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Venkataravanappa V, Ashwathappa KV, Hiremath S, Manjunatha L, Shankarappa KS, Krishna Reddy M, Lakshminarayana Reddy CN. Begomovirus and DNA-satellites association with mosaic and leaf curl disease of Solanum nigrum and Physalis minima: the new hosts for chilli leaf curl virus. Virusdisease 2023; 34:504-513. [PMID: 38046062 PMCID: PMC10686937 DOI: 10.1007/s13337-023-00850-x] [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: 07/05/2023] [Accepted: 11/03/2023] [Indexed: 12/05/2023] Open
Abstract
The numerous plants of Solanum nigrum L, and Physalis minima L, well-known weeds with medicinal properties in agriculture and horticulture crops exhibiting severe mosaic, enation and leaf curl symptoms, were collected from the Varanasi and Mirzapur districts of Uttar Pradesh, India. The begomovirus infection in S. nigrum and P. minima was validated by PCR using virus-specific primers. The whole genome of the represented isolate of S. nigrum (SN1), P. minima (PM1), and beta satellite was amplified, cloned and sequenced. The SDT analysis showed that the DNA-A of PM1 and SN1 isolate showed the highest nt identity of 87.4 to 99.1%, with several chilli leaf curl virus (ChiLCuV) isolates from India and Oman, respectively. The betasatellite sequence (PM1β) obtained from the PM1 isolate showed a very low identity of 83.1-84.5%. A demarcation threshold of 91% for betasatellite species delineation has led to identifying a new betasatellite in the PM1 sample. This unique betasatellite has been named "physalis minima leaf curl betasatellite," indicating its novelty with the plant. Whereas, betasatellite sequence (SN1β) obtained from the SN1 sample showed 86.8-91.2% nucleotide identity with ChiLCB isolates infecting several crops in Indian subcontinents. The RDP analysis of the viral genome and betasatellite of SN1 and PM1 isolates revealed recombination in substantial portions of their genetic makeup, which appeared to have originated from pre-existing begomoviruses known to infect diverse host species. The present research also highlights the potential role of these plants as significant reservoir hosts for ChiLCuV in chili plants. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-023-00850-x.
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Affiliation(s)
- V. Venkataravanappa
- Division of Crop Protection, Central Horticultural Experimental Station (CHES), ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Chettalli, Madikeri District, Bengaluru, Karnataka 560089 India
- Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences, GKVK, Bengaluru, Karnataka 560065 India
| | - K. V. Ashwathappa
- Division of Crop Protection, Central Horticultural Experimental Station (CHES), ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Chettalli, Madikeri District, Bengaluru, Karnataka 560089 India
| | - Shridhar Hiremath
- Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences, GKVK, Bengaluru, Karnataka 560065 India
- Centre for Infectious Diseases, CSIR- North East Institute of Science and Technology, Jorhat, Assam 785006 India
| | - L. Manjunatha
- Crop Protection, Indian Institute of Horticultural Research, Bangalore, India
| | - K. S. Shankarappa
- Department of Plant Pathology, College of Horticulture, Bengaluru, 560 065 India
- University of Horticultural Sciences, Bagalkot, Karnataka India
| | - M. Krishna Reddy
- Division of Crop Protection, Central Horticultural Experimental Station (CHES), ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Chettalli, Madikeri District, Bengaluru, Karnataka 560089 India
| | - C. N. Lakshminarayana Reddy
- Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences, GKVK, Bengaluru, Karnataka 560065 India
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Vignesh S, Renukadevi P, Nagendran K, Senthil N, Kumar RV, SwarnaPriya R, Behera TK, Karthikeyan G. A distinct strain of tomato leaf curl New Delhi virus that causes mosaic disease in ash gourd and other cucurbitaceous crops. Front Microbiol 2023; 14:1268333. [PMID: 37965544 PMCID: PMC10641021 DOI: 10.3389/fmicb.2023.1268333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/05/2023] [Indexed: 11/16/2023] Open
Abstract
Ash gourd (Benincasa hispida) is a cucurbitaceous crop cultivated as an edible vegetable rich in vitamins, minerals, dietary fibers and antioxidants. In a field survey conducted in the Udumalpet region of Tamil Nadu during 2019, the incidence of mosaic disease on ash gourd crop was observed to be 75%. The DNA-A and DNA-B components of begomovirus genome have been identified as associated with this disease. Both the cloned DNA-A and DNA-B genomic components shared highest pairwise sequence identities with the isolates of tomato leaf curl New Delhi virus (ToLCNDV), a bipartite begomovirus. Recombinant analysis showed that both the components are possibly evolved through intra-species recombination between ToLCNDV isolates. Tomato leaf curl Bangladesh betasatellite (ToLCBB) is not naturally associated with this sample. The results of infectivity studies on ash gourd and other cucurbitaceous crops demonstrates the Koch's postulates, when co-inoculation of DNA-A and DNA-B of ToLCNDV was undertaken. However, the inoculation of non-cognate ToLCBB along with DNA-A and DNA-B enhances the symptom expression and reduces the time taken for symptom development. Thus, Koch's postulates were proved for these virus complexes on cucurbitaceous crops. Furthermore, an enhanced accumulation of DNA-A component was detected in the cucurbits co-inoculated with ToLCNDV and ToLCBB. This report highlights the importance of investigating the spread of these disease complexes with other cucurbitaceous crops in India.
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Affiliation(s)
- S. Vignesh
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - P. Renukadevi
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - K. Nagendran
- Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - N. Senthil
- Department of Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - R. Vinoth Kumar
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - R. SwarnaPriya
- Floriculture Research Station, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | | | - G. Karthikeyan
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
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Nalla MK, Schafleitner R, Pappu HR, Barchenger DW. Current status, breeding strategies and future prospects for managing chilli leaf curl virus disease and associated begomoviruses in Chilli ( Capsicum spp.). FRONTIERS IN PLANT SCIENCE 2023; 14:1223982. [PMID: 37936944 PMCID: PMC10626458 DOI: 10.3389/fpls.2023.1223982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/09/2023] [Indexed: 11/09/2023]
Abstract
Chilli leaf curl virus disease caused by begomoviruses, has emerged as a major threat to global chilli production, causing severe yield losses and economic harm. Begomoviruses are a highly successful and emerging group of plant viruses that are primarily transmitted by whiteflies belonging to the Bemisia tabaci complex. The most effective method for mitigating chilli leaf curl virus disease losses is breeding for host resistance to Begomovirus. This review highlights the current situation of chilli leaf curl virus disease and associated begomoviruses in chilli production, stressing the significant issues that breeders and growers confront. In addition, the various breeding methods used to generate begomovirus resistant chilli cultivars, and also the complicated connections between the host plant, vector and the virus are discussed. This review highlights the importance of resistance breeding, emphasising the importance of multidisciplinary approaches that combine the best of traditional breeding with cutting-edge genomic technologies. subsequently, the article highlights the challenges that must be overcome in order to effectively deploy begomovirus resistant chilli varieties across diverse agroecological zones and farming systems, as well as understanding the pathogen thus providing the opportunities for improving the sustainability and profitability of chilli production.
