University, Beijing, China
| | - Anam Munawar
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Imran Amin
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Waheed S Khan
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Sadia Zafar Bajwa
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.
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11
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Khan AJ, Akhtar S, Al-Zaidi AM, Singh AK, Briddon RW. Genetic diversity and distribution of a distinct strain of Chili leaf curl virus and associated betasatellite infecting tomato and pepper in Oman. Virus Res 2013; 177:87-97. [PMID: 23911631 DOI: 10.1016/j.virusres.2013.07.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Revised: 07/12/2013] [Accepted: 07/20/2013] [Indexed: 11/28/2022]
Abstract
Tomato and pepper are widely grown in Oman for local consumption. A countrywide survey was conducted during 2010-2011 to collect samples and assess the diversity of begomoviruses associated with leaf curl disease of tomato and pepper. A virus previously only identified on the Indian subcontinent, chili leaf curl virus (ChLCV), was found associated with tomato and pepper diseases in all vegetable grown areas of Oman. Some of the infected plant samples were also found to contain a betasatellite. A total of 19 potentially full-length begomovirus and eight betasatellite clones were sequenced. The begomovirus clones showed >96% nucleotide sequence identity, showing them to represent a single species. Comparisons to sequences available in the databases showed the highest levels of nucleotide sequence identity (88.0-91.1%) to isolates of the "Pakistan" strain of ChLCV (ChLCV-PK), indicating the virus from Oman to be a distinct strain, for which the name Oman strain (ChLCV-OM) is proposed. An analysis for recombination showed ChLCV-OM likely to have originated by recombination between ChLCV-PK (the major parent), pepper leaf curl Lahore virus and a third strain of ChLCV. The betasatellite sequences obtained were shown to have high levels of identity to isolates of tomato leaf curl betasatellite (ToLCB) previous shown to be present in Oman. For the disease in tomato Koch's postulates were satisfied by Agrobacterium-mediated inoculation of virus and betasatellites clones. This showed the symptoms induced by the virus in the presence of the betasatellite to be enhanced, although viral DNA levels were not affected. ChLCV-OM is the fourth begomovirus identified in tomato in Oman and the first in Capsicum. The significance of these findings is discussed.
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Affiliation(s)
- Akhtar J Khan
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, P.O. Box-34, Al-Khod 123, Oman.
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A new begomovirus-betasatellite complex is associated with chilli leaf curl disease in Sri Lanka. Virus Genes 2012; 46:128-39. [PMID: 23090833 DOI: 10.1007/s11262-012-0836-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 10/05/2012] [Indexed: 10/27/2022]
Abstract
Leaf curl disease of chilli (LCDC) is a major constraint in production of chilli in the Indian subcontinent. The objective of this study was to identify the begomovirus species occurring in chilli in Sri Lanka, where the LCDC was initially recorded in 1938. The virus samples were collected from the North Central Province, the major chilli growing region in Sri Lanka with a history of epidemic prevalence of LCDC. The virus could be readily transmitted by Bemisia tabaci to chilli, tomato and tobacco, where vein clearing followed by leaf curl developed. The genome analysis of two isolates obtained from two distantly located fields showing 100 % LCDC, revealed that the DNA-A genome (2754 nucleotides) shared 89.5 % sequence identity with each other and 68.80-84.40 % sequence identity with the other begomoviruses occurring in the Indian subcontinent. The closest identity (84.40 %) of the virus isolates was with Tomato leaf curl Sri Lanka virus (ToLCLKV). The results support that a new begomovirus species is affecting chilli in Sri Lanka and the name Chilli leaf curl Sri Lanka virus (ChiLCSLV) is proposed. Recombination analysis indicated that ChiLCSLV was a recombinant virus potentially originated from the begomoviruses prevailing in southern India and Sri Lanka. The genome of betasatellite associated with the two isolates consisted of 1366 and 1371 nucleotides and shared 95.2 % sequence identity with each other and 41.50-73.70 % sequence identity with the other betasatellite species. The results suggest that a new begomovirus betasatellite, Chilli leaf curl Sri Lanka betasatellite is associated with LCDC in Sri Lanka. This study demonstrates a new species of begomovirus and betasatellite complex is occurring in chilli in Sri Lanka and further shows that diverse begomovirus species are affecting chilli production in the Indian subcontinent.
