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Mubin M, Shabbir A, Nahid N, Liaqat I, Hassan M, Aljarba NH, Qahtani AA, Fauquet CM, Ye J, Nawaz-ul-Rehman MS. Patterns of Genetic Diversity among Alphasatellites Infecting Gossypium Species. Pathogens 2022; 11:pathogens11070763. [PMID: 35890008 PMCID: PMC9319557 DOI: 10.3390/pathogens11070763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/30/2022] [Accepted: 07/03/2022] [Indexed: 02/04/2023] Open
Abstract
Alphasatellites are small single-stranded circular DNA molecules associated with geminiviruses and nanoviruses. In this study, a meta-analysis of known alphasatellites isolated from the genus Gossypium (cotton) over the last two decades was performed. The phylogenetic and pairwise sequence identity analysis suggested that cotton-infecting begomoviruses were associated with at least 12 different alphasatellites globally. Three out of twelve alphasatellite were associated with cotton leaf curl geminiviruses but were not isolated from cotton plants. The cotton leaf curl Multan alphasatellite, which was initially isolated from cotton, has now been reported in several plant species, including monocot plants such as sugarcane. Our recombination analysis suggested that four alphasatellites, namely cotton leaf curl Lucknow alphasatellites, cotton leaf curl Multan alphasatellites, Ageratum yellow vein Indian alphasatellites and Ageratum enation alphasatellites, evolved through recombination. Additionally, high genetic variability was detected among the cotton-infecting alphasatellites at the genome level. The nucleotide substitution rate for the replication protein of alphasatellites (alpha-Rep) was estimated to be relatively high (~1.56 × 10−3). However, unlike other begomoviruses and satellites, the first codon position of alpha-Rep rapidly changed compared to the second and third codon positions. This study highlights the biodiversity and recombination of alphasatellites associated with the leaf curl diseases of cotton crops.
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Affiliation(s)
- Muhammad Mubin
- Virology Lab, CABB University of Agriculture, Jail Road, Faisalabad 38000, Pakistan; (M.M.); (A.S.); (M.H.)
| | - Arzoo Shabbir
- Virology Lab, CABB University of Agriculture, Jail Road, Faisalabad 38000, Pakistan; (M.M.); (A.S.); (M.H.)
| | - Nazia Nahid
- Department of Bioinformatics and Biotechnology, GC University Faisalabad, Faisalabad 38000, Pakistan;
| | - Iram Liaqat
- Microbiology Laboratory, Department of Zoology, GC University Lahore, Lahore 54000, Pakistan;
| | - Muhammad Hassan
- Virology Lab, CABB University of Agriculture, Jail Road, Faisalabad 38000, Pakistan; (M.M.); (A.S.); (M.H.)
| | - Nada H. Aljarba
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia;
| | - Ahmed Al Qahtani
- Department of Infection and Immunity, Research Center, King FaisaI Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia;
- Department of Microbiology and Immunology, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | | | - Jian Ye
- Laboratory of Vector-Borne Diseases, State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Muhammad Shah Nawaz-ul-Rehman
- Virology Lab, CABB University of Agriculture, Jail Road, Faisalabad 38000, Pakistan; (M.M.); (A.S.); (M.H.)
- Correspondence:
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Srivastava A, Gupta T, Srivastava S, Dhir S, Kumar P, Singhal T, Rani A, Rishi N. Development of a new Collateral Cleavage-independent CRISPR/Cas12a based easy detection system for plant viruses. J Virol Methods 2021; 300:114432. [PMID: 34919973 DOI: 10.1016/j.jviromet.2021.114432] [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: 09/11/2021] [Revised: 12/07/2021] [Accepted: 12/13/2021] [Indexed: 11/17/2022]
Abstract
Plant virus spread through various means, from mechanically to the insect vectors and act as obligate parasite, therefore, are extremely challenging to eradicate. Geminiviruses are an important class of viruses which have reported extensively in last two decades on several new hosts. They infect wide range of annual crops and perineal shrubs, therefore, essentially required to detect them on field and dispose to check their vector transmission to healthy crops. In this study, we have chosen two important begomovirus viz. Mungbean yellow mosaic India virus which infect wide range of leguminous crops while Ageratum enation virus is reported to infect a wide range of crops from weed to opium poppy. Here, we have utilized the binding and cleaving ability of LbaCas12a protein with target to detect the virus infection on field. We proposed here a new Collateral Cleavage Independent CRISPR/Cas12a based detection system (CCI-CRISPR) for plant viruses.
