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Iqbal Z, Shafiq M, Sattar MN, Ali I, Khurshid M, Farooq U, Munir M. Genetic Diversity, Evolutionary Dynamics, and Ongoing Spread of Pedilanthus Leaf Curl Virus. Viruses 2023; 15:2358. [PMID: 38140599 PMCID: PMC10747432 DOI: 10.3390/v15122358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Pedilanthus leaf curl virus (PeLCV) is a monopartite begomovirus (family Geminiviridae) discovered just a few decades ago. Since then, it has become a widely encountered virus, with reports from ca. 25 plant species across Pakistan and India, indicative of its notable evolutionary success. Viruses mutate at such a swift rate that their ecological and evolutionary behaviors are inextricably linked, and all of these behaviors are imprinted on their genomes as genetic diversity. So, all these imprints can be mapped by computational methods. This study was designed to map the sequence variation dynamics, genetic heterogeneity, regional diversity, phylogeny, and recombination events imprinted on the PeLCV genome. Phylogenetic and network analysis grouped the full-length genome sequences of 52 PeLCV isolates into 7 major clades, displaying some regional delineation but lacking host-specific demarcation. The progenitor of PeLCV was found to have originated in Multan, Pakistan, in 1977, from where it spread concurrently to India and various regions of Pakistan. A high proportion of recombination events, distributed unevenly throughout the genome and involving both inter- and intraspecies recombinants, were inferred. The findings of this study highlight that the PeLCV population is expanding under a high degree of genetic diversity (π = 0.073%), a high rate of mean nucleotide substitution (1.54 × 10-3), demographic selection, and a high rate of recombination. This sets PeLCV apart as a distinctive begomovirus among other begomoviruses. These factors could further exacerbate the PeLCV divergence and adaptation to new hosts. The insights of this study that pinpoint the emergence of PeLCV are outlined.
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Affiliation(s)
- Zafar Iqbal
- Central Laboratories, King Faisal University, Al-Ahsa P.O. Box 55110, Saudi Arabia;
| | - Muhammad Shafiq
- Department of Biotechnology, University of Management and Technology, Sialkot Campus, Sialkot P.O. Box 51340, Pakistan;
| | | | - Irfan Ali
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad P.O. Box 38000, Pakistan;
| | - Muhammad Khurshid
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore P.O. Box 54590, Pakistan;
| | - Umer Farooq
- Department of Biotechnology, University of Sialkot, Sialkot P.O. Box 51340, Pakistan;
| | - Muhammad Munir
- Date Palm Research Center of Excellence, King Faisal University, Al-Ahsa P.O. Box 31982, Saudi Arabia;
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Al-Ali E, Al-Hashash H, Akbar A, Al-Aqeel H, Al-Shayji N, Alotaibi M, Ben Hejji A. Genetic recombination among tomato yellow leaf curl virus isolates in commercial tomato crops in Kuwait drives emergence of virus diversity: a comparative genomic analysis. BMC Res Notes 2023; 16:71. [PMID: 37150821 PMCID: PMC10164301 DOI: 10.1186/s13104-023-06319-w] [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: 07/08/2022] [Accepted: 03/30/2023] [Indexed: 05/09/2023] Open
Abstract
OBJECTIVE Whitefly-transmitted tomato yellow leaf curl virus (TYLCV) continues to be a major constraint to tomato production in Kuwait. However, very limited information is available about the population structure and genetic diversity of TYLCV infecting tomato in Kuwait. RESULTS Whole genome sequences of 31 isolates of TYLCV, collected from commercial tomato crops grown in northern (Abdally) and southern (Al Wafra) parts of Kuwait, were deciphered. Eighteen isolates of TYLCV are identified as potential genetic recombinants. The isolates Abdally 6A and Abdally 3B reported in this study were identified to be potential recombinants. Compared to the 15 isolates from the Abdally area, and the three previously reported KISR isolates of Kuwait, six out of sixteen Al Wafra isolates showed an insertion of 19 extra nucleotides near the 5'-end. There are also four nucleotide variations before the 19-extra-nucleotides. The additional 19 nucleotides observed in nine isolates indicate that these isolates might have resulted from a single gene recombination/insertion event. Molecular phylogeny based on complete genome sequences of TYLCV isolates suggests transboundary movement of virus isolates due to geographic proximity. The information presented herein is quite useful for the comprehension of TYLCV biology, epidemiology and would aid in the management of disease in the long run.
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Affiliation(s)
- Ebtisam Al-Ali
- Kuwait Institute for Scientific Research, Environmental and Life Science Research Center, Biotechnology Program, 13109, Safat, Kuwait.
| | - Hanadi Al-Hashash
- Kuwait Institute for Scientific Research, Environmental and Life Science Research Center, Biotechnology Program, 13109, Safat, Kuwait
| | - Abrar Akbar
- Kuwait Institute for Scientific Research, Environmental and Life Science Research Center, Biotechnology Program, 13109, Safat, Kuwait
| | - Hamed Al-Aqeel
- Kuwait Institute for Scientific Research, Environmental and Life Science Research Center, Biotechnology Program, 13109, Safat, Kuwait
| | - Nabila Al-Shayji
- Kuwait Institute for Scientific Research, Environmental and Life Science Research Center, Biotechnology Program, 13109, Safat, Kuwait
| | - Mohammed Alotaibi
- Kuwait Institute for Scientific Research, Environmental and Life Science Research Center, Biotechnology Program, 13109, Safat, Kuwait
| | - Ahmed Ben Hejji
- Kuwait Institute for Scientific Research, Environmental and Life Science Research Center, Biotechnology Program, 13109, Safat, Kuwait
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Venkataravanappa V, Ashwathappa KV, Kallingappa P, Shridhar H, Hemachandra Reddy P, Reddy MK, Reddy CNL. Diversity and phylogeography of begomoviruses and DNA satellites associated with the leaf curl and mosaic disease complex of eggplant. Microb Pathog 2023; 180:106127. [PMID: 37119939 DOI: 10.1016/j.micpath.2023.106127] [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: 01/12/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/01/2023]
Abstract
Eggplant is one of the important vegetable crops grown across the world, and its production is threatened by both biotic and abiotic stresses. Diseases caused by viruses are becoming major limiting factors for its successful cultivation. A survey for begomovirus-like symptoms in 72 eggplant fields located in six different Indian states revealed a prevalence of disease ranging from 5.2 to 40.2%, and the symptoms recorded were mosaic, mottling, petiole bending, yellowing, and upward curling, vein thickening, and enation of the leaves, and stunting of plants. The causal agent associated with these plants was transmitted from infected leaf samples to healthy eggplant seedlings via grafting and whiteflies (Bemisia tabaci). The presence of begomovirus was confirmed in 72 infected eggplant samples collected from the surveyed fields exhibiting leaf curl and mosaic disease by PCR using begomovirus specifc primers (DNA-A componet), which resulted in an expected amplicon of 1.2 kb. The partial genome sequence obtained from amplified 1.2 kb from all samples indicated that they are closely related begomovirus species, tomato leaf Karnataka virus (ToLCKV, two samples), tomato leaf curl Palampur virus (ToLCPalV, fifty eggplant samples), and chilli leaf curl virus (ChLCuV, twenty samples). Based on the partial genome sequence analysis, fourteen representative samples were selected for full viral genome amplification by the rolling circle DNA amplification (RCA) technique. Analyses of fourteen eggplant isolates genome sequences using the Sequence Demarcation Tool (SDT) indicated that one isolate had the maximum nucleotide (nt) identity with ToLCKV and eight isolates with ToLCPalV. Whereas, four isolates four isolates (BLC1-CH, BLC2-CH, BLC3-CH, BLC4-CH) are showing nucleotide identity of less than 91% with chilli infecting viruses begomoviruses with chilli infecting begomoviruses and as per the guidelines given by the ICTV study group for the classification of begomoviruses these isolates are considered as one novel begomovirus species, for which name, Eggplant leaf curl Chhattisgarh virus (EgLCuChV) is proposed. For DNA-B component, seven eggplant isolates had the highest nt identity with ToLCPalV infecting other crops. Further, DNA satellites sequence analysis indicated that four betasatellites identified shared maximum nucleotide identity with the tomato leaf curl betasatellite and five alphasatellites shared maximum nucleotide identity with the ageratum enation alphasatellite. Recombination and GC plot analyses indicated that the bulk of begomovirus genome and associated satellites presumably originated from of previously known mono and bipartite begomoviruses and DNA satellites. To the best of our knowledge, this is India's first report of ToLCKV and a noval virus, eggplant leaf curl Chhattisgarh virus associated with eggplant leaf curl disease.
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Affiliation(s)
- V Venkataravanappa
- Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bangalore, 560089, Karnataka, India.
| | - K V Ashwathappa
- Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bangalore, 560089, Karnataka, India
| | | | - Hiremath Shridhar
- Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences, GKVK, Bengaluru, 560 065, Karnataka, India
| | - P Hemachandra Reddy
- Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bangalore, 560089, Karnataka, India
| | - M Krishna Reddy
- Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bangalore, 560089, Karnataka, India
| | - C N Lakshminarayana Reddy
- Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences, GKVK, Bengaluru, 560 065, Karnataka, India.
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Qureshi MA, Lal A, Nawaz-ul-Rehman MS, Vo TTB, Sanjaya GNPW, Ho PT, Nattanong B, Kil EJ, Jahan SMH, Lee KY, Tsai CW, Dao HT, Hoat TX, Aye TT, Win NK, Lee J, Kim SM, Lee S. Emergence of Asian endemic begomoviruses as a pandemic threat. FRONTIERS IN PLANT SCIENCE 2022; 13:970941. [PMID: 36247535 PMCID: PMC9554542 DOI: 10.3389/fpls.2022.970941] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/05/2022] [Indexed: 06/16/2023]
Abstract
Plant viruses are responsible for the most devastating and commercially significant plant diseases, especially in tropical and subtropical regions. The genus begomovirus is the largest one in the family Geminiviridae, with a single-stranded DNA genome, either monopartite or bipartite. Begomoviruses are transmitted by insect vectors, such as Bemisia tabaci. Begomoviruses are the major causative agents of diseases in agriculture globally. Because of their diversity and mode of evolution, they are thought to be geographic specific. The emerging begomoviruses are of serious concern due to their increasing host range and geographical expansion. Several begomoviruses of Asiatic origin have been reported in Europe, causing massive economic losses; insect-borne transmission of viruses is a critical factor in virus outbreaks in new geographical regions. This review highlights crucial information regarding Asia's four emerging and highly destructive begomoviruses. We also provided information regarding several less common but still potentially important pathogens of different crops. This information will aid possible direction of future studies in adopting preventive measures to combat these emerging viruses.