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Affiliation(s)
- Manoj Kumar Nalla
- World Vegetable Center, South and Central Asia Regional Office, Hyderabad, India
| | | | - Hanu R. Pappu
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
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Mo C, Tang Y, Chen J, Cui L, Xie H, Qin B, Cai J, Li Z. Characteristics of the Complete Genome of Ageratum Yellow Vein China Virus Infecting Sonchus oleraceus. PLANT DISEASE 2023; 107:2944-2948. [PMID: 37125842 DOI: 10.1094/pdis-11-22-2688-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Sonchus (Sonchus oleraceus) originated from Europe and is now cultivated worldwide. The wild resources of sonchus are very abundant, and it has rich nutritional and medicinal value. In this study, 15 sonchus samples with typical symptoms showing leaf curling, vein thickening, and enations were collected from Guigang and Baise City of Guangxi, China. Diseased sonchus were identified by PCR detection, whole genome sequence amplification, and phylogenetic and recombination analysis. The results showed that all the samples were confirmed infected by begomoviruses, and three full-length viral genomes were obtained from 15 sonchus, named GG7-13, GG8-6, and BS63-5. The full genome lengths were 2,584, 2,735, and 2,746 nt, respectively. The nucleotide identities among the three isolates ranged from 92.67 to 99.93%. All of them shared the highest identities (greater than 91.69%) with other isolates of ageratum yellow vein China virus (AYVCNV) (available on GenBank). According to the guidelines of classification of begomoviruses, the virus isolates obtained in this study are different isolates of AYVCNV; a phylogenetic tree analysis showed that these isolates formed a large branch with three other Guangxi isolates of AYVCNV, indicating their close evolution. The genome structures of GG8-6 and BS63-5 are consistent with the monopartite genome virus of the begomoviruses, and both have six open reading frames (ORFs), while GG7-13 has a 151-nt deletion between C2 and C3, resulting in a mutant strain of only five ORFs. This study is the first report on S. oleraceus infected by ageratum yellow vein China virus.
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Affiliation(s)
- Cuiping Mo
- Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences; Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs; Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Nanning, Guangxi 530007, China
| | - Yafei Tang
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, Guangdong 510640, China
| | - Jinqing Chen
- Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences; Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs; Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Nanning, Guangxi 530007, China
| | - Lixian Cui
- Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences; Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs; Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Nanning, Guangxi 530007, China
| | - Huiting Xie
- Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences; Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs; Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Nanning, Guangxi 530007, China
| | - Bixia Qin
- Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences; Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs; Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Nanning, Guangxi 530007, China
| | - Jianhe Cai
- Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences; Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs; Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Nanning, Guangxi 530007, China
| | - Zhanbiao Li
- Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences; Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs; Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Nanning, Guangxi 530007, China
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Mastrochirico M, Spanò R, De Miccolis Angelini RM, Mascia T. Molecular Characterization of a Recombinant Isolate of Tomato Leaf Curl New Delhi Virus Associated with Severe Outbreaks in Zucchini Squash in Southern Italy. PLANTS (BASEL, SWITZERLAND) 2023; 12:2399. [PMID: 37446959 DOI: 10.3390/plants12132399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/07/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023]
Abstract
The molecular characterization of a tomato leaf curl New Delhi virus (ToLCNDV) isolate, denoted ToLCNDV-Le, is reported. The virus was associated with severe and recurrent outbreaks in protected crops of zucchini squash grown in the Province of Lecce (Apulia, southern Italy). The fully sequenced genome of ToLCNDV-Le consists of two genomic components named DNA-A and DNA-B of 2738 and 2683 nt in size, respectively. Like other ToLCNDV isolates, ToLCNDV-Le DNA-A contains the AV2 and AV1 open reading frames (ORFs) in the virion-sense orientation and five additional ORFs named AC1, AC2, AC3, AC4 and AC5 in the complementary-sense orientation. The DNA-B contains BV1 ORF in the virion-sense orientation and BC1 ORF in the complementary-sense orientation. No DNA betasatellites were found associated with ToLCNDV-Le in naturally infected samples. Phylogenetic analysis clustered ToLCNDV-Le with the ToLCNDV-ES strain of western Mediterranean Basin isolates. Consequently, the ToLCNDV-ES-[IT-Zu-Le18] name is proposed as the descriptor for ToLCNDV-Le. Using recombination detection program RDP4, one putative recombination breakpoint (Rbp) was identified close to nucleotide positions 2197-2727, covering approximately half of the AC1 region, including the AC4 ORF and the 3' UTR. RDP4 indicated the event represents an Rbp of an isolate similar to ToLCNDV [Pk-06] (Acc. No. EF620534) found in Luffa acutangula in Pakistan and identified as putative minor parent into the background of ToLCNDV [BG-Jes-Svr-05] (Acc. No. AJ875157), found in tomato in Bangladesh, and identified as putative major parent. To the best of our knowledge, this is the first report of a ToLCNDV-ES recombinant isolate in the AC1-AC4 region in Italy.