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Affiliation(s)
- Ashish Srivastava
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, 201313, India.
| | - Taruna Gupta
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, 201313, India
| | - Sonal Srivastava
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, 201313, India
| | - Sunny Dhir
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, 201313, India
| | - Prashant Kumar
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, 201313, India
| | - Tripti Singhal
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, 201313, India
| | - Asha Rani
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, 201313, India
| | - Narayan Rishi
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, 201313, India
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Construction of Infectious Clones of Begomoviruses: Strategies, Techniques and Applications. BIOLOGY 2021; 10:biology10070604. [PMID: 34209952 PMCID: PMC8301103 DOI: 10.3390/biology10070604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 11/24/2022]
Abstract
Simple Summary Begomovirus has a wide host range and threatens a significant amount of economic damage to many important crops such as tomatoes, beans, cassava, squash and cotton. There are many efforts directed at controlling this disease including the use of insecticides to control the insect vector as well as screening the resistant varieties. The use of synthetic virus or infectious clones approaches has allowed plant virologists to characterize and exploit the genome virus at the molecular and biological levels. By exploiting the DNA of the virus using the infectious clones strategy, the viral genome can be manipulated at specific regions to study functional genes for host–virus interactions. Thus, this review will provide an overview of the strategy to construct infectious clones of Begomovirus. The significance of established infectious clones in Begomovirus study will also be discussed. Abstract Begomovirus has become a potential threat to the agriculture sector. It causes significant losses to several economically important crops. Given this considerable loss, the development of tools to study viral genomes and function is needed. Infectious clones approaches and applications have allowed the direct exploitation of virus genomes. Infectious clones of DNA viruses are the critical instrument for functional characterization of the notable and newly discovered virus. Understanding of structure and composition of viruses has contributed to the evolution of molecular plant pathology. Therefore, this review provides extensive guidelines on the strategy to construct infectious clones of Begomovirus. Also, this technique’s impacts and benefits in controlling and understanding the Begomovirus infection will be discussed.
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Rishishwar R, Dasgupta I. Suppressors of RNA silencing encoded by geminiviruses and associated DNA satellites. Virusdisease 2019; 30:58-65. [PMID: 31143832 PMCID: PMC6517462 DOI: 10.1007/s13337-018-0418-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 01/05/2018] [Indexed: 12/31/2022] Open
Abstract
In plants, RNA silencing provides a major line of defence against viruses. This antiviral immunity involves production of virus-derived small interfering RNAs (vsiRNAs) and results in specific silencing of viruses by vsiRNAs-guided effector complexes. As a counterattack against RNA silencing, many plant viruses encode suppressors of RNA silencing called viral suppressors of RNA silencing (VSRs), which interfere with the silencing pathway by various mechanisms. This review describes various methods that are being used to characterize viral proteins for suppressor function, VSRs found in geminiviruses and associated DNA satellites and their mechanisms of action.
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Affiliation(s)
- Rashmi Rishishwar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021 India
| | - Indranil Dasgupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021 India
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Jeske H. Barcoding of Plant Viruses with Circular Single-Stranded DNA Based on Rolling Circle Amplification. Viruses 2018; 10:E469. [PMID: 30200312 PMCID: PMC6164888 DOI: 10.3390/v10090469] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 08/28/2018] [Accepted: 08/30/2018] [Indexed: 01/10/2023] Open
Abstract
The experience with a diagnostic technology based on rolling circle amplification (RCA), restriction fragment length polymorphism (RFLP) analyses, and direct or deep sequencing (Circomics) over the past 15 years is surveyed for the plant infecting geminiviruses, nanoviruses and associated satellite DNAs, which have had increasing impact on agricultural and horticultural losses due to global transportation and recombination-aided diversification. Current state methods for quarantine measures are described to identify individual DNA components with great accuracy and to recognize the crucial role of the molecular viral population structure as an important factor for sustainable plant protection.