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Affiliation(s)
- Muhammad Amir Qureshi
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Aamir Lal
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | | | - Thuy Thi Bich Vo
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | | | - Phuong Thi Ho
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Bupi Nattanong
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Eui-Joon Kil
- Department of Plant Medicals, Andong National University, Andong, South Korea
| | | | - Kyeong-Yeoll Lee
- Division of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Chi-Wei Tsai
- Department of Entomology, National Taiwan University, Taipei, Taiwan
| | - Hang Thi Dao
- Plant Protection Research Institute, Hanoi, Vietnam
| | | | - Tin-Tin Aye
- Department of Entomology, Yezin Agricultural University, Yezin, Myanmar
| | - Nang Kyu Win
- Department of Plant Pathology, Yezin Agricultural University, Yezin, Myanmar
| | - Jangha Lee
- Crop Breeding Research Center, NongWoo Bio, Yeoju, South Korea
| | - Sang-Mok Kim
- Plant Quarantine Technology Center, Animal and Plant Quarantine Agency, Gimcheon, South Korea
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
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Yadav S, Kumar V. A prey–predator model approach to increase the production of crops: Mathematical modeling and qualitative analysis. INT J BIOMATH 2022. [DOI: 10.1142/s1793524522500425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
This paper expresses the concepts, methods, and applications of mathematical models in agriculture. We propose and analyze an ecosystem consisting of two types of preys and their predators; here the prey-I like sugarcane crops that take a long time to grow and prey-II like vegetables, which have a short life, are grown with sugarcane crops and predators that harm both prey-I and prey-II. The various equilibria of the system are obtained, and the stability conditions are analyzed. Furthermore, a comprehensive analysis of the optimal control strategy is also performed. The optimal control model includes the use of three control variables, such as pesticide application rate, biomass application rate, and control of Cassava mosaic virus in the system. Finally, we apply Pontryagin’s maximum principle to find the optimal control. Furthermore, analytical results are verified by numerical simulations.
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Affiliation(s)
- Sudhakar Yadav
- Department of Applied Mathematics, Delhi Technological University, New Delhi 110042, India
| | - Vivek Kumar
- Department of Applied Mathematics, Delhi Technological University, New Delhi 110042, India
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Gambley C, Nimmo P, McDonald J, Campbell P. The Establishment and Spread of a Newly Introduced Begomovirus in a Dry Tropical Environment Using Tomato Yellow Leaf Curl Virus as a Case Study. PLANTS 2022; 11:plants11060776. [PMID: 35336658 PMCID: PMC8952566 DOI: 10.3390/plants11060776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/18/2022] [Accepted: 03/10/2022] [Indexed: 11/23/2022]
Abstract
Early detection of tomato yellow leaf curl virus (TYLCV) in a previously unaffected tomato production district in Australia allowed its spread to be evaluated spatially and temporally. The population dynamics of the TYLCV vector, Bemisia argentifolii (silverleaf whitefly, SLW), were also evaluated. The district is a dry tropical environment with a clear break to commercial production during the summer wet season. The incidence of TYLCV within crops and its prevalence through the district was influenced by weather, location, vector movements, and the use of Ty-1 virus-resistant hybrids. Rainfall had an important influence, with late summer and early autumn rain suppressing the levels of SLW and, by contrast, a dry summer supporting faster population growth. The use of Ty-1 hybrids appears to have reduced the incidence of TYLCV in this district. There was limited use of Ty-1 hybrids during 2013, and by season end, crops had moderate levels of SLW and high virus incidence. The 2015 and early 2016 season had high SLW populations, but TYLCV incidence was lower than in 2013, possibly due to the widespread adoption of the Ty-1 hybrids reducing virus spread. This study provides valuable epidemiology data for future incursions of begomoviruses, and other viruses spread by SLW.
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Vo TTB, Lal A, Ho PT, Troiano E, Parrella G, Kil EJ, Lee S. Different Infectivity of Mediterranean and Southern Asian Tomato Leaf Curl New Delhi Virus Isolates in Cucurbit Crops. PLANTS (BASEL, SWITZERLAND) 2022; 11:704. [PMID: 35270174 PMCID: PMC8912351 DOI: 10.3390/plants11050704] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
Tomato leaf curl New Delhi virus (ToLCNDV) became an alerting virus in Europe from 2017 to 2020 because of its significant damage to Cucurbitaceae cultivation. Until now, just some cucurbit crops including sponge gourd, melon, pumpkin, and cucumber were reported to be resistant to ToLCNDV, but no commercial cultivars are available. In this study, a new isolate of ToLCNDV was identified in Pakistan and analyzed together with ToLCNDV-ES which was previously isolated in Italy. Furthermore, infectious clones of two ToLCNDV isolates were constructed and agroinoculated into different cucurbit crops to verify their infectivity. Results showed that both isolates exhibited severe infection on all tested cucurbit (>70%) except watermelon. Thus, those cultivars may be good candidates in the first step of screening genetic resources for resistance on both Southeast Asian and Mediterranean ToLCNDV isolates. Additional, comparison pathogenicity of different geographical ToLCNDV isolates will be aided to understand viral characterization as such knowledge could facilitate breeding resistance to this virus.
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Affiliation(s)
- Thuy T. B. Vo
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea; (T.T.B.V.); (A.L.); (P.T.H.)
| | - Aamir Lal
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea; (T.T.B.V.); (A.L.); (P.T.H.)
| | - Phuong T. Ho
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea; (T.T.B.V.); (A.L.); (P.T.H.)
| | - Elisa Troiano
- Institute for Sustainable Plant Protection of the National Research Council (IPSP-CNR), 80055 Portici, Italy;
| | - Giuseppe Parrella
- Institute for Sustainable Plant Protection of the National Research Council (IPSP-CNR), 80055 Portici, Italy;
| | - Eui-Joon Kil
- Department of Plant Medicals, Andong National University, Andong 36729, Korea
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea; (T.T.B.V.); (A.L.); (P.T.H.)
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Maity S, Mandal PS. A Comparison of Deterministic and Stochastic Plant-Vector-Virus Models Based on Probability of Disease Extinction and Outbreak. Bull Math Biol 2022; 84:41. [PMID: 35150332 DOI: 10.1007/s11538-022-01001-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 01/24/2022] [Indexed: 11/02/2022]
Abstract
In this investigation, we formulate and analyse a stochastic epidemic model using the continuous-time Markov chain model for the propagation of a vector-borne cassava mosaic disease in a single population. The stochastic model is based upon a pre-existing deterministic plant-vector-virus model. To see how demographic stochasticity affects the vector-borne cassava mosaic disease dynamics, we compare the disease dynamics of both deterministic and stochastic models through disease extinction process. The probability of disease extinction and therefore the major outbreak are estimated analytically using the multitype Galton-Watson branching process (GWbp) approximation. Also, we have found the approximate probabilities of disease extinction numerically based on 30000 sample paths, and it is shown to be good estimate with the calculated probabilities from GWbp approximation. In particular, it is observed that there is a very high probability of disease extinction when the disease is introduced via the infected vectors rather than through infected plants.
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Affiliation(s)
- Sunil Maity
- Department of Mathematics, NIT Patna, Patna, Bihar, India
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Deb S, Choudhury A, Kharbyngar B, Satyawada RR. Applications of CRISPR/Cas9 technology for modification of the plant genome. Genetica 2022; 150:1-12. [PMID: 35018532 DOI: 10.1007/s10709-021-00146-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/02/2021] [Indexed: 12/26/2022]
Abstract
The CRISPR/Cas (Clustered regularly interspaced short palindromic repeats/ CRISPR associated protein 9) system was discovered in bacteria and archea as an acquired immune response to protect the cells from infection. This technology has now evolved to become an efficient genome editing tool, and is replacing older gene editing technologies. This technique uses programmable sgRNAs to guide the Cas9 endonuclease to the target DNA location. sgRNA is a vital component of the CRISPR technology, since without it the Cas nuclease cannot reach to its target location. Over the years, many tools have been developed for designing sgRNAs, the details of which have been extensively reviewed here. It has proven to be a promising tool in the field of genetic engineering and has successfully generated many plant varieties with better and desirable qualities. In the present review, we attempted to collect,collate and summarize information related to the development of CRISPR/Cas9 system as a tool and subsequently into a technique having a wide array of applications in the field of plant genome editing in attaining desirable traits like resistance to various diseases, nutritional enhancement etc. In addition, the probable future prospects and the various bio-safety concerns associated with CRISPR gene editing technology have been discussed in detail.
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Affiliation(s)
- Sohini Deb
- Plant Biotechnology Laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya, 793022, India
| | - Amrita Choudhury
- Plant Biotechnology Laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya, 793022, India
| | - Banridor Kharbyngar
- Plant Biotechnology Laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya, 793022, India
| | - Rama Rao Satyawada
- Plant Biotechnology Laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya, 793022, India.
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Ali Z, Mahfouz MM. CRISPR/Cas systems versus plant viruses: engineering plant immunity and beyond. PLANT PHYSIOLOGY 2021; 186:1770-1785. [PMID: 35237805 PMCID: PMC8331158 DOI: 10.1093/plphys/kiab220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 04/16/2021] [Indexed: 05/02/2023]
Abstract
Molecular engineering of plant immunity to confer resistance against plant viruses holds great promise for mitigating crop losses and improving plant productivity and yields, thereby enhancing food security. Several approaches have been employed to boost immunity in plants by interfering with the transmission or lifecycles of viruses. In this review, we discuss the successful application of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) (CRISPR/Cas) systems to engineer plant immunity, increase plant resistance to viruses, and develop viral diagnostic tools. Furthermore, we examine the use of plant viruses as delivery systems to engineer virus resistance in plants and provide insight into the limitations of current CRISPR/Cas approaches and the potential of newly discovered CRISPR/Cas systems to engineer better immunity and develop better diagnostics tools for plant viruses. Finally, we outline potential solutions to key challenges in the field to enable the practical use of these systems for crop protection and viral diagnostics.