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Affiliation(s)
| | - Roberta Spanò
- Department of Soil, Plant and Food Sciences, University of Bari "Aldo Moro", 70126 Bari, Italy
| | | | - Tiziana Mascia
- Department of Soil, Plant and Food Sciences, University of Bari "Aldo Moro", 70126 Bari, Italy
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Khan A, Saeed ST, Sinha S, Yadav SS, Samad A. Identification and characterization of a novel begomovirus, Withania leaf curl virus associated with leaf curl disease of Withania somnifera. 3 Biotech 2023; 13:178. [PMID: 37188293 PMCID: PMC10175521 DOI: 10.1007/s13205-023-03606-y] [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: 12/09/2022] [Accepted: 05/03/2023] [Indexed: 05/17/2023] Open
Abstract
Begomovirus is the largest genus of the family Geminiviridae with wide host range and responsible for a considerable amount of economic damage to many important crops globally. Withania somnifera (Indian ginseng) is an important medicinal plant with high demand in pharmaceutical industries worldwide. During the routine survey in 2019, typical characteristic viral symptoms such as severe leaf curling, downward rolling of the leaves, vein clearing, and poor growth of Withania plants with 17-20% disease incidence were observed in Lucknow, India. Typical symptoms, abundant presence of whiteflies, PCR and RCA based detection indicated the amplification of ~ 2.7 kb and suspected the causal pathogen to be a begomovirus, associated with a betasatellite (~ 1.3 kb). Transmission electron microscopy revealed the presence of twinned particles of ~ 18-20 nm in diameter. Full genome sequencing (2758 bp) of the virus and its analysis showed only 88% sequence identity with the begomovirus sequences present in the database. Hence, based on the nomenclature guidelines we concluded that the virus associated with the present disease of W. somnifera is a novel begomovirus and its name is proposed as Withania leaf curl virus.
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Affiliation(s)
- Asifa Khan
- Plant Pathology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015 India
| | - Sana Tabanda Saeed
- Plant Pathology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015 India
| | - Soumya Sinha
- Plant Pathology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015 India
| | - Sujata Singh Yadav
- Plant Pathology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015 India
| | - Abdul Samad
- Plant Pathology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015 India
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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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Sangeeta, Kumar RV, Yadav BK, Bhatt BS, Krishna R, Krishnan N, Karkute SG, Kumar S, Singh B, Singh AK. Diverse begomovirus-betasatellite complexes cause tomato leaf curl disease in the western India. Virus Res 2023; 328:199079. [PMID: 36813240 DOI: 10.1016/j.virusres.2023.199079] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023]
Abstract
In the Indian sub-continent, tomato leaf curl disease (ToLCD) of tomato caused by begomoviruses has emerged as a major limiting factor for tomato cultivation. Despite the spread of this disease in the western India, a systematic study on the characterization of virus complexes with ToLCD is lacking. Here, we report the identification of a complex of begomoviruses including 19 DNA-A and 4 DNA-B as well as 15 betasatellites with ToLCD in the western part of the country. Additionally, a novel betasatellite and an alphasatellite were also identified. The recombination breakpoints were detected in the cloned begomoviruses and betasatellites. The cloned infectious DNA constructs cause disease on the tomato (a moderately virus-resistant cultivar) plants, thus fulfilling Koch's postulates for these virus complexes. Further, the role of non-cognate DNA B/betasatellite with ToLCD-associated begomoviruses on disease development was demonstrated. It also emphasizes the evolutionary potential of these virus complexes in breaking disease resistance and plausible expansion of its host range. This necessitates to investigate the mechanism of the interaction between resistance breaking virus complexes and the infected host.
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Affiliation(s)
- Sangeeta
- School of Life Sciences, Central University of Gujarat, Gandhinagar, Gujarat 382 030, India; Present address-Department of Science & Technology, Gujarat Council of Science & Technology, Gandhinagar, Gujarat 382 011, India
| | - R Vinoth Kumar
- Department of Biotechnology, College of Science & Humanities, SRM Institute of Science & Technology, Ramapuram, Chennai, Tamil Nadu 600 089, India
| | - Brijesh K Yadav
- School of Life Sciences, Central University of Gujarat, Gandhinagar, Gujarat 382 030, India; Faculty of Education and Methodology, Jayoti Vidyapeeth Women's University, Jaipur, Rajasthan 303 122, India
| | - Bhavin S Bhatt
- School of Life Sciences, Central University of Gujarat, Gandhinagar, Gujarat 382 030, India; Faculty of Science, Sarvajanik University, Surat, Gujarat 395 001, India
| | - Ram Krishna
- Crop Improvement Division, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221 305, India
| | - Nagendran Krishnan
- Crop Improvement Division, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221 305, India
| | - Suhas G Karkute
- Crop Improvement Division, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221 305, India
| | - Sudhir Kumar
- Crop Improvement Division, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221 305, India
| | - Bijendra Singh
- Crop Improvement Division, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221 305, India
| | - Achuit K Singh
- Crop Improvement Division, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221 305, India.
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Bupi N, Sangaraju VK, Phan LT, Lal A, Vo TTB, Ho PT, Qureshi MA, Tabassum M, Lee S, Manavalan B. An Effective Integrated Machine Learning Framework for Identifying Severity of Tomato Yellow Leaf Curl Virus and Their Experimental Validation. RESEARCH (WASHINGTON, D.C.) 2023; 6:0016. [PMID: 36930763 PMCID: PMC10013792 DOI: 10.34133/research.0016] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/07/2022] [Indexed: 01/13/2023]
Abstract
Tomato yellow leaf curl virus (TYLCV) dispersed across different countries, specifically to subtropical regions, associated with more severe symptoms. Since TYLCV was first isolated in 1931, it has been a menace to tomato industrial production worldwide over the past century. Three groups were newly isolated from TYLCV-resistant tomatoes in 2022; however, their functions are unknown. The development of machine learning (ML)-based models using characterized sequences and evaluating blind predictions is one of the major challenges in interdisciplinary research. The purpose of this study was to develop an integrated computational framework for the accurate identification of symptoms (mild or severe) based on TYLCV sequences (isolated in Korea). For the development of the framework, we first extracted 11 different feature encodings and hybrid features from the training data and then explored 8 different classifiers and developed their respective prediction models by using randomized 10-fold cross-validation. Subsequently, we carried out a systematic evaluation of these 96 developed models and selected the top 90 models, whose predicted class labels were combined and considered as reduced features. On the basis of these features, a multilayer perceptron was applied and developed the final prediction model (IML-TYLCVs). We conducted blind prediction on 3 groups using IML-TYLCVs, and the results indicated that 2 groups were severe and 1 group was mild. Furthermore, we confirmed the prediction with virus-challenging experiments of tomato plant phenotypes using infectious clones from 3 groups. Plant virologists and plant breeding professionals can access the user-friendly online IML-TYLCVs web server at https://balalab-skku.org/IML-TYLCVs, which can guide them in developing new protection strategies for newly emerging viruses.