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Affiliation(s)
- Holger Jeske
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart, Germany.
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Srivastava A, Agrawal L, Raj R, Jaidi M, Raj SK, Gupta S, Dixit R, Singh PC, Tripathi T, Sidhu OP, Singh BN, Shukla S, Chauhan PS, Kumar S. Ageratum enation virus Infection Induces Programmed Cell Death and Alters Metabolite Biosynthesis in Papaver somniferum. FRONTIERS IN PLANT SCIENCE 2017; 8:1172. [PMID: 28729873 PMCID: PMC5498505 DOI: 10.3389/fpls.2017.01172] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 06/19/2017] [Indexed: 05/06/2023]
Abstract
A previously unknown disease which causes severe vein thickening and inward leaf curl was observed in a number of opium poppy (Papaver somniferum L.) plants. The sequence analysis of full-length viral genome and associated betasatellite reveals the occurrence of Ageratum enation virus (AEV) and Ageratum leaf curl betasatellite (ALCB), respectively. Co-infiltration of cloned agroinfectious DNAs of AEV and ALCB induces the leaf curl and vein thickening symptoms as were observed naturally. Infectivity assay confirmed this complex as the cause of disease and also satisfied the Koch's postulates. Comprehensive microscopic analysis of infiltrated plants reveals severe structural anomalies in leaf and stem tissues represented by unorganized cell architecture and vascular bundles. Moreover, the characteristic blebs and membranous vesicles formed due to the virus-induced disintegration of the plasma membrane and intracellular organelles were also present. An accelerated nuclear DNA fragmentation was observed by Comet assay and confirmed by TUNEL and Hoechst dye staining assays suggesting virus-induced programmed cell death. Virus-infection altered the biosynthesis of several important metabolites. The biosynthesis potential of morphine, thebaine, codeine, and papaverine alkaloids reduced significantly in infected plants except for noscapine whose biosynthesis was comparatively enhanced. The expression analysis of corresponding alkaloid pathway genes by real time-PCR corroborated well with the results of HPLC analysis for alkaloid perturbations. The changes in the metabolite and alkaloid contents affect the commercial value of the poppy plants.
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Affiliation(s)
- Ashish Srivastava
- Plant Molecular Virology Laboratory, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
- Amity Institute of Virology and Immunology, Amity UniversityNoida, India
| | - Lalit Agrawal
- Division of Plant Microbe Interaction, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
| | - Rashmi Raj
- Plant Molecular Virology Laboratory, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
| | - Meraj Jaidi
- Plant Molecular Virology Laboratory, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
| | - Shri K. Raj
- Plant Molecular Virology Laboratory, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
| | - Swati Gupta
- Division of Plant Microbe Interaction, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
| | - Ritu Dixit
- Division of Plant Microbe Interaction, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
| | - Poonam C. Singh
- Division of Plant Microbe Interaction, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
| | - Tusha Tripathi
- Division of Phytochemistry, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
| | - Om P. Sidhu
- Division of Phytochemistry, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
| | - Brahma N. Singh
- Division of Pharmacognosy and Ethnopharmacology, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
| | - Sudhir Shukla
- Plant Breeding Laboratory, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
| | - Puneet S. Chauhan
- Division of Plant Microbe Interaction, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
| | - Susheel Kumar
- Plant Molecular Virology Laboratory, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
- *Correspondence: Susheel Kumar,
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Srivastava A, Kumar S, Raj SK. Molecular Characterization of a Begomovirus and Betasatellite Causing Yellow Vein Net Disease of Ageratum houstonianum. PLANT DISEASE 2015; 99:627-631. [PMID: 30699689 DOI: 10.1094/pdis-03-14-0333-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Ageratum houstonianum was introduced in India as an annual ornamental plant and is grown in beds for blue head flowers. Yellow vein net disease was observed on A. houstonianum plants with about 9.0% disease incidence during a survey in February 2012 at gardens of NBRI, Lucknow, India. Association of a begomovirus and betasatellite with the disease was characterized based on sequence analyses of their cloned full length genome isolated from diseased A. houstonianum. Sequence analysis of the begomovirus showed presence of the six open reading frames in its genome, similar to the arrangement of Old World begomoviruses. The begomoviral genome shared 95 to 97% sequence identities with various strains of Ageratum enation virus (AEV); however, it showed distinct phylogenetic relationships with them, and hence was identified as a variant of AEV based on more than 94% sequence homology, the criteria defined by ICTV. The sequence analysis of associated betasatellite revealed highest 93% sequence identity and close phylogenetic relationships with Ageratum leaf curl betasatellite (ALCB) molecules; therefore, it was identified as an isolate of ALCB (based on 93% sequence homology). Agroinfiltration of partial dimers of the AEV variant and ALCB induced similar systemic yellow vein net and leaf curl symptoms on A. houstonianum when infiltrated in combination, fulfilling Koch's postulates. Characterization of AEV and ALCB causing yellow vein net disease of A. houstonianum is being reported for the first time.