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Affiliation(s)
- Zahir Ali
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Author for communication:
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Mugerwa H, Colvin J, Alicai T, Omongo CA, Kabaalu R, Visendi P, Sseruwagi P, Seal SE. Genetic diversity of whitefly ( Bemisia spp.) on crop and uncultivated plants in Uganda: implications for the control of this devastating pest species complex in Africa. JOURNAL OF PEST SCIENCE 2021; 94:1307-1330. [PMID: 34720787 PMCID: PMC8550740 DOI: 10.1007/s10340-021-01355-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/09/2021] [Accepted: 02/18/2021] [Indexed: 05/12/2023]
Abstract
UNLABELLED Over the past three decades, highly increased whitefly (Bemisia tabaci) populations have been observed on the staple food crop cassava in eastern Africa and associated with ensuing viral disease pandemics and food insecurity. Increased whitefly numbers have also been observed in other key agricultural crops and weeds. Factors behind the population surges on different crops and their interrelationships are unclear, although in cassava they have been associated with specific populations within the Bemisia tabaci species complex known to infest cassava crops in Africa. This study carried out an in-depth survey to understand the distribution of B. tabaci populations infesting crops and uncultivated plant hosts in Uganda, a centre of origin for this pest complex. Whitefly samples were collected from 59 identified plant species and 25 unidentified weeds in a countrywide survey. Identities of 870 individual adult whiteflies were determined through mitochondrial cytochrome oxidase 1 sequences (651 bp) in the 3' barcode region used for B. tabaci systematics. Sixteen B. tabaci and five related whitefly putative species were identified based on > 4.0% nucleotide divergence, of which three are proposed as novel B. tabaci putative species and four as novel closely related whitefly species. The most prevalent whiteflies were classified as B. tabaci MED-ASL (30.5% of samples), sub-Saharan Africa 1 (SSA1, 22.7%) and Bemisia Uganda1 (12.1%). These species were also indicated to be the most polyphagous occurring on 33, 40 and 25 identified plant species, respectively. Multiple (≥ 3) whitefly species occurred on specific crops (bean, eggplant, pumpkin and tomato) and weeds (Sida acuta and Ocimum gratissimum). These plants may have increased potential to act as reservoirs for mixed infections of whitefly-vectored viruses. Management of whitefly pest populations in eastern Africa will require an integration of approaches that consider their degree of polyphagy and a climate that enables the continuous presence of crop and uncultivated plant hosts. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10340-021-01355-6.
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Affiliation(s)
- Habibu Mugerwa
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB UK
- Department of Entomology, University of Georgia, 1109 Experiment Street, Griffin, GA 30223 USA
| | - John Colvin
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB UK
| | - Titus Alicai
- Root Crops Programme, National Crops Resources Research Institute, P. O. Box 7084, Kampala, Uganda
| | - Christopher A. Omongo
- Root Crops Programme, National Crops Resources Research Institute, P. O. Box 7084, Kampala, Uganda
| | - Richard Kabaalu
- Root Crops Programme, National Crops Resources Research Institute, P. O. Box 7084, Kampala, Uganda
| | - Paul Visendi
- Centre for Agriculture and Bioeconomy, Queensland University of Technology, Brisbane, 4001 Australia
| | - Peter Sseruwagi
- Biotechnology Department, Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar es Salaam, Tanzania
| | - Susan E. Seal
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB UK
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Khatun MF, Hwang HS, Shim JK, Kil EJ, Lee S, Lee KY. Identification of begomoviruses from different cryptic species of Bemisia tabaci in Bangladesh. Microb Pathog 2020; 142:104069. [PMID: 32061918 DOI: 10.1016/j.micpath.2020.104069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 01/20/2020] [Accepted: 02/12/2020] [Indexed: 11/21/2022]
Abstract
Bemisia tabaci is a global species complex consisting of at least 40 cryptic species. It is also a vector for at least 100 species of begomovirus, many of which cause severe crop damage. The relationship between begomoviruses and cryptic species of the B. tabaci species complex, however, remains unclear. Our previous study [13] was identified four cryptic species (Asia I, Asia II 1, Asia II 5, and Asia II 10) of B. tabaci from Bangladesh. Using those 110 whitefly samples, vector-based PCR analysis identified 8 different begomovirus species: BYVMV, BGYVV, OELCV, SLCCV, SLCV, TbCSV, ToLCBV, and ToLCNDV. The overall rate of virus infection was 26.4%, and BYVMV and ToLCNDV were the most frequently detected in the B. tabaci vector. Virus infection rates for Asia I, Asia II 1, Asia II 5, and Asia II 10 were 22.4% (15/67), 35% (7/20), 27.3% (6/22), and 100% (1/1), respectively. Each cryptic species infected multiple virus species, but SLCCV, TbCSV, and BGYVV were each only detected in, Asia I, Asia II 1, and Asia II 5, respectively. This study demonstrates the geographic distribution of various begomoviruses in Bangladesh and their relationships with cryptic species of B. tabaci.
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Affiliation(s)
- Mst Fatema Khatun
- Division of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea; Department of Entomology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Dhaka, Bangladesh
| | - Hwal-Su Hwang
- Division of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea; Institute of Plant Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Jae-Kyoung Shim
- Division of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea; Institute of Plant Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Eui-Joon Kil
- Department of Genetic Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Sukchan Lee
- Department of Genetic Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Kyeong-Yeoll Lee
- Division of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea; Institute of Plant Medicine, Kyungpook National University, Daegu, Republic of Korea; Institute of Agricultural Science and Technology, Kyungpook National University, Daegu, Republic of Korea.
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13
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Mushtaq M, Mukhtar S, Sakina A, Dar AA, Bhat R, Deshmukh R, Molla K, Kundoo AA, Dar MS. Tweaking genome-editing approaches for virus interference in crop plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 147:242-250. [PMID: 31881433 DOI: 10.1016/j.plaphy.2019.12.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 12/18/2019] [Accepted: 12/18/2019] [Indexed: 05/13/2023]
Abstract
Plant viruses infect various economically important crops and cause a serious threat to agriculture. As of now, conventional strategies employed are inadequate to circumvent the proliferation of rapidly evolving plant viruses. In this regard, recent advancement in genome-editing approach looks promising to produce plants resistant to DNA/RNA virus infections. Clustered regularly interspaced palindromic repeats (CRISPR) system has been emerged as a promising genome-editing tool that has received special interest because of its ease, competence and reproducibility. Recent studies have demonstrated that CRISPR/Cas9 system has great potential to confer plant immunity by either directly targeting or cleaving the viral genome in both RNA and DNA viruses. Similarly, the approach can be used for targeting the host susceptibility genes more particularly in case of RNA viruses. In the present review, different approaches and strategies being used to improve plant resistance against devastating viruses are discussed in view of recent advances in CRISPR systems. This review also describes the major pitfalls of CRISPR/Cas9 system that utilizes highly efficient and novel platforms to engineer interference to single and multiple plant RNA viruses.
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Affiliation(s)
- Muntazir Mushtaq
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, J&K, 180009, India
| | - Shazia Mukhtar
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, J&K, 180009, India
| | - Aafreen Sakina
- Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, J&K, 190025, India
| | - Aejaz Ahmad Dar
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, J&K, 180009, India.
| | - Rohini Bhat
- ICAR-Directorate of Onion and Garlic Research, Rajagurunagar, Pune, Maharashtra, 410505, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute, Sector 81, Sahibzada Ajit Singh Nagar, Punjab, 140308, India
| | - Kutubuddin Molla
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, 16801, USA
| | - Ajaz Ahmad Kundoo
- Division of Entomology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, J&K, 190025, India
| | - Mohd Saleem Dar
- Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, J&K, 190025, India
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Bokil VA, Allen LJS, Jeger MJ, Lenhart S. Optimal control of a vectored plant disease model for a crop with continuous replanting. JOURNAL OF BIOLOGICAL DYNAMICS 2019; 13:325-353. [PMID: 31149889 DOI: 10.1080/17513758.2019.1622808] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 04/28/2019] [Indexed: 06/09/2023]
Abstract
Vector-transmitted diseases of plants have had devastating effects on agricultural production worldwide, resulting in drastic reductions in yield for crops such as cotton, soybean, tomato, and cassava. Plant-vector-virus models with continuous replanting are investigated in terms of the effects of selection of cuttings, roguing, and insecticide use on disease prevalence in plants. Previous models are extended to include two replanting strategies: frequencyreplanting and abundance-replanting. In frequency-replanting, replanting of infected cuttings depends on the selection frequency parameter ε, whereas in abundance-replanting, replanting depends on plant abundance via a selection rate parameter also denoted as ε. The two models are analysed and new thresholds for disease elimination are defined for each model. Parameter values for cassava, whiteflies, and African cassava mosaic virus serve as a case study. A numerical sensitivity analysis illustrates how the equilibrium densities of healthy and infected plants vary with parameter values. Optimal control theory is used to investigate the effects of roguing and insecticide use with a goal of maximizing the healthy plants that are harvested. Differences in the control strategies in the two models are seen for large values of ε. Also, the combined strategy of roguing and insecticide use performs better than a single control.
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Affiliation(s)
- V A Bokil
- a Department of Mathematics, Oregon State University , Corvallis , OR , USA
| | - L J S Allen
- b Department of Mathematics & Statistics, Texas Tech University , Lubbock , TX , USA
| | - M J Jeger
- c Centre for Environmental Policy, Imperial College , London , UK
| | - S Lenhart
- d Department of Mathematics, University of Tennessee , Knoxville , TN , USA
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15
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Maio F, Arroyo-Mateos M, Bobay BG, Bejarano ER, Prins M, van den Burg HA. A Lysine Residue Essential for Geminivirus Replication Also Controls Nuclear Localization of the Tomato Yellow Leaf Curl Virus Rep Protein. J Virol 2019; 93:e01910-18. [PMID: 30842320 PMCID: PMC6498046 DOI: 10.1128/jvi.01910-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/20/2019] [Indexed: 02/07/2023] Open
Abstract
Geminiviruses are single-stranded DNA (ssDNA) viruses that infect a wide range of plants. To promote viral replication, geminiviruses manipulate the host cell cycle. The viral protein Rep is essential to reprogram the cell cycle and then initiate viral DNA replication by interacting with a plethora of nuclear host factors. Even though many protein domains of Rep have been characterized, little is known about its nuclear targeting. Here, we show that one conserved lysine in the N-terminal part of Rep is pivotal for nuclear localization of the Rep protein from Tomato yellow leaf curl virus (TYLCV), with two other lysines also contributing to its nuclear import. Previous work had identified that these residues are essential for Rep from Tomato golden mosaic virus (TGMV) to interact with the E2 SUMO-conjugating enzyme (SCE1). We here show that mutating these lysines leads to nuclear exclusion of TYLCV Rep without compromising its interaction with SCE1. Moreover, the ability of TYLCV Rep to promote viral DNA replication also depends on this highly conserved lysine independently of its role in nuclear import of Rep. Our data thus reveal that this lysine potentially has a broad role in geminivirus replication, but its role in nuclear import and SCE1 binding differs depending on the Rep protein examined.IMPORTANCE Nuclear activity of the replication initiator protein (Rep) of geminiviruses is essential for viral replication. We now define that one highly conserved lysine is important for nuclear import of Rep from three different begomoviruses. To our knowledge, this is the first time that nuclear localization has been mapped for any geminiviral Rep protein. Our data add another key function to this lysine residue, besides its roles in viral DNA replication and interaction with host factors, such as the SUMO E2-conjugating enzyme.