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Shafiq M, Asad S, Zafar Y, Briddon RW, Mansoor S. Pepper leaf curl Lahore virus requires the DNA B component of Tomato leaf curl New Delhi virus to cause leaf curl symptoms. Virol J 2010; 7:367. [PMID: 21144019 PMCID: PMC3017532 DOI: 10.1186/1743-422x-7-367] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2010] [Accepted: 12/13/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Begomoviruses are whitefly-transmitted geminiviruses with genomes that consist of either two components (known as DNA A and DNA B) or a single component (homologous to the DNA A component of bipartite begomoviruses). Monopartite begomoviruses are often associated with a symptom-modulating DNA satellite (collectively known as betasatellites). Both bipartite and monopartite begomoviruses with associated satellites have previously been identified in chillies showing leaf curl symptoms in Pakistan. RESULTS A chilli plant (Capsicum annum) with chilli leaf curl disease symptoms was found to contain a begomovirus, a betasatellite and the DNA B component of Tomato leaf curl New Delhi virus (ToLCNDV). The begomovirus consisted of 2747 nucleotides and had the highest sequence identity (99%) with Pepper leaf curl Lahore virus (PepLCLV-[PK: Lah:04], acc. no. AM404179). Agrobacterium-mediated inoculation of the clone to Nicotiana benthamiana, induced very mild symptoms and low levels of viral DNA, detected in systemically infected leaves by PCR. No symptoms were induced in Nicotiana tabacum or chillies either in the presence or absence of a betasatellite. However, inoculation of PepLCLV with the DNA B component of ToLCNDV induced leaf curl symptoms in N. benthamiana, N. tabacum and chillies and viral DNA accumulated to higher levels in comparison to plants infected with just PepLCLV. CONCLUSIONS Based on our previous efforts aimed at understanding of diversity of begomoviruses associated with chillies, we propose that PepLCLV was recently mobilized into chillies upon its interaction with DNA B of ToLCNDV. Interestingly, the putative rep-binding iterons found on PepLCLV (GGGGAC) differ at two base positions from those of ToLCNDV (GGTGTC). This is the first experimental demonstration of the infectivity for a bipartite begomovirus causing chilli leaf curl disease in chillies from Pakistan and suggests that component capture is contributing to the emerging complexity of begomovirus diseases in the region.
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Affiliation(s)
- Muhammad Shafiq
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), P O Box 577, Jhang Road, Faisalabad, Pakistan
| | - Shaheen Asad
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), P O Box 577, Jhang Road, Faisalabad, Pakistan
| | - Yusuf Zafar
- 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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Mubin M, Briddon RW, Mansoor S. Complete nucleotide sequence of chili leaf curl virus and its associated satellites naturally infecting potato in Pakistan. Arch Virol 2009; 154:365-8. [DOI: 10.1007/s00705-008-0296-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Accepted: 12/04/2008] [Indexed: 11/30/2022]
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Infectivity of the cloned components of a begomovirus: DNA beta complex causing chilli leaf curl disease in India. Arch Virol 2008; 153:533-9. [DOI: 10.1007/s00705-007-0017-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Accepted: 11/22/2007] [Indexed: 11/27/2022]
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Briddon RW, Stanley J. Subviral agents associated with plant single-stranded DNA viruses. Virology 2006; 344:198-210. [PMID: 16364750 DOI: 10.1016/j.virol.2005.09.042] [Citation(s) in RCA: 216] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2005] [Accepted: 09/16/2005] [Indexed: 11/18/2022]
Abstract
Begomoviruses (family Geminiviridae) are responsible for many economically important crop diseases worldwide. The majority of these diseases are caused by bipartite begomovirus infections, although a rapidly growing number of diseases of the Old World are associated with monopartite begomoviruses. With the exception of several diseases of tomato, most of these are caused by a monopartite begomovirus in association with a recently discovered essential satellite component (DNA-beta). These begomovirus/satellite disease complexes are widespread and diverse and collectively infect a wide variety of crops, weeds and ornamental plants. Non-essential subviral components (DNA-1) originating from nanoviruses are frequently associated with these disease complexes, and there are tantalizing hints that further novel satellites may also be associated with some begomovirus diseases. DNA-beta components can be maintained in permissive plants by more than one distinct begomovirus, reflecting less stringent requirements for trans-replication that will undoubtedly encourage diversification and adaptation as a consequence of component exchange and recombination. In view of their impact on agriculture, there is a pressing need to develop a more comprehensive picture of the diversity and distribution of the disease complexes. A greater understanding of how they elicit the host response may provide useful information for their control as well as an insight into plant developmental processes.
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Affiliation(s)
- R W Briddon
- Plant Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Jhang Road, Faisalabad, Pakistan
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