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Affiliation(s)
- Nattanong Bupi
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
| | - Vinoth Kumar Sangaraju
- Computational Biology and Bioinformatics Laboratory, Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
| | - Le Thi Phan
- Computational Biology and Bioinformatics Laboratory, Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
| | - Aamir Lal
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
| | - Thuy Thi Bich Vo
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
| | - Phuong Thi Ho
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
| | - Muhammad Amir Qureshi
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
| | - Marjia Tabassum
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
| | - Sukchan Lee
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
| | - Balachandran Manavalan
- Computational Biology and Bioinformatics Laboratory, Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
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10
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Sattar MN, Khurshid M, El-Beltagi HS, Iqbal Z. Identification and estimation of sequence variation dynamics of Tomato Leaf curl Palampur virus and betasatellite complex infecting a new weed host. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2112911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Affiliation(s)
- Muhammad Naeem Sattar
- Central Laboratories, Department of Biotechnology, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Muhammad Khurshid
- School of Biochemistry and Biotechnology, Faculty of Life Sciences, University of the Punjab, Lahore, Pakistan
| | - Hossam S. El-Beltagi
- Department of Biotechnology, College of Agricultural and Food Sciences, King Faisal University, Al-Ahsa, Saudi Arabia
- Biochemistry Department, Faculty of Agriculture, Cairo University, Cairo, Egypt
| | - Zafar Iqbal
- Central Laboratories, Department of Biotechnology, King Faisal University, Al-Ahsa, Saudi Arabia
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11
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Multiple begomoviruses infecting soybean; a case study in Faisalabad, Pakistan. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01290-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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12
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Lal A, Kil EJ, Vo TTB, Wira Sanjaya IGNP, Qureshi MA, Nattanong B, Ali M, Shuja MN, Lee S. Interspecies Recombination-Led Speciation of a Novel Geminivirus in Pakistan. Viruses 2022; 14:v14102166. [PMID: 36298721 PMCID: PMC9612148 DOI: 10.3390/v14102166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 11/25/2022] Open
Abstract
Recombination between isolates of different virus species has been known to be one of the sources of speciation. Weeds serve as mixing vessels for begomoviruses, infecting a wide range of economically important plants, thereby facilitating recombination. Chenopodium album is an economically important weed spread worldwide. Here, we present the molecular characterization of a novel recombinant begomovirus identified from C. album in Lahore, Pakistan. The complete DNA- A genome of the virus associated with the leaf distortion occurred in the infected C. album plants was cloned and sequenced. DNA sequence analysis showed that the nucleotide sequence of the virus shared 93% identity with those of the rose leaf curl virus and the duranta leaf curl virus. Interestingly, this newly identified virus is composed of open reading frames (ORFs) from different origins. Phylogenetic networks and complementary recombination detection methods revealed extensive recombination among the sequences. The infectious clone of the newly detected virus was found to be fully infectious in C. album and Nicotiana benthamiana as the viral DNA was successfully reconstituted from systemically infected tissues of inoculated plants, thus fulfilling Koch's postulates. Our study reveals a new speciation of an emergent ssDNA plant virus associated with C. album through recombination and therefore, proposed the tentative name 'Chenopodium leaf distortion virus' (CLDV).
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Affiliation(s)
- Aamir Lal
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea
- Department of Plant Medicals, College of Life Sciences, Andong National University, Andong 36729, Korea
- Agricultural Science and Technology Research Institute, Andong National University, Andong 36729, Korea
| | - Eui-Joon Kil
- Department of Plant Medicals, College of Life Sciences, Andong National University, Andong 36729, Korea
| | - Thuy T. B. Vo
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea
| | | | - Muhammad Amir Qureshi
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea
| | - Bupi Nattanong
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea
| | - Muhammad Ali
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore 54770, Pakistan
| | - Malik Nawaz Shuja
- Department of Microbiology, Kohat University of Science and Technology, Kohat 26000, Pakistan
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea
- Correspondence:
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13
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Krishnan N, Reddy BR, Kumari S, Singh AK. Development of agro-infectious clones for screening resistance against recombinant mungbean yellow mosaic India virus causing golden mosaic disease in vegetable cowpea. 3 Biotech 2022; 12:145. [PMID: 35694238 DOI: 10.1007/s13205-022-03206-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 05/13/2022] [Indexed: 11/27/2022] Open
Abstract
Begomovirus associated with golden mosaic disease on vegetable cowpea has been characterized through rolling circle amplification. The genomic components (DNA A and DNA B) were cloned and sequenced. Nucleotide sequence analysis of DNA A (MT671430) and DNA B (MT671431) component had > 98% identity toward the mungbean yellow mosaic India virus (MYMIV) reported previously from India on various legumes. In phylogenetic analysis, study isolate shared common ancestry with MYMIV isolates of India, Pakistan and Nepal infecting legumes. Based on the recombination analysis, this cowpea isolate appears to be evolved through recombination of MYMIV sequences both at DNA A (Major parent: AF481855; Minor parent: AF416742) and DNA B (Major parent: AF416741; Minor parent: MN698281) level. Furthermore, Agrobacterium-based dimeric clone constructs were found highly infectious on cowpea host upon co-inoculation of DNA-A and DNA-B components by producing typical golden mosaic symptoms 42 days post-inoculation. Upon inoculation of these agro-infectious clones, vegetable cowpea germplasm lines were categorized as resistant, moderately resistant and susceptible to golden mosaic disease. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03206-2.