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Affiliation(s)
- Francesca Maio
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Manuel Arroyo-Mateos
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento Biología Celular, Genética y Fisiología, Universidad de Málaga, Campus Teatinos, Málaga, Spain
| | - Benjamin G Bobay
- Duke University NMR Center, Duke University Medical Center, Durham, North Carolina, USA
- Department of Biochemistry, Duke University, Durham, North Carolina, USA
- Department of Radiology, Duke University, Durham, North Carolina, USA
| | - Eduardo R Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento Biología Celular, Genética y Fisiología, Universidad de Málaga, Campus Teatinos, Málaga, Spain
| | - Marcel Prins
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
- Keygene N.V., Wageningen, the Netherlands
| | - Harrold A van den Burg
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
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16
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Zhao L, Rosario K, Breitbart M, Duffy S. Eukaryotic Circular Rep-Encoding Single-Stranded DNA (CRESS DNA) Viruses: Ubiquitous Viruses With Small Genomes and a Diverse Host Range. Adv Virus Res 2018; 103:71-133. [PMID: 30635078 DOI: 10.1016/bs.aivir.2018.10.001] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
While single-stranded DNA (ssDNA) was once thought to be a relatively rare genomic architecture for viruses, modern metagenomics sequencing has revealed circular ssDNA viruses in most environments and in association with diverse hosts. In particular, circular ssDNA viruses encoding a homologous replication-associated protein (Rep) have been identified in the majority of eukaryotic supergroups, generating interest in the ecological effects and evolutionary history of circular Rep-encoding ssDNA viruses (CRESS DNA) viruses. This review surveys the explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade, highlights similarities between the well-studied geminiviruses and circoviruses with newly identified groups known only through their genome sequences, discusses the ecology and evolution of eukaryotic CRESS DNA viruses, and speculates on future research horizons.
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Affiliation(s)
- Lele Zhao
- Department of Ecology, Evolution and Natural Resources, Rutgers, the State University of New Jersey, New Brunswick, NJ, United States
| | - Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers, the State University of New Jersey, New Brunswick, NJ, United States.
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17
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Al Basir F, Blyuss KB, Ray S. Modelling the effects of awareness-based interventions to control the mosaic disease of Jatropha curcas. ECOLOGICAL COMPLEXITY 2018. [DOI: 10.1016/j.ecocom.2018.07.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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18
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Torre C, Donaire L, Gómez-Aix C, Juárez M, Peterschmitt M, Urbino C, Hernando Y, Agüero J, Aranda MA. Characterization of Begomoviruses Sampled during Severe Epidemics in Tomato Cultivars Carrying the Ty-1 Gene. Int J Mol Sci 2018; 19:E2614. [PMID: 30177671 PMCID: PMC6164481 DOI: 10.3390/ijms19092614] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 08/25/2018] [Accepted: 08/28/2018] [Indexed: 12/27/2022] Open
Abstract
Tomato yellow leaf curl virus (TYLCV, genus Begomovirus, family Geminiviridae) is a major species that causes a tomato disease for which resistant tomato hybrids (mainly carriers of the Ty-1/Ty-3 gene) are being used widely. We have characterized begomoviruses severely affecting resistant tomato crops in Southeast Spain. Circular DNA was prepared from samples by rolling circle amplification, and sequenced by massive sequencing (2015) or cloning and Sanger sequencing (2016). Thus, 23 complete sequences were determined, all belonging to the TYLCV Israel strain (TYLCV-IL). Massive sequencing also revealed the absence of other geminiviral and beta-satellite sequences. A phylogenetic analysis showed that the Spanish isolates belonged to two groups, one related to early TYLCV-IL isolates in the area (Group 1), and another (Group 2) closely related to El Jadida (Morocco) isolates, suggesting a recent introduction. The most parsimonious evolutionary scenario suggested that the TYLCV isolates of Group 2 are back recombinant isolates derived from TYLCV-IS76, a recombinant virus currently predominating in Moroccan epidemics. Thus, an infectious Group 2 clone (TYLCV-Mu15) was constructed and used in in planta competition assays against TYLCV-IS76. TYLCV-Mu15 predominated in single infections, whereas TYLCV-IS76 did so in mixed infections, providing credibility to a scenario of co-occurrence of both types of isolates.
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Affiliation(s)
- Covadonga Torre
- Abiopep S.L., Departamento de I + D + i, Parque Científico de Murcia, Ctra. de Madrid, Km 388, Complejo de Espinardo, Edf. R, 2°, 30100 Murcia, Spain.
| | - Livia Donaire
- Centro de Edafología y Biología Aplicada del Segura (CEBAS)-CSIC, Departamento de Biología del Estrés y Patología Vegetal, P.O. Box 164, 30100 Murcia, Spain.
| | - Cristina Gómez-Aix
- Abiopep S.L., Departamento de I + D + i, Parque Científico de Murcia, Ctra. de Madrid, Km 388, Complejo de Espinardo, Edf. R, 2°, 30100 Murcia, Spain.
| | - Miguel Juárez
- Escuela Politécnica Superior de Orihuela, Universidad Miguel Hernández de Elche, Ctra. de Beniel, Km 3.2, 03312 Alicante, Spain.
| | - Michel Peterschmitt
- Centre de Coopération Internationale en Recherche Agronomique Pour le Développement (CIRAD), UMR-BGPI, Equipe Interactions Virus-Insecte-Plante, TA A-54/K, Campus International de Baillarguet, CEDEX 5, 34398 Monptellier, France.
| | - Cica Urbino
- Centre de Coopération Internationale en Recherche Agronomique Pour le Développement (CIRAD), UMR-BGPI, Equipe Interactions Virus-Insecte-Plante, TA A-54/K, Campus International de Baillarguet, CEDEX 5, 34398 Monptellier, France.
| | - Yolanda Hernando
- Abiopep S.L., Departamento de I + D + i, Parque Científico de Murcia, Ctra. de Madrid, Km 388, Complejo de Espinardo, Edf. R, 2°, 30100 Murcia, Spain.
| | - Jesús Agüero
- Abiopep S.L., Departamento de I + D + i, Parque Científico de Murcia, Ctra. de Madrid, Km 388, Complejo de Espinardo, Edf. R, 2°, 30100 Murcia, Spain.
| | - Miguel A Aranda
- Centro de Edafología y Biología Aplicada del Segura (CEBAS)-CSIC, Departamento de Biología del Estrés y Patología Vegetal, P.O. Box 164, 30100 Murcia, Spain.
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19
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Jeger MJ, Madden LV, van den Bosch F. Plant Virus Epidemiology: Applications and Prospects for Mathematical Modeling and Analysis to Improve Understanding and Disease Control. PLANT DISEASE 2018; 102:837-854. [PMID: 30673389 DOI: 10.1094/pdis-04-17-0612-fe] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In recent years, mathematical modeling has increasingly been used to complement experimental and observational studies of biological phenomena across different levels of organization. In this article, we consider the contribution of mathematical models developed using a wide range of techniques and uses to the study of plant virus disease epidemics. Our emphasis is on the extent to which models have contributed to answering biological questions and indeed raised questions related to the epidemiology and ecology of plant viruses and the diseases caused. In some cases, models have led to direct applications in disease control, but arguably their impact is better judged through their influence in guiding research direction and improving understanding across the characteristic spatiotemporal scales of plant virus epidemics. We restrict this article to plant virus diseases for reasons of length and to maintain focus even though we recognize that modeling has played a major and perhaps greater part in the epidemiology of other plant pathogen taxa, including vector-borne bacteria and phytoplasmas.
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Affiliation(s)
- M J Jeger
- Centre for Environmental Policy, Imperial College London, Silwood Park, Ascot SL5 7PY, United Kingdom
| | - L V Madden
- Department of Plant Pathology, Ohio State University, Wooster, OH 44691
| | - F van den Bosch
- Computational and Systems Biology, Rothamsted Research, Harpenden AL5 2JQ, United Kingdom
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20
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Survey, symptomatology, transmission, host range and characterization of begomovirus associated with yellow mosaic disease of ridge gourd in southern India. Virusdisease 2017; 28:146-155. [PMID: 28770240 DOI: 10.1007/s13337-017-0376-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 04/19/2017] [Indexed: 10/19/2022] Open
Abstract
Ridge gourd is an important vegetable crop and is affected by several biotic and abiotic factors. Among the different biotic factors, ridge gourd yellow mosaic disease (RgYMD) is new emerging threat for the production of ridge gourd. The incidence of the RgYMD varied from 30 to 100% in southern India with highest disease incidence of 100% observed in Belagavi district of Karnataka state. The infected plants showed chlorosis, mosaic, cupping of leaves, blistering, reduction in leaf size and stunted growth. The varieties/hybrids grown in the farmer's fields were found to be susceptible to the disease. Begomovirus was detected in 61 out 64 samples collected from different areas of southern India. Further, all the samples failed to give amplification for beta and alpha satellites. The transmission studies revealed that single whitefly (Bemisia tabaci) is enough to transmit the virus, however, 100% transmission was observed with 10 whiteflies. The minimum acquisition access period and inoculation access period for transmission of virus by whitefly was 15 min. Among the 56 host plants belonging to diversified families tested for host range, sponge gourd, ash gourd, bottle gourd, pumpkin, cucumber, summer squash, cluster bean, tobacco and datura were shown to be susceptible. Seventy six varieties/hybrids evaluated for identifying the resistance source for RgYMD, all were found highly susceptible. Sequence analysis of DNA-A revealed that the causal virus shared highest nucleotide sequence identity (92.3%) with Tomato leaf curl New Delhi virus (ToLCNDV) infecting sponge gourd from northern India. Sequence and phylogenetic analysis of both DNA-A and DNA-B components showed that the begomovirus associated with RgYMD is found to be strain of ToLCNDV. This is first report of ToLCNDV association with RgYMD from southern India.
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21
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Dennehy JJ. Evolutionary ecology of virus emergence. Ann N Y Acad Sci 2016; 1389:124-146. [PMID: 28036113 PMCID: PMC7167663 DOI: 10.1111/nyas.13304] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/24/2016] [Accepted: 11/09/2016] [Indexed: 12/22/2022]
Abstract
The cross-species transmission of viruses into new host populations, termed virus emergence, is a significant issue in public health, agriculture, wildlife management, and related fields. Virus emergence requires overlap between host populations, alterations in virus genetics to permit infection of new hosts, and adaptation to novel hosts such that between-host transmission is sustainable, all of which are the purview of the fields of ecology and evolution. A firm understanding of the ecology of viruses and how they evolve is required for understanding how and why viruses emerge. In this paper, I address the evolutionary mechanisms of virus emergence and how they relate to virus ecology. I argue that, while virus acquisition of the ability to infect new hosts is not difficult, limited evolutionary trajectories to sustained virus between-host transmission and the combined effects of mutational meltdown, bottlenecking, demographic stochasticity, density dependence, and genetic erosion in ecological sinks limit most emergence events to dead-end spillover infections. Despite the relative rarity of pandemic emerging viruses, the potential of viruses to search evolutionary space and find means to spread epidemically and the consequences of pandemic viruses that do emerge necessitate sustained attention to virus research, surveillance, prophylaxis, and treatment.