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Affiliation(s)
- Ashish Srivastava
- Plant Molecular Virology Laboratory, CSIR-National Botanical Research Institute (NBRI), Rana Pratap Marg, Lucknow 226001, India
| | - Susheel Kumar
- Plant Molecular Virology Laboratory, CSIR-National Botanical Research Institute (NBRI), Rana Pratap Marg, Lucknow 226001, India
| | - Shri Krishna Raj
- Plant Molecular Virology Laboratory, CSIR-National Botanical Research Institute (NBRI), Rana Pratap Marg, Lucknow 226001, India
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Srivastava A, Kumar S, Jaidi M, Raj SK. Characterization of a novel begomovirus associated with yellow mosaic disease of three ornamental species of Jatropha grown in India. Virus Res 2015; 201:41-9. [PMID: 25720372 DOI: 10.1016/j.virusres.2015.02.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 02/10/2015] [Accepted: 02/14/2015] [Indexed: 11/30/2022]
Abstract
Severe yellow mosaic disease was observed in three ornamental species of Jatropha: J. integerrima, J. podagrica and J. multifida grown in gardens at Lucknow, India, during a survey in 2013. The causal pathogen was successfully transmitted from diseased to healthy plants of these species by whitefly (Bemisia tabaci). The infection of begomovirus was initially detected in naturally infected plant samples by PCR using begomovirus universal primers. The begomovirus was characterized having a monopartite genome based on sequence analyses of the cloned ∼2.9kb DNA-A genome amplified by rolling circle amplification using Phi-29 DNA polymerase. The genome contained 2844 nucleotides that could be translated into seven potential open reading frames. The nucleotide sequences of DNA-A genome of the begomovirus isolates: JI (KC513823), JP (KF652078) and JM (KF652077) shared 94-95% identities together and 93-95% identities with an uncharacterized begomovirus isolated from J. curcas (the only sequences available in GenBank database as GU451249 and EU798996 under the name jatropha leaf curl virus). These shared highest identity of 61% and highly distant phylogenetic relationships with other begomoviruses reported worldwide. Based on 61% sequence identities (much less than 89%, the species demarcation criteria for a new begomovirus) the isolates under study were identified as members of a new Begomovirus species for which the name was proposed as "Jatropha mosaic Lucknow virus (JMLV)". The recombination analysis also suggested that JMLV was not a recombinant species, hence considered as unidentified Begomovirus species. Koch's postulates were also established by agroinfiltration assay of agroinfectious clone of JMLV. Characterization of JMLV associated with yellow mosaic disease of J. integerrima, J. podagrica and J. multifida is being reported for the first time.
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Affiliation(s)
- Ashish Srivastava
- Plant Molecular Virology, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, Uttar Pradesh, India
| | - Susheel Kumar
- Plant Molecular Virology, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, Uttar Pradesh, India
| | - Meraj Jaidi
- Plant Molecular Virology, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, Uttar Pradesh, India
| | - Shri Krishna Raj
- Plant Molecular Virology, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, Uttar Pradesh, India.
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