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Affiliation(s)
- Nagendran Krishnan
- Division of Crop Protection, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221305 India
| | - B Rajasekhar Reddy
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221305 India
| | - Shweta Kumari
- Division of Crop Protection, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221305 India
| | - Achuit Kumar Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221305 India
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14
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Venkataravanappa V, Vinaykumar HD, Hiremath S, Mantesh M, Shankarappa KS, Basha CRJ, Reddy MK, Reddy CNL. Molecular characterization of novel bipartite begomovirus associated with enation leaf disease of Garden croton (Codiaeum variegatum L.). Virusdisease 2022; 33:194-207. [DOI: 10.1007/s13337-022-00772-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 06/06/2022] [Indexed: 10/17/2022] Open
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15
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Nawaz-Ul-Rehman MS, Liaqat I, Nahid N, Saleem F, Alkahtani S, Al Qahtani A, Ye J, Mubin M. Alternanthera yellow vein virus (AYVV); a betasatellite independent begomovirus infecting Sonchus palustris in Pakistan. BRAZ J BIOL 2022; 82:e262248. [PMID: 35703634 DOI: 10.1590/1519-6984.262248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/13/2022] [Indexed: 11/22/2022] Open
Abstract
Satellites associated begomoviruses are the most diverse group of plant viruses in tropical and subtropical regions. In Pakistan, during field surveys in 2019-2020, Sonchus palustris (a weed plant) was observed showing begomovirus symptoms i.e., vein yellowing and mosaic patterns on leaves. Rolling circle amplification from total isolated DNA of symptomatic leaves was performed to amplify circular viral genomes. Subsequent cloning and sequencing showed that a new strain of Alternanthera yellow vein virus (AlYVV) is associated with vein yellowing disease of S. palustris. The identity percentage analysis through BLAST search and SDT analysis showed that the new strain is 94-98% identical to AlYVV isolates reported from Pakistan, India and China. In phylogenetic tree, it clustered with AlYVV-[PK:E prostrata:15-KX710155], AlYVV-[PK:E prostrata:13]-KX906697] and AlYVV-[PK:E prostrata:11]-KX906694] previously reported from Pakistan. There was no detectable level of betasatellite or any other satellite molecule in the samples studied here. Phylogenetic analysis of Rep and CP genes of AlYVV with corresponding genes of closely related viruses circulating in Southeast Asia showed intra-specific recombination involving both complementary and virion sense region of virus. Relaxed clock and Bayesian Skyline Plot analysis based on CP gene sequences indicated slight higher substitution rates (4.75 x 10-3 substitutions/nucleotide/year). In the Indian subcontinent satellite-associated monopartite begomoviruses predominately infect crops and non-crop plants. But AlYVV is found infecting mostly non-crop plants independent of satellite molecules. We hypothesize here that AlYVV evolved as a true monopartite begomovirus in the Indian sub-continent and could be a great threat to introduced crops under suitable conditions. Such studies are crucial to understand probable future epidemics of begomoviruses in the region.
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Affiliation(s)
- M S Nawaz-Ul-Rehman
- University of Agriculture, Centre of Agricultural Biochemistry and Biotechnology, Faisalabad, Pakistan
| | - I Liaqat
- GC University Lahore, Department of Zoology, Lahore, Pakistan
| | - N Nahid
- GC University Faisalabad, Department of Bioinformatics and Biotechnology, Faisalabad, Pakistan
| | - F Saleem
- University of Agriculture, Centre of Agricultural Biochemistry and Biotechnology, Faisalabad, Pakistan
| | - S Alkahtani
- King Saud University, College of Science, Department of Zoology, Riyadh, Saudi Arabia
| | - A Al Qahtani
- King Faisal Specialist Hospital and Research Center, Research Center, Department of Infection and Immunity, Riyadh, Saudi Arabia
| | - J Ye
- Chinese Academy of Sciences, Institute of Microbiology, Laboratory of Vector-Borne Diseases, State Key Laboratory of Plant Genomics, Beijing, PR China
| | - M Mubin
- University of Agriculture, Centre of Agricultural Biochemistry and Biotechnology, Faisalabad, Pakistan.,Chinese Academy of Sciences, Institute of Microbiology, Laboratory of Vector-Borne Diseases, State Key Laboratory of Plant Genomics, Beijing, PR China
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16
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Azeem H, Perveen R, Tahir MN, Umar UUD, Ölmez F, Ali A. Prevalence, transmission and molecular characterization of Cotton leaf curl Multan virus infecting hollyhock plants in Pakistan. Mol Biol Rep 2022; 49:5635-5644. [DOI: 10.1007/s11033-022-07557-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 05/03/2022] [Indexed: 11/30/2022]
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17
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Gawande SP, Raghavendra KP, Monga D, Nagrale DT, Prabhulinga T, Hiremani N, Meshram M, Kranthi S, Gokte-Narkhedkar N, Waghmare VN. Development of Loop Mediated Isothermal Amplification (LAMP): A new tool for rapid diagnosis of cotton leaf curl viral disease. J Virol Methods 2022; 306:114541. [PMID: 35568082 DOI: 10.1016/j.jviromet.2022.114541] [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: 12/17/2020] [Revised: 05/05/2022] [Accepted: 05/08/2022] [Indexed: 10/18/2022]
Abstract
Cotton leaf curl disease (CLCuD) ranks top among all endemic diseases transmitted by whitefly (Bemisia tabaci) affecting cotton (Gossypium hirsutum) causing severe economic losses to the cotton growers in the Indian subcontinent. For its effective management, robust tools for detection are a prerequisite and it is important to diagnose the virus titre in early stage of infection in plants as well as in the disease transmitting vector. Considering the limitations in current PCR-based techniques we have standardized rapid and sensitive Loop Mediated Isothermal Amplification (LAMP) protocol for the diagnosis of cotton leaf curl virus (CLCuV) in cotton leaves and in its transmitting vector whitefly. Perhaps, this is the first report of use of LAMP tool for rapid diagnosis of CLCuV in cotton and its transmitting vector the whitefly. Further, the colorimetric detection for diagnostic simplicity of amplified LAMP product by using different dyes lead to enhanced applicability of this technique in the field of disease diagnostics. The merit of present study is that the diagnostic failure of PCR and LAMP due to low virus titre in the infected leaf has been circumvented through the combination of rolling circle amplification (RCA) with LAMP. Thus RCA-LAMP can be an option for ultra-sensitive detection of samples with low virus titre. The potential applications of this advanced diagnostic tool in laboratory research on diagnosis of CLCuV, an important viral pathogen of cotton have been discussed.