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Affiliation(s)
- John J Dennehy
- Biology Department, Queens College of the City University of New York, Queens, New York and The Graduate Center of the City University of New York, New York, New York
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22
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Yasmeen A, Kiani S, Butt A, Rao AQ, Akram F, Ahmad A, Nasir IA, Husnain T, Mansoor S, Amin I, Aftab S, Zubair M, Tahir MN, Akhtar S, Scheffler J, Scheffler B. Amplicon-Based RNA Interference Targeting V2 Gene of Cotton Leaf Curl Kokhran Virus-Burewala Strain Can Provide Resistance in Transgenic Cotton Plants. Mol Biotechnol 2016; 58:807-820. [PMID: 27757798 PMCID: PMC5102983 DOI: 10.1007/s12033-016-9980-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The conserved coat or V2 gene of begomoviruses is responsible for viral movement in the plant cells. RNAi technology was used to silence V2 gene for resistance against these viruses in transgenic plants. The transformation of the RNAi-based gene construct targeting V2 gene of CLCuKoV-Bur, cloned under 35S promoter, was done in two elite cotton varieties MNH-786 and VH-289 using shoot apex cut method of gene transformation. The transformation efficiency was found to be 3.75 and 2.88 % in MNH-786 and VH-289, respectively. Confirmation of successful transformation was done through PCR in T 0, T 1, and T 2 generations using gene-specific primers. Transgenic cotton plants were categorized on the basis of the virus disease index in T 1 generation. Copy number and transgene location were observed using FISH and karyotyping in T 2 generation which confirmed random integration of V2 RNAi amplicon at chromosome 6 and 16. Real-time quantitative PCR analyses of promising transgenic lines showed low virus titer compared to wild-type control plants upon challenging them with viruliferous whiteflies in a contained environment. From the results, it was concluded that amplicon V2 RNAi construct was able to limit virus replication and can be used to control CLCuV in the field.
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Affiliation(s)
- Aneela Yasmeen
- Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Sarfraz Kiani
- Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Afshan Butt
- Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Abdul Qayyum Rao
- Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan.
| | - Faheem Akram
- Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Aftab Ahmad
- Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Idrees Ahmad Nasir
- Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Tayyab Husnain
- Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Shahid Mansoor
- National Institute of Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Imran Amin
- National Institute of Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Shaheen Aftab
- National Institute of Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Muhammad Zubair
- National Institute of Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | | | - Sohail Akhtar
- National Institute of Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Jodi Scheffler
- Jamie Whitten Delta States Research Center, USDA, Stoneville, MS, 38776, USA
| | - Brian Scheffler
- Jamie Whitten Delta States Research Center, USDA, Stoneville, MS, 38776, USA
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Zaidi SSEA, Tashkandi M, Mansoor S, Mahfouz MM. Engineering Plant Immunity: Using CRISPR/Cas9 to Generate Virus Resistance. FRONTIERS IN PLANT SCIENCE 2016; 7:1673. [PMID: 27877187 PMCID: PMC5099147 DOI: 10.3389/fpls.2016.01673] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/24/2016] [Indexed: 05/19/2023]
Abstract
Plant viruses infect many economically important crops, including wheat, cotton, maize, cassava, and other vegetables. These viruses pose a serious threat to agriculture worldwide, as decreases in cropland area per capita may cause production to fall short of that required to feed the increasing world population. Under these circumstances, conventional strategies can fail to control rapidly evolving and emerging plant viruses. Genome-engineering strategies have recently emerged as promising tools to introduce desirable traits in many eukaryotic species, including plants. Among these genome engineering technologies, the CRISPR (clustered regularly interspaced palindromic repeats)/CRISPR-associated 9 (CRISPR/Cas9) system has received special interest because of its simplicity, efficiency, and reproducibility. Recent studies have used CRISPR/Cas9 to engineer virus resistance in plants, either by directly targeting and cleaving the viral genome, or by modifying the host plant genome to introduce viral immunity. Here, we briefly describe the biology of the CRISPR/Cas9 system and plant viruses, and how different genome engineering technologies have been used to target these viruses. We further describe the main findings from recent studies of CRISPR/Cas9-mediated viral interference and discuss how these findings can be applied to improve global agriculture. We conclude by pinpointing the gaps in our knowledge and the outstanding questions regarding CRISPR/Cas9-mediated viral immunity.
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Affiliation(s)
- Syed Shan-e-Ali Zaidi
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
- National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| | - Manal Tashkandi
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| | - Magdy M. Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
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Synthesis and biological activity evaluation of novel amino acid derivatives as potential elicitors against Tomato yellow leaf curl virus. Amino Acids 2015; 47:2495-503. [PMID: 26162434 DOI: 10.1007/s00726-015-2040-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 06/24/2015] [Indexed: 10/23/2022]
Abstract
Disease caused by Tomato yellow leaf curl virus (TYLCV) brings serious production losses of cultivated tomato worldwide. In our previous study, two novel amino acid derivatives exerted satisfactory antiviral activities against TYLCV. In this study, the variation of TYLCV, the transcriptional expression level of Ty-1 and the enzyme activities of POD and PPO in tomato were monitored after treatment with two amino acid derivatives to illustrate the antiviral mechanism. The results showed the symptom severity caused by TYLCV was reduced significantly by two compounds and was associated with the inhibition of viral DNA level at the early stage. Among three levels of concentration, the highest inhibition rate of CNBF-His was 40.66% at 1000 mg/L, for CNBF-Asn, the highest inhibition rate was 36.26% at 2000 mg/L 30 days post-inoculation. Two compounds could also enhance the activities of PPO and POD and the transcriptional expression level of Ty-1 which correlates with plant resistance in tomato. In the field test, two compounds increased the yields of tomato and the maximum increase of yield was 37.66%. This is the first report of novel amino acid derivatives inducing resistance in tomato plant against TYLCV. It is suggested that amino acid derivatives have the potential to be an effective approach against TYLCV in tomato plant.
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Bioinformatic analysis reveals genome size reduction and the emergence of tyrosine phosphorylation site in the movement protein of New World bipartite begomoviruses. PLoS One 2014; 9:e111957. [PMID: 25383632 PMCID: PMC4226511 DOI: 10.1371/journal.pone.0111957] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 10/09/2014] [Indexed: 11/19/2022] Open
Abstract
Begomovirus (genus Begomovirus, family Geminiviridae) infection is devastating to a wide variety of agricultural crops including tomato, squash, and cassava. Thus, understanding the replication and adaptation of begomoviruses has important translational value in alleviating substantial economic loss, particularly in developing countries. The bipartite genome of begomoviruses prevalent in the New World and their counterparts in the Old World share a high degree of genome homology except for a partially overlapping reading frame encoding the pre-coat protein (PCP, or AV2). PCP contributes to the essential functions of intercellular movement and suppression of host RNA silencing, but it is only present in the Old World viruses. In this study, we analyzed a set of non-redundant bipartite begomovirus genomes originating from the Old World (N = 28) and the New World (N = 65). Our bioinformatic analysis suggests ∼ 120 nucleotides were deleted from PCP's proximal promoter region that may have contributed to its loss in the New World viruses. Consequently, genomes of the New World viruses are smaller than the Old World counterparts, possibly compensating for the loss of the intercellular movement functions of PCP. Additionally, we detected substantial purifying selection on a portion of the New World DNA-B movement protein (MP, or BC1). Further analysis of the New World MP gene revealed the emergence of a putative tyrosine phosphorylation site, which likely explains the increased purifying selection in that region. These findings provide important information about the strategies adopted by bipartite begomoviruses in adapting to new environment and suggest future in planta experiments.
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Rodríguez-Negrete E, Lozano-Durán R, Piedra-Aguilera A, Cruzado L, Bejarano ER, Castillo AG. Geminivirus Rep protein interferes with the plant DNA methylation machinery and suppresses transcriptional gene silencing. THE NEW PHYTOLOGIST 2013; 199:464-475. [PMID: 23614786 DOI: 10.1111/nph.12286] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 03/13/2013] [Indexed: 05/17/2023]
Abstract
Cytosine methylation is an epigenetic mark that promotes gene silencing and plays an important role in genome defence against transposons and invading DNA viruses. Previous data showed that the largest family of single-stranded DNA viruses, Geminiviridae, prevents methylation-mediated transcriptional gene silencing (TGS) by interfering with the proper functioning of the plant methylation cycle. Here, we describe a novel counter-defence strategy used by geminiviruses, which reduces the expression of the plant maintenance DNA methyltransferases, METHYLTRANSFERASE 1 (MET1) and CHROMOMETHYLASE 3 (CMT3), in both locally and systemically infected tissues. We demonstrated that the virus-mediated repression of these two maintenance DNA methyltransferases is widespread among geminivirus species. Additionally, we identified Rep (Replication associated protein) as the geminiviral protein responsible for the repression of MET1 and CMT3, and another viral protein, C4, as an ancillary player in MET1 down-regulation. The presence of Rep suppressed TGS of an Arabidopsis thaliana transgene and of host loci whose expression was strongly controlled by CG methylation. Bisulfite sequencing analyses showed that the expression of Rep caused a substantial reduction in the levels of DNA methylation at CG sites. Our findings suggest that Rep, the only viral protein essential for replication, displays TGS suppressor activity through a mechanism distinct from that thus far described for geminiviruses.
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Affiliation(s)
- Edgar Rodríguez-Negrete
- Area de Genética, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus Teatinos, 29071, Málaga, Spain
| | - Rosa Lozano-Durán
- Area de Genética, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus Teatinos, 29071, Málaga, Spain
| | - Alvaro Piedra-Aguilera
- Area de Genética, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus Teatinos, 29071, Málaga, Spain
| | - Lucia Cruzado
- Area de Genética, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus Teatinos, 29071, Málaga, Spain
| | - Eduardo R Bejarano
- Area de Genética, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus Teatinos, 29071, Málaga, Spain
| | - Araceli G Castillo
- Area de Genética, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus Teatinos, 29071, Málaga, Spain
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27
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Lima ATM, Sobrinho RR, González-Aguilera J, Rocha CS, Silva SJC, Xavier CAD, Silva FN, Duffy S, Zerbini FM. Synonymous site variation due to recombination explains higher genetic variability in begomovirus populations infecting non-cultivated hosts. J Gen Virol 2013; 94:418-431. [DOI: 10.1099/vir.0.047241-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Begomoviruses are ssDNA plant viruses that cause serious epidemics in economically important crops worldwide. Non-cultivated plants also harbour many begomoviruses, and it is believed that these hosts may act as reservoirs and as mixing vessels where recombination may occur. Begomoviruses are notoriously recombination-prone, and also display nucleotide substitution rates equivalent to those of RNA viruses. In Brazil, several indigenous begomoviruses have been described infecting tomatoes following the introduction of a novel biotype of the whitefly vector in the mid-1990s. More recently, a number of viruses from non-cultivated hosts have also been described. Previous work has suggested that viruses infecting non-cultivated hosts have a higher degree of genetic variability compared with crop-infecting viruses. We intensively sampled cultivated and non-cultivated plants in similarly sized geographical areas known to harbour either the weed-infecting Macroptilium yellow spot virus (MaYSV) or the crop-infecting Tomato severe rugose virus (ToSRV), and compared the molecular evolution and population genetics of these two distantly related begomoviruses. The results reinforce the assertion that infection of non-cultivated plant species leads to higher levels of standing genetic variability, and indicate that recombination, not adaptive selection, explains the higher begomovirus variability in non-cultivated hosts.
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Affiliation(s)
- Alison T. M. Lima
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - Roberto R. Sobrinho
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - Jorge González-Aguilera
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - Carolina S. Rocha
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - Sarah J. C. Silva
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - César A. D. Xavier
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - Fábio N. Silva
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - F. Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
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28
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Pramesh D, Mandal B, Phaneendra C, Muniyappa V. Host range and genetic diversity of croton yellow vein mosaic virus, a weed-infecting monopartite begomovirus causing leaf curl disease in tomato. Arch Virol 2012; 158:531-42. [PMID: 23096697 DOI: 10.1007/s00705-012-1511-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 09/09/2012] [Indexed: 10/27/2022]
Abstract
Croton yellow vein mosaic virus (CYVMV) is a widely occurring begomovirus in Croton bonplandianum, a common weed in the Indian subcontinent. In this study, CYVMV (genus Begomovirus, family Geminiviridae) was transmitted by whiteflies (Bemisia tabaci) to as many as 35 plant species belonging to 11 families, including many vegetables, tobacco varieties, ornamentals and weeds. CYVMV produced bright yellow vein symptoms in croton, whereas in all the other host species, the virus produced leaf curl symptoms. CYVMV produced leaf curl in 13 tobacco species and 22 cultivars of Nicotiana tabacum and resembled tobacco leaf curl virus (TobLCV) in host reactions. However, CYVMV was distinguished from TobLCV in four differential hosts, Ageratum conyzoides, C. bonplandianum, Euphorbia geniculata and Sonchus bracyotis. The complete genome sequences of four isolates originating from northern, eastern and southern India revealed that a single species of DNA-A and a betasatellite, croton yellow vein mosaic betasatellite (CroYVMB) were associated with the yellow vein mosaic disease of croton. The sequence identity among the isolates of CYVMV DNA-A and CroYVMB occurring in diverse plant species was 91.8-97.9 % and 83.3-100 %, respectively. The CYVMV DNA-A and CroYVMB generated through rolling-circle amplification of the cloned DNAs produced typical symptoms of yellow vein mosaic and leaf curling in croton and tomato, respectively. The progeny virus from both the croton and tomato plants was transmitted successfully by B. tabaci. The present study establishes the etiology of yellow vein mosaic disease of C. bonplandianum and provides molecular evidence that a weed-infecting monopartite begomovirus causes leaf curl in tomato.
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Affiliation(s)
- D Pramesh
- Division of Plant Pathology, Advanced Centre for Plant Virology, Indian Agricultural Research Institute, New Delhi 110012, India
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29
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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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30
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Luna AP, Morilla G, Voinnet O, Bejarano ER. Functional analysis of gene-silencing suppressors from tomato yellow leaf curl disease viruses. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:1294-306. [PMID: 22712505 DOI: 10.1094/mpmi-04-12-0094-r] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Tomato yellow leaf curl disease (TYLCD) is caused by a complex of phylogenetically related Begomovirus spp. that produce similar symptoms when they infect tomato plants but have different host ranges. In this work, we have evaluated the gene-silencing-suppression activity of C2, C4, and V2 viral proteins isolated from the four main TYLCD-causing strains in Spain in Nicotiana benthamiana. We observed varying degrees of local silencing suppression for each viral protein tested, with V2 proteins from all four viruses exhibiting the strongest suppression activity. None of the suppressors were able to avoid the spread of the systemic silencing, although most produced a delay. In order to test the silencing-suppression activity of Tomato yellow leaf curl virus (TYLCV) and Tomato yellow leaf curl Sardinia virus (TYLCSV) proteins in a shared (tomato) and nonshared (bean) host, we established novel patch assays. Using these tools, we found that viral proteins from TYLCV were able to suppress silencing in both hosts, whereas TYLCSV proteins were only effective in tomato. This is the first time that viral suppressors from a complex of disease-causing geminiviruses have been subject to a comprehensive analysis using two economically important crop hosts, as well as the established N. benthamiana plant model.
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Affiliation(s)
- Ana P Luna
- Departamento de Genetica, Universidad de Malaga, Malaga, Spain
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31
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Rey MEC, Ndunguru J, Berrie LC, Paximadis M, Berry S, Cossa N, Nuaila VN, Mabasa KG, Abraham N, Rybicki EP, Martin D, Pietersen G, Esterhuizen LL. Diversity of dicotyledenous-infecting geminiviruses and their associated DNA molecules in southern Africa, including the South-west Indian ocean islands. Viruses 2012; 4:1753-91. [PMID: 23170182 PMCID: PMC3499829 DOI: 10.3390/v4091753] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 09/04/2012] [Accepted: 09/05/2012] [Indexed: 11/16/2022] Open
Abstract
The family Geminiviridae comprises a group of plant-infecting circular ssDNA viruses that severely constrain agricultural production throughout the temperate regions of the world, and are a particularly serious threat to food security in sub-Saharan Africa. While geminiviruses exhibit considerable diversity in terms of their nucleotide sequences, genome structures, host ranges and insect vectors, the best characterised and economically most important of these viruses are those in the genus Begomovirus. Whereas begomoviruses are generally considered to be either monopartite (one ssDNA component) or bipartite (two circular ssDNA components called DNA-A and DNA-B), many apparently monopartite begomoviruses are associated with additional subviral ssDNA satellite components, called alpha- (DNA-αs) or betasatellites (DNA-βs). Additionally, subgenomic molecules, also known as defective interfering (DIs) DNAs that are usually derived from the parent helper virus through deletions of parts of its genome, are also associated with bipartite and monopartite begomoviruses. The past three decades have witnessed the emergence and diversification of various new begomoviral species and associated DI DNAs, in southern Africa, East Africa, and proximal Indian Ocean islands, which today threaten important vegetable and commercial crops such as, tobacco, cassava, tomato, sweet potato, and beans. This review aims to describe what is known about these viruses and their impacts on sustainable production in this sensitive region of the world.
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Affiliation(s)
- Marie E. C. Rey
- Department of Biochemistry, University of Johannesburg, PO Box 524, Auckland Park, 2006, Johannesburg, South Africa;
| | - Joseph Ndunguru
- Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar es Salaam, Tanzania;
| | - Leigh C. Berrie
- National Institute for Communicable Diseases, Private Bag X4, Sandringham, Johannesburg, 2131, South Africa
- Department of Biochemistry, University of Johannesburg, PO Box 524, Auckland Park, 2006, Johannesburg, South Africa;
| | - Maria Paximadis
- National Institute for Communicable Diseases, Private Bag X4, Sandringham, Johannesburg, 2131, South Africa
- Department of Biochemistry, University of Johannesburg, PO Box 524, Auckland Park, 2006, Johannesburg, South Africa;
| | - Shaun Berry
- South African Sugarcane Research Institute, 170 Flanders Drive, Private Bag X02, Mount Edgecombe, 4300, South Africa
- Department of Biochemistry, University of Johannesburg, PO Box 524, Auckland Park, 2006, Johannesburg, South Africa;
| | - Nurbibi Cossa
- The Institute of Agricultural Research of Mozambique, Av. Das FPLM, No. 269 C.P. 3658, Maputo, Mozambique;
| | - Valter N. Nuaila
- Biotechnology Center, Eduardo Mondlane University, Praca 25 de Junho. Caixa, Potal 257, Maputo, Mozambique
- Department of Biochemistry, University of Johannesburg, PO Box 524, Auckland Park, 2006, Johannesburg, South Africa;
| | - Ken G. Mabasa
- Crop Protection and Diagnostic Center, ARC-Roodeplaat-VOPI, Private Bag X134, Pretoria, 0001, South Africa
- Department of Biochemistry, University of Johannesburg, PO Box 524, Auckland Park, 2006, Johannesburg, South Africa;
| | - Natasha Abraham
- Department of Biochemistry, University of Johannesburg, PO Box 524, Auckland Park, 2006, Johannesburg, South Africa;
| | - Edward P. Rybicki
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa; (E.P.R.); (D.M.)
| | - Darren Martin
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa; (E.P.R.); (D.M.)
| | - Gerhard Pietersen
- ARC-Plant Protection Research Institute and University of Pretoria, Private Bag X134, Pretoria, 0001, South Africa;
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Caracuel Z, Lozano-Durán R, Huguet S, Arroyo-Mateos M, Rodríguez-Negrete EA, Bejarano ER. C2 from Beet curly top virus promotes a cell environment suitable for efficient replication of geminiviruses, providing a novel mechanism of viral synergism. THE NEW PHYTOLOGIST 2012; 194:846-858. [PMID: 22404507 DOI: 10.1111/j.1469-8137.2012.04080.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
• Geminiviruses are plant viruses with circular, single-stranded (ss) DNA genomes that infect a wide range of species and cause important losses in agriculture. Geminiviruses do not encode their own DNA polymerase, and rely on the host cell machinery for their replication. • Here, we identify a positive effect of the curtovirus Beet curly top virus (BCTV) on the begomovirus Tomato yellow leaf curl Sardinia virus (TYLCSV) infection in Nicotiana benthamiana plants. • Our results show that this positive effect is caused by the promotion of TYLCSV replication by BCTV C2. Transcriptomic analyses of plants expressing C2 unveil an up-regulation of cell cycle-related genes induced on cell cycle re-entry; experiments with two mutated versions of C2 indicate that this function resides in the N-terminal part of C2, which is also sufficient to enhance geminiviral replication. Moreover, C2 expression promotes the replication of other geminiviral species, but not of RNA viruses. • We conclude that BCTV C2 has a novel function in the promotion of viral replication, probably by restoring the DNA replication competency of the infected cells and thus creating a favourable cell environment for viral spread. Because C2 seems to have a broad impact on the replication of geminiviruses, this mechanism might have important epidemiological implications.