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Affiliation(s)
- S P Gawande
- ICAR-Central Institute for Cotton Research (ICAR-CICR), Nagpur-440010, India.
| | - K P Raghavendra
- ICAR-Central Institute for Cotton Research (ICAR-CICR), Nagpur-440010, India
| | - D Monga
- ICAR- Central Institute for Cotton Research Regional Station (ICAR-CICR RS), Sirsa -125055, India
| | - D T Nagrale
- ICAR-Central Institute for Cotton Research (ICAR-CICR), Nagpur-440010, India
| | - T Prabhulinga
- ICAR-Central Institute for Cotton Research (ICAR-CICR), Nagpur-440010, India
| | - N Hiremani
- ICAR-Central Institute for Cotton Research (ICAR-CICR), Nagpur-440010, India
| | - M Meshram
- ICAR-Central Institute for Cotton Research (ICAR-CICR), Nagpur-440010, India
| | - Sandhya Kranthi
- Project Consultant, International Cotton Advisory Committee (ICAC), Washington DC, USA
| | | | - V N Waghmare
- ICAR-Central Institute for Cotton Research (ICAR-CICR), Nagpur-440010, India
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18
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Chowdary VT, Kumar VM, Varma PK, Selvarajan R, Balasubramanian V. New record of mungbean yellow mosaic India virus in Desmodium laxiflorum and association of bhendi yellow vein mosaic betasatellite in Abelmoschus moschatus in Andhra Pradesh, India. Virusdisease 2022; 33:119-121. [PMID: 35493751 PMCID: PMC9005597 DOI: 10.1007/s13337-021-00749-5] [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: 08/07/2021] [Accepted: 10/07/2021] [Indexed: 10/19/2022] Open
Abstract
Mungbean yellow mosaic India virus (MYMIV) is one of the most serious commonly occurring yellow mosaic virus (YMV's) group in majority of the pulses especially black gram and green gram in southern India compared to previously reported mungbean yellow mosaic virus. In January 2020 Desmodium laxiflorum and Abelmoscus moschatus showing mosaic symptoms and vein yellowing were collected from Guntur and Prakasam districts respectively in Andhra Pradesh. PCR analysis using MYMIV and betasatellite specific primers gave desired expected amplification from the infected samples of A. moschatus (YMV-ABEL) whereas only MYMIV specific amplification was obtained in D. laxiflorum (YMV-DES). However, no PCR amplification was obtained in respective healthy leaf samples of both plants. Sequence analysis showed that the CP sequence of YMV-ABEL and YMV-DES showed a similarity of 99.19% with MYMIV (KP677496) and 99.75% with MYMIV (JN181003) respectively. The full-length betasatellite (1356 bp) showed highest identity of 90% with bhendi yellow vein mosaic betasatellite (BYVMB) (GU111977). Phylogenetic analysis clustered the test isolates with south Indian isolates of MYMIV whereas the betasatellite sequence clustered with various isolates of BYVMB, tomato leaf curl New Delhi virus betasatellite and okra leaf curl betasatellite reported from India and Pakistan. To the best of our knowledge, this is the first report of a MYMIV in D. laxiflorum and A. moschatus and MYMIV betasatellite complex in A. moschatus.
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Affiliation(s)
- Vallabhaneni Tilak Chowdary
- Department of Plant Pathology, Agricultural College, Bapatla, Acharya N.G. Ranga Agricultural University, Guntur, Andhra Pradesh India
| | - V. Manoj Kumar
- Department of Plant Pathology, Agricultural College, Bapatla, Acharya N.G. Ranga Agricultural University, Guntur, Andhra Pradesh India
| | - P. Kishore Varma
- Department of Plant pathology, RARS, Anakapalle, Acharya N.G. Ranga Agricultural University, Guntur, Andhra Pradesh India
| | - R. Selvarajan
- ICAR National Research Centre for Banana, Thayanur Post, Tiruchirapalli, 620102 India
| | - V. Balasubramanian
- ICAR National Research Centre for Banana, Thayanur Post, Tiruchirapalli, 620102 India
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19
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Du M, Wang Y, Chen C, Li X, Feng R, Zhou X, Yang X. Molecular Characterization and Pathogenicity of a Novel Soybean-Infecting Monopartite Geminivirus in China. Viruses 2022; 14:341. [PMID: 35215936 PMCID: PMC8877103 DOI: 10.3390/v14020341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/31/2022] [Accepted: 02/06/2022] [Indexed: 02/06/2023] Open
Abstract
Soybean is a major legume crop that plays an important role in food production, industrial production, and animal husbandry. Here, we characterize a novel soybean-infecting monopartite geminivirus identified in China. Analysis of the contigs de novo assembled from sequenced small interfering RNAs, followed by PCR, cloning, and sequencing, the complete viral genome was determined to be 2782 nucleotides. The genome contains the conserved nonanucleotide sequence, TAATATTAC and other sequence features typical of the family Geminiviridae, and encodes two and four open reading frames in the virion-sense and the complementary-sense strands, respectively. Genome-wide pairwise identity analysis revealed that the novel virus shares less than 65.6% identity with previously characterized geminiviruses. Phylogenetic and recombination analysis indicated that this virus was placed in a unique taxon within the family Geminiviridae and potentially arose from recombination. An infectious clone of this virus was further constructed and its infectivity was tested in different species of plants. Successful infection and characteristic symptoms were observed in Glycine max, Nicotiana benthamiana, N. tabacum, N. glutinosa, and N. tabacum cv. Samsun plants. Taken together, this virus represents a member of an unclassified genus of the family Geminiviridae, for which the name soybean yellow leaf curl virus is proposed.
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Affiliation(s)
- Min Du
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (M.D.); (Y.W.); (C.C.); (R.F.)
| | - Yongzhi Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (M.D.); (Y.W.); (C.C.); (R.F.)
- Key Laboratory of Integrated Pest Management on Crops in Northeast, Ministry of Agriculture, Jilin Academy of Agricultural Sciences, Changchun 130033, China;
| | - Cheng Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (M.D.); (Y.W.); (C.C.); (R.F.)
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Institute of Plant Protection, Ministry of Agriculture, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Xiaoyu Li
- Key Laboratory of Integrated Pest Management on Crops in Northeast, Ministry of Agriculture, Jilin Academy of Agricultural Sciences, Changchun 130033, China;
| | - Runzi Feng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (M.D.); (Y.W.); (C.C.); (R.F.)
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (M.D.); (Y.W.); (C.C.); (R.F.)
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xiuling Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (M.D.); (Y.W.); (C.C.); (R.F.)