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Affiliation(s)
- Zaira Caracuel
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento Biología Celular, Genética y Fisiología, Universidad de Málaga, Campus Teatinos, 29071 Málaga, Spain
| | - Rosa Lozano-Durán
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento Biología Celular, Genética y Fisiología, Universidad de Málaga, Campus Teatinos, 29071 Málaga, Spain
| | - Stéphanie Huguet
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 rue G. Crémieux, CP 5708, F-91057 Evry Cedex, France
| | - Manuel Arroyo-Mateos
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento Biología Celular, Genética y Fisiología, Universidad de Málaga, Campus Teatinos, 29071 Málaga, Spain
| | - Edgar A Rodríguez-Negrete
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento Biología Celular, Genética y Fisiología, Universidad de Málaga, Campus Teatinos, 29071 Málaga, Spain
| | - Eduardo R Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento Biología Celular, Genética y Fisiología, Universidad de Málaga, Campus Teatinos, 29071 Málaga, Spain
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33
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Thierry M, Lefeuvre P, Hoareau M, Péréfarres F, Delatte H, Reynaud B, Martin DP, Lett JM. Differential disease phenotype of begomoviruses associated with tobacco leaf curl disease in Comoros. Arch Virol 2012; 157:545-50. [PMID: 22187103 DOI: 10.1007/s00705-011-1199-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 11/17/2011] [Indexed: 11/24/2022]
Abstract
In the 2000s, tobacco plantations on the Comoros Islands were afflicted with a previously unobserved tobacco leaf curl disease characterised by symptoms of severe leaf curling and deformation. Previous molecular characterization of potential viral pathogens revealed a complex of African monopartite tobacco leaf curl begomovirus (TbLCVs). Our molecular investigation allowed the characterization of a new monopartite virus involved in the disease: tomato leaf curl Namakely virus (ToLCNamV). Agroinoculation experiments indicated that TbLCVs and tomato leaf curl viruses (ToLCVs) can infect both tomato and tobacco but that infectivity and symptom expression fluctuate depending on the virus and the plant cultivar combination.
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Affiliation(s)
- M Thierry
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 97410 Saint-Pierre, Ile de La Réunion, France.
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34
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da Silva SJC, Castillo-Urquiza GP, Hora Júnior BT, Assunção IP, Lima GSA, Pio-Ribeiro G, Mizubuti ESG, Zerbini FM. High genetic variability and recombination in a begomovirus population infecting the ubiquitous weed Cleome affinis in northeastern Brazil. Arch Virol 2011; 156:2205-13. [PMID: 22006043 DOI: 10.1007/s00705-011-1119-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2011] [Accepted: 09/14/2011] [Indexed: 11/25/2022]
Abstract
Diseases caused by begomoviruses are a serious constraint to crop production in many tropical and subtropical areas of the world, including Brazil. Begomoviruses are whitefly-transmitted, single-stranded DNA viruses that are often associated with weed plants, which may act as natural reservoirs of viruses that cause epidemics in crop plants. Cleome affinis (family Capparaceae) is an annual weed that is frequently associated with leguminous crops in Brazil. Samples of C. affinis were collected in four states in the northeast of Brazil. Analysis of 14 full-length DNA-A components revealed that only one begomovirus was present, with 91-96% identity to cleome leaf crumple virus (ClLCrV). In a phylogenetic tree, ClLCrV forms a basal group relative to all other Brazilian begomoviruses. Evidence of multiple recombination events was detected among the ClLCrV isolates, which also display a high degree of genetic variability. Despite ClLCrV being the only begomovirus found, its phylogenetic placement, high genetic variability and recombinant nature suggest that C. affinis may act as a source of novel viruses for crop plants. Alternatively, ClLCrV could be a genetically isolated begomovirus. Further studies on the biological properties of ClLCrV should help to clarify the role of C. affinis in the epidemiological scenario of Brazilian begomoviruses.
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Affiliation(s)
- Sarah J C da Silva
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, MG, Brazil
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35
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Sánchez-Durán MA, Dallas MB, Ascencio-Ibañez JT, Reyes MI, Arroyo-Mateos M, Ruiz-Albert J, Hanley-Bowdoin L, Bejarano ER. Interaction between geminivirus replication protein and the SUMO-conjugating enzyme is required for viral infection. J Virol 2011; 85:9789-800. [PMID: 21775461 PMCID: PMC3196459 DOI: 10.1128/jvi.02566-10] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Accepted: 07/08/2011] [Indexed: 12/11/2022] Open
Abstract
Geminiviruses are small DNA viruses that replicate in nuclei of infected plant cells by using plant DNA polymerases. These viruses encode a protein designated AL1, Rep, or AC1 that is essential for viral replication. AL1 is an oligomeric protein that binds to double-stranded DNA, catalyzes the cleavage and ligation of single-stranded DNA, and induces the accumulation of host replication machinery. It also interacts with several host proteins, including the cell cycle regulator retinoblastoma-related protein (RBR), the DNA replication protein PCNA (proliferating cellular nuclear antigen), and the sumoylation enzyme that conjugates SUMO to target proteins (SUMO-conjugating enzyme [SCE1]). The SCE1-binding motif was mapped by deletion to a region encompassing AL1 amino acids 85 to 114. Alanine mutagenesis of lysine residues in the binding region either reduced or eliminated the interaction with SCE1, but no defects were observed for other AL1 functions, such as oligomerization, DNA binding, DNA cleavage, and interaction with AL3 or RBR. The lysine mutations reduced or abolished virus infectivity in plants and viral DNA accumulation in transient-replication assays, suggesting that the AL1-SCE1 interaction is required for viral DNA replication. Ectopic AL1 expression did not result in broad changes in the sumoylation pattern of plant cells, but specific changes were detected, indicating that AL1 modifies the sumoylation state of selected host proteins. These results established the importance of AL1-SCE1 interactions during geminivirus infection of plants and suggested that AL1 alters the sumoylation of selected host factors to create an environment suitable for viral infection.
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Affiliation(s)
- Miguel A. Sánchez-Durán
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departmento de Biología Celular, Genética y Fisiología, Universidad de Málaga, Campus Teatinos, 29071 Málaga, Spain
| | - Mary B. Dallas
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7622
| | - José T. Ascencio-Ibañez
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7622
| | - Maria Ines Reyes
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7622
| | - Manuel Arroyo-Mateos
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departmento de Biología Celular, Genética y Fisiología, Universidad de Málaga, Campus Teatinos, 29071 Málaga, Spain
| | - Javier Ruiz-Albert
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departmento de Biología Celular, Genética y Fisiología, Universidad de Málaga, Campus Teatinos, 29071 Málaga, Spain
| | - Linda Hanley-Bowdoin
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7622
| | - Eduardo R. Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departmento de Biología Celular, Genética y Fisiología, Universidad de Málaga, Campus Teatinos, 29071 Málaga, Spain
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36
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Mubin M, Hussain M, Briddon RW, Mansoor S. Selection of target sequences as well as sequence identity determine the outcome of RNAi approach for resistance against cotton leaf curl geminivirus complex. Virol J 2011; 8:122. [PMID: 21410988 PMCID: PMC3315792 DOI: 10.1186/1743-422x-8-122] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Accepted: 03/16/2011] [Indexed: 11/11/2022] Open
Abstract
Cotton leaf curl disease is caused by a geminivirus complex that involves multiple distinct begomoviruses and a disease-specific DNA satellite, cotton leaf curl Multan betasatellite (CLCuMB), which is essential to induce disease symptoms. Here we have investigated the use of RNA interference (RNAi) for obtaining resistance against one of the viruses, Cotton leaf curl Multan virus (CLCuMV), associated with the disease. Three hairpin RNAi constructs were produced containing either complementary-sense genes essential for replication/pathogenicity or non-coding regulatory sequences of CLCuMV. In transient assays all three RNAi constructs significantly reduced the replication of the virus in inoculated tissues. However, only one of the constructs, that targeting the overlapping genes involved in virus replication and pathogenicity (the replication-associated protein (Rep), the transcriptional activator protein and the replication enhancer protein) was able to prevent systemic movement of the virus, although the other constructs significantly reduced the levels of virus in systemic tissues. In the presence of CLCuMB, however, a small number of plants co-inoculated with even the most efficient RNAi construct developed symptoms of virus infection, suggesting that the betasatellite may compromise resistance. Further analyses, using Rep gene sequences of distinct begomoviruses expressed from a PVX vector as the target, are consistent with the idea that the success of the RNAi approach depends on sequence identity to the target virus. The results show that selection of both the target sequence, as well as the levels of identity between the construct and target sequence, determine the outcome of RNAi-based resistance against geminivirus complexes.
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Affiliation(s)
- Muhammad Mubin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Jhang Road, Faisalabad, Pakistan
| | - Mazhar Hussain
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Jhang Road, Faisalabad, Pakistan
| | - Rob W Briddon
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Jhang Road, Faisalabad, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Jhang Road, Faisalabad, Pakistan
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Chen LF, Rojas M, Kon T, Gamby K, Xoconostle-Cazares B, Gilbertson RL. A severe symptom phenotype in tomato in Mali is caused by a reassortant between a novel recombinant begomovirus (Tomato yellow leaf curl Mali virus) and a betasatellite. MOLECULAR PLANT PATHOLOGY 2009; 10:415-30. [PMID: 19400843 PMCID: PMC6640326 DOI: 10.1111/j.1364-3703.2009.00541.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Tomato production in West Africa has been severely affected by begomovirus diseases, including yellow leaf curl and a severe symptom phenotype, characterized by extremely stunted and distorted growth and small deformed leaves. Here, a novel recombinant begomovirus from Mali, Tomato yellow leaf curl Mali virus (TYLCMLV), is described that, alone, causes tomato yellow leaf curl disease or, in combination with a betasatellite, causes the severe symptom phenotype. TYLCMLV is an Old World monopartite begomovirus with a hybrid genome composed of sequences from Tomato yellow leaf curl virus-Mild (TYLCV-Mld) and Hollyhock leaf crumple virus (HoLCrV). A TYLCMLV infectious clone induced leaf curl and yellowing in tomato, leaf curl, crumpling and yellowing in Nicotiana benthamiana and common bean, mild symptoms in N. glutinosa, and a symptomless infection in Datura stramonium. In a field-collected sample from a tomato plant showing the severe symptom phenotype in Mali, TYLCMLV was detected together with a betasatellite, identified as Cotton leaf curl Gezira betasatellite (CLCuGB). Tomato plants co-agroinoculated with TYLCMLV and CLCuGB developed severely stunted and distorted growth and small crumpled leaves. These symptoms were more severe than those induced by TYLCMLV alone, and were similar to the severe symptom phenotype observed in the field in Mali and in other West African countries. TYLCMLV and CLCuGB also induced more severe symptoms than TYLCMLV in the other solanaceous hosts, but not in common bean. The increased symptom severity was associated with hyperplasia of phloem-associated cells, but relatively little increase in TYLCMLV DNA levels. In surveys of tomato virus diseases in West Africa, TYLCMLV was commonly detected in plants with leaf curl and yellow leaf curl symptoms, whereas CLCuGB was infrequently detected and always in association with the severe symptom phenotype. Together, these results indicate that TYLCMLV causes tomato yellow leaf curl disease throughout West Africa, whereas TYLCMLV and CLCuGB represent a reassortant that causes the severe symptom phenotype in tomato.
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Affiliation(s)
- Li-Fang Chen
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
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38
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Kon T, Rojas MR, Abdourhamane IK, Gilbertson RL. Roles and interactions of begomoviruses and satellite DNAs associated with okra leaf curl disease in Mali, West Africa. J Gen Virol 2009; 90:1001-1013. [PMID: 19264648 DOI: 10.1099/vir.0.008102-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Okra leaf curl disease (OLCD) is a major constraint on okra (Abelmoschus esculentus) production in West Africa. Two monopartite begomoviruses (okra virus-1 and okra virus-2), a betasatellite and a DNA1 satellite are associated with OLCD in Mali. Okra virus-1 is an isolate of okra yellow crinkle virus (OYCrV), okra virus-2 is a recombinant isolate of cotton leaf curl Gezira virus (CLCuGV) and the betasatellite is a variant of cotton leaf curl Gezira betasatellite (CLCuGB). Cloned DNA of OYCrV and CLCuGV were infectious and induced leaf curl symptoms in Nicotiana benthamiana plants, but did not induce OLCD in okra. However, when these clones were individually co-inoculated with the cloned CLCuGB DNA, symptom severity and viral DNA levels were increased in N. benthamiana plants and typical OLCD symptoms were induced in okra. The CLCuGB was also replicated by, and increased symptom severity of, three monopartite tomato-infecting begomoviruses, including two from West Africa. The sequence of the DNA1 satellite was highly divergent, indicating that it represents a distinct West African lineage. DNA1 replicated autonomously, and replication required the DNA1-encoded Rep protein. Although DNA1 reduced helper begomovirus DNA levels, symptoms were not attenuated. In the presence of CLCuGB, DNA levels of the helper begomoviruses and DNA1 were substantially increased. Together, these findings establish that OLCD in Mali is caused by a complex of monopartite begomoviruses and a promiscuous betasatellite with an associated parasitic DNA1 satellite. These findings are discussed in terms of the aetiology of OLCD and the evolution of new begomovirus/satellite DNA complexes.
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Affiliation(s)
- Tatsuya Kon
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Maria R Rojas
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | | | - Robert L Gilbertson
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
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Lett JM, Lefeuvre P, Couston L, Hoareau M, Thierry M, Reynaud B, Martin DP, Varsani A. Complete genomic sequences of Tomato yellow leaf curl Mali virus isolates infecting tomato and pepper from the North Province of Cameroon. Arch Virol 2009; 154:535-40. [DOI: 10.1007/s00705-009-0313-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Accepted: 12/18/2008] [Indexed: 11/30/2022]
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40
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Jones RAC. Plant virus emergence and evolution: origins, new encounter scenarios, factors driving emergence, effects of changing world conditions, and prospects for control. Virus Res 2009; 141:113-30. [PMID: 19159652 DOI: 10.1016/j.virusres.2008.07.028] [Citation(s) in RCA: 185] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2008] [Indexed: 11/25/2022]
Abstract
This review focuses on virus-plant pathosystems at the interface between managed and natural vegetation, and describes how rapid expansion in human activity and climate change are likely to impact on plants, vectors and viruses causing increasing instability. It starts by considering virus invasion of cultivated plants from their wild ancestors in the centres of plant domestication in different parts of the world and subsequent long distance movement away from these centres to other continents. It then describes the diverse virus-plant pathosystem scenarios possible at the interface between managed and natural vegetation and gives examples that illustrate situations where indigenous viruses emerge to damage introduced cultivated plants and newly introduced viruses become potential threats to biodiversity. These examples demonstrate how human activities increasingly facilitate damaging new encounters between plants and viruses worldwide. The likely effects of climate change on virus emergence are emphasised, and the major factors driving virus emergence, evolution and greater epidemic severity at the interface are analysed and explained. Finally, the kinds of challenges posed by rapidly changing world conditions to achieving effective control of epidemics of emerging plant viruses, and the approaches needed to address them, are described.
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Affiliation(s)
- Roger A C Jones
- Agricultural Research Western Australia, Bentley Delivery Centre, WA, Australia.
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41
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Wu B, Melcher U, Guo X, Wang X, Fan L, Zhou G. Assessment of codivergence of mastreviruses with their plant hosts. BMC Evol Biol 2008; 8:335. [PMID: 19094195 PMCID: PMC2630985 DOI: 10.1186/1471-2148-8-335] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Accepted: 12/18/2008] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Viruses that have spent most of their evolutionary time associated with a single host lineage should have sequences that reflect codivergence of virus and host. Several examples for RNA viruses of host-virus tree congruence are being challenged. DNA viruses, such as mastreviruses, are more likely than RNA viruses to have maintained a record of host lineage association. RESULTS The full genomes of 28 isolates of Wheat dwarf virus (WDV), a member of the Mastrevirus genus, from different regions of China were sequenced. The analysis of these 28 entire genomes and 18 entire genome sequences of cereal mastreviruses from other countries support the designation of wheat, barley and oat mastrevirus isolates as separate species. They revealed that relative divergence times for the viruses WDV, Barley dwarf virus (BDV), Oat dwarf virus (ODV) and Maize streak virus (MSV) are proportional to divergence times of their hosts, suggesting codivergence. Considerable diversity among Chinese isolates was found and was concentrated in hot spots in the Rep A, SIR, LIR, and intron regions in WDV genomes. Two probable recombination events were detected in Chinese WDV isolates. Analysis including further Mastrevirus genomes concentrated on coding regions to avoid difficulties due to recombination and hyperdiversity. The analysis demonstrated congruence of trees in two branches of the genus, but not in the third. Assuming codivergence, an evolutionary rate of 10-8 substitutions per site per year was calculated. The low rate implies stronger constraints against change than are obtained by other methods of estimating the rate. CONCLUSION We report tests of the hypothesis that mastreviruses have codiverged with their monocotyledonous hosts over 50 million years of evolution. The tests support the hypothesis for WDV, BDV and ODV, but not for MSV and other African streak viruses.
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Affiliation(s)
- Beilei Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanming Rd, Beijing 100193, PR China
| | - Ulrich Melcher
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078-3035, USA
| | - Xingyi Guo
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310029, PR China
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanming Rd, Beijing 100193, PR China
| | - Longjiang Fan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310029, PR China
| | - Guanghe Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanming Rd, Beijing 100193, PR China
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Radhakrishnan GK, Splitter GA, Usha R. DNA recognition properties of the cell-to-cell movement protein (MP) of soybean isolate of Mungbean yellow mosaic India virus (MYMIV-Sb). Virus Res 2008; 131:152-9. [PMID: 17949843 DOI: 10.1016/j.virusres.2007.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2007] [Revised: 09/03/2007] [Accepted: 09/03/2007] [Indexed: 11/26/2022]
Abstract
Bipartite geminiviruses possess two movement proteins (NSP and MP), which mediate the intra- and intercellular movement. In order to accomplish the transport process the movement proteins interact with viral nucleic acids in a sequence non-specific manner. To investigate the nucleic acid recognition properties of MP of MYMIV-Sb, the protein was expressed in Escherichia coli as a fusion protein with maltose-binding protein (MBP) and purified in native condition. Gel mobility shift assay was employed for analyzing the DNA recognition properties of purified MBP-MP fusion protein. The analyses demonstrated the sequence non-specific binding of MYMIV-Sb MP to both ds and ssDNA and its high affinity for ssDNA. MP of MYMIV-Sb did not show any specificity towards various forms of plasmid DNA but displayed size selection towards linear dsDNA.
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Affiliation(s)
- Girish K Radhakrishnan
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, India
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Gilligan CA, van den Bosch F. Epidemiological models for invasion and persistence of pathogens. ANNUAL REVIEW OF PHYTOPATHOLOGY 2008; 46:385-418. [PMID: 18680429 DOI: 10.1146/annurev.phyto.45.062806.094357] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Motivated by questions such as "Why do some diseases take off, while others die out?" and "How can we optimize the deployment of control methods," we introduce simple epidemiological concepts for the invasion and persistence of plant pathogens. An overarching modeling framework is then presented that can be used to analyze disease invasion and persistence at a range of scales from the microscopic to the regional. Criteria for invasion and persistence are introduced, initially for simple models of epidemics, and then for models with greater biological realism. Some ways in which epidemiological models are used to identify optimal strategies for the control of disease are discussed. Particular attention is given to the spatial structure of host populations and to the role of chance events in determining invasion and persistence of plant pathogens. Finally, three brief case studies are used to illustrate the practical applications of epidemiological theory to understand invasion and persistence of plant pathogens. These comprise long-term predictions for the persistence and control of Dutch elm disease; identification of methods to manage the spread of rhizomania on sugar beet in the U.K. by matching the scale of control with the spatial and temporal scales of the disease; and analysis of evolutionary change in virus control to identify risks of inadvertent selection for damaging virus strains.
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Affiliation(s)
- Christopher A Gilligan
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom.
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Arguello-Astorga G, Ascencio-Ibáñez JT, Dallas MB, Orozco BM, Hanley-Bowdoin L. High-frequency reversion of geminivirus replication protein mutants during infection. J Virol 2007; 81:11005-15. [PMID: 17670823 PMCID: PMC2045516 DOI: 10.1128/jvi.00925-07] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The geminivirus replication protein AL1 interacts with retinoblastoma-related protein (RBR), a key regulator of the plant division cell cycle, to induce conditions permissive for viral DNA replication. Previous studies of tomato golden mosaic virus (TGMV) AL1 showed that amino acid L148 in the conserved helix 4 motif is critical for RBR binding. In this work, we examined the effect of an L148V mutation on TGMV replication in tobacco cells and during infection of Nicotiana benthamiana plants. The L148V mutant replicated 100 times less efficiently than wild-type TGMV in protoplasts but produced severe symptoms that were delayed compared to those of wild-type infection in plants. Analysis of progeny viruses revealed that the L148V mutation reverted at 100% frequency in planta to methionine, leucine, isoleucine, or a second-site mutation depending on the valine codon in the initial DNA sequence. Similar results were seen with another geminivirus, cabbage leaf curl virus (CaLCuV), carrying an L145A mutation in the equivalent residue. Valine was the predominant amino acid recovered from N. benthamiana plants inoculated with the CaLCuV L145A mutant, while threonine was the major residue in Arabidopsis thaliana plants. Together, these data demonstrated that there is strong selection for reversion of the TGMV L148V and CaLCuV L145A mutations but that the nature of the selected revertants is influenced by both the viral background and host components. These data also suggested that high mutation rates contribute to the rapid evolution of geminivirus genomes in plants.
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Affiliation(s)
- Gerardo Arguello-Astorga
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, USA
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