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20
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Jiang N, Gai X, Yin D, Zhang G, Lu C, Guo J, Ma J, Xia Z. Tobacco leaf curl Puer virus: a novel monopartite begomovirus infecting Nicotiana tabacum in China. Arch Virol 2022; 167:229-232. [PMID: 34652555 DOI: 10.1007/s00705-021-05267-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/26/2021] [Indexed: 10/20/2022]
Abstract
Begomoviruses (family Geminiviridae) cause serious diseases in many crops. In this study, we characterized a begomovirus isolated from a tobacco plant with leaf curl in Puer, Yunnan Province, China. Analysis of the viral genome obtained from a symptomatic Nicotiana tabacum plant showed that it belonged to a novel monopartite begomovirus. The genome (2741 nt) shared the highest nucleotide sequence identity (83.43%) with that of tomato yellow leaf curl Vietnam virus (TYLCVV). Based on the current taxonomic criteria of the International Committee on Taxonomy of Viruses, this virus, for which the name "tobacco leaf curl Puer virus" is proposed, represents a new species of begomovirus.
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Affiliation(s)
- Ning Jiang
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China.
| | - Xiaotong Gai
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Duan Yin
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Guanghai Zhang
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Canhua Lu
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Jian Guo
- Yunnan Tobacco Company, Honghe Branch, Honghe, 652399, Yunnan Province, China
| | - Junhong Ma
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Zhenyuan Xia
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
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21
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Lal A, Kim YH, Vo TTB, Wira Sanjaya IGNP, Ho PT, Byun HS, Choi HS, Kil EJ, Lee S. Identification of a Novel Geminivirus in Fraxinus rhynchophylla in Korea. Viruses 2021; 13:2385. [PMID: 34960653 PMCID: PMC8705360 DOI: 10.3390/v13122385] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/20/2021] [Accepted: 11/22/2021] [Indexed: 02/07/2023] Open
Abstract
Fraxinus rhynchophylla, common name ash, belongs to the family Oleaceae and is found in China, Korea, North America, the Indian subcontinent, and eastern Russia. It has been used as a traditional herbal medicine in Korea and various parts of the world due to its chemical constituents. During a field survey in March 2019, mild vein thickening (almost negligible) was observed in a few ash trees. High-throughput sequencing of libraries of total DNA from ash trees, rolling-circle amplification (RCA), and polymerase chain reaction (PCR) allowed the identification of a Fraxinus symptomless virus. This virus has five confirmed open reading frames along with a possible sixth open reading frame that encodes the movement protein and is almost 2.7 kb in size, with a nonanucleotide and stem loop structure identical to begomoviruses. In terms of its size and structure, this virus strongly resembles begomoviruses, but does not show any significant sequence identity with them. To confirm movement of the virus within the trees, different parts of infected trees were examined, and viral movement was successfully observed. No satellite molecules or DNA B were identified. Two-step PCR confirmed the virion and complementary strands during replication in both freshly collected infected samples of ash tree and Nicotiana benthamiana samples agro-inoculated with infectious clones. This taxon is so distantly grouped from other known geminiviruses that it likely represents a new geminivirus genus.
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Affiliation(s)
- Aamir Lal
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea; (A.L.); (T.T.B.V.); (I.G.N.P.W.S.); (P.T.H.)
| | - Yong-Ho Kim
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 55365, Korea; (Y.-H.K.); (H.-S.B.)
| | - Thuy Thi Bich Vo
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea; (A.L.); (T.T.B.V.); (I.G.N.P.W.S.); (P.T.H.)
| | | | - Phuong Thi Ho
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea; (A.L.); (T.T.B.V.); (I.G.N.P.W.S.); (P.T.H.)
| | - Hee-Seong Byun
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 55365, Korea; (Y.-H.K.); (H.-S.B.)
| | - Hong-Soo Choi
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 55365, Korea; (Y.-H.K.); (H.-S.B.)
| | - Eui-Joon Kil
- Department of Plant Medicals, Andong National University, Andong 36729, Korea
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea; (A.L.); (T.T.B.V.); (I.G.N.P.W.S.); (P.T.H.)
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22
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Palchoudhury S, Khare VK, Balram N, Bhattacharyya UK, Das S, Shukla P, Chakraborty P, Biswas KK. A multiplex polymerase chain reaction for the simultaneous detection of the virus and satellite components associated with cotton leaf curl begomovirus disease complex. J Virol Methods 2021; 300:114369. [PMID: 34813823 DOI: 10.1016/j.jviromet.2021.114369] [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: 03/11/2019] [Revised: 09/22/2021] [Accepted: 11/18/2021] [Indexed: 11/18/2022]
Abstract
Cotton leaf curl disease (CLCuD) is caused by a complex of several whiteflies (Bemisia tabaci Genn.)-transmitted begomovirus species, Cotton leaf curl Multan virus (CLCuMuV), Cotton leaf curl Kokhran virus (CLCuKoV) and Cotton leaf curl Alabad virus (CLCuAlV) by individual of mixed infection, associated with Cotton leaf curl Multan betasatellite (CLCuMB) and several alphasatellites. The disease causes major economic losses in cotton in the Indian subcontinent. For monitoring of epidemiology and development of management strategies of CLCuD, a quick, sensitive and effective method capable of detecting all the begomovirus, betasatellite and alphasatellite components associated with CLCuD is required. With this objective, a multiplex polymerase chain reaction (mPCR) assay was developed for the simultaneous detection of these three viral components associated with CLCuD of cotton. Primers for each component were designed based on the retrieved reference sequences from the GenBank. Each pair of primers, designed for each of the respective component, was evaluated for its sensitivity and specificity in both the component-specific simplex polymerase chain reaction (sPCR) and mPCR assay. This report identified three viral component-specific pairs of primers which, in all combinations, amplified simultaneously the CP gene (780 nts) of the begomovirus, the βC1gene (375 nts) of the betasatellite and the Rep gene (452 nts) of the alphasatellite associated with CLCuD in the mPCR assays. The amplified products specific to each component produced by these assays were identified based on their amplicon sizes, and the identities of the viral components amplified were confirmed by cloning and sequencing the amplicons obtained in the mPCR. The mPCR assay was validated using naturally CLCuD-affected cotton plants of the fields. This assay will be useful for rapid detection of CLCuD-associated begomovirus, betasatellite and alphasatellite DNA in field samples, extensive resistance screening in resistance breeding programme, and also monitoring epidemiology for detection of virus and its components when symptoms are mild or absent in the plant.
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Affiliation(s)
- S Palchoudhury
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - V K Khare
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - N Balram
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - U K Bhattacharyya
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - S Das
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - P Shukla
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - P Chakraborty
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - K K Biswas
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India.
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Natural occurrence of mesta yellow vein mosaic virus and DNA-satellites in ornamental sunflower ( Helianthus spp.) in Pakistan. Saudi J Biol Sci 2021; 28:6621-6630. [PMID: 34764778 PMCID: PMC8568841 DOI: 10.1016/j.sjbs.2021.07.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/07/2021] [Accepted: 07/11/2021] [Indexed: 11/23/2022] Open
Abstract
Weeds and ornamental plants serve as a reservoir for geminiviruses and contribute to their dissemination, genome recombination and/or satellite capture. Ornamental sunflower (Helianthus spp.) plants exhibiting mild leaf curl symptoms were subjected to begomovirus and DNA-satellites isolation. The full-length genome of the isolated begomovirus clone (Od1-A) showed 96.8% nucleotide (nt) sequence identity with mesta yellow vein mosaic virus (MeYVMV; accession no. FR772081) whereas, alphasatellite (Od1-a) and betasatellite (Od1-b) clones showed their highest nt sequence identities at 97.4% and 98.2% with ageratum enation alphasatellite (AEA; accession no. FR772085) and papaya leaf curl betasatellite (PaLCuB; accession. no. LN878112), respectively. The evolutionary relationships, average evolutionary divergence and the recombination events were also inferred. The MeYVMV exhibited 9.5% average evolutionary divergence and its CP and Rep had 9.3% and 12.2%, concomitantly; the alphasatellite and the betasatellite had 8.3% and 5.2%, respectively. The nt substitution rates (site-1 year−1) were found to be 6.983 × 10-04 and 5.702 × 10-05 in the CP and Rep of MeYVMV, respectively. The dN/dS ratio and the Tajima D value of MeYVMV CP demonstrated its possible role in host switching. The absolute quantification of the begomovirus demonstrated that mild symptoms might have a correlation with low virus titer. This is the first identification of MeYVMV and associated DNA-satellites from ornamental sunflower in Pakistan. The role of sequence divergence, recombination and importance of MeYVMV along with DNA-satellites in extending its host range is discussed.
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Alabi OJ, Diaz-Lara A, Erickson TM, Al Rwahnih M. Olea europaea geminivirus is present in a germplasm repository and in California and Texas olive (Olea europaea L.) groves. Arch Virol 2021; 166:3399-3404. [PMID: 34546432 DOI: 10.1007/s00705-021-05218-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 07/15/2021] [Indexed: 11/30/2022]
Abstract
Olea europaea geminivirus (OEGV) from olive accessions in Italy was characterized recently. OEGV was also detected during routine high-throughput sequencing screening of olive (cv. Leccino) material, and its complete bipartite genome segments were sequenced and shown to be 100% identical to those of the isolate from Italy. Using two pairs of newly designed primers targeting the AV1 and BV1 genes, OEGV was detected in randomly sampled olive trees from the U.S. Department of Agriculture National Clonal Germplasm Repository (USDA-NCGR) (21.4% or 6/28), commercial and residential settings in California (47.6% or 10/21), and an orchard in Texas (60% or 30/50). The cuttings for the USDA-NCGR-positive trees originated from the former Serbia and Montenegro, Spain, Italy, and Greece. Comparative analysis of the directly sequenced gene fragments from randomly selected samples showed that OEGV isolates from the different sources were 100% identical to each other. The results indicate that OEGV spread was likely facilitated by inadvertent movement of contaminated olive germplasm.
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Affiliation(s)
- Olufemi J Alabi
- Department of Plant Pathology and Microbiology, Texas A&M AgriLife Research and Extension Center, Weslaco, TX, 78596, USA
| | - Alfredo Diaz-Lara
- Department of Plant Pathology, University of California-Davis, Davis, CA, 95616, USA
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, 76130, Querétaro, Mexico
| | - Teresa M Erickson
- Department of Plant Pathology, University of California-Davis, Davis, CA, 95616, USA
| | - Maher Al Rwahnih
- Department of Plant Pathology, University of California-Davis, Davis, CA, 95616, USA.
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25
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Singh AK, Yadav BK, Krishna R, Kumar RV, Mishra GP, Karkute SG, Krishnan N, Seth T, Kumari S, Singh B, Singh PM, Singh J. Bhendi Yellow Vein Mosaic Virus and Bhendi Yellow Vein Mosaic Betasatellite Cause Enation Leaf Curl Disease and Alter Host Phytochemical Contents in Okra. PLANT DISEASE 2021; 105:2595-2600. [PMID: 33393356 DOI: 10.1094/pdis-12-20-2655-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Whitefly (Bemisia tabaci)-transmitted begomoviruses cause severe diseases in numerous economically important dicotyledonous plants. Okra enation leaf curl disease (OELCuD) has emerged as a serious threat to okra (Abelmoschus esculentus L. Moench) cultivation in the Indian subcontinent. This study reports the association of a monopartite begomovirus (bhendi yellow vein mosaic virus; BYVMV) and betasatellite (bhendi yellow vein mosaic betasatellite; BYVB) with OELCuD in the Mau region of Uttar Pradesh, India. The BYVMV alone inoculated Nicotiana benthamiana and A. esculentus cv. Pusa Sawani plants developed mild symptoms. Co-inoculation of BYVMV and BYVB resulted in a reduced incubation period, an increased symptom severity, and an enhanced BYVMV accumulation by Southern hybridization and quantitative real-time PCR. This is the first study that satisfies Koch's postulates for OELCuD in its natural host. Activities of various antioxidative enzymes were significantly increased in the virus-inoculated okra plants. Differential responses in various biochemical components (such as photosynthetic pigments, phenol, proline, and sugar) in diseased okra plants were observed. This change in phytochemical responses is significant in understanding its impact on virus pathogenesis and disease development.
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Affiliation(s)
- Achuit K Singh
- Indian Council of Agricultural Research, Indian Institute of Vegetable Research, Varanasi 221 305, Uttar Pradesh, India
| | - Brijesh K Yadav
- Indian Council of Agricultural Research, Indian Institute of Vegetable Research, Varanasi 221 305, Uttar Pradesh, India
| | - Ram Krishna
- Indian Council of Agricultural Research, Indian Institute of Vegetable Research, Varanasi 221 305, Uttar Pradesh, India
| | - R Vinoth Kumar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110 067, Delhi, India
| | - Gyan P Mishra
- Indian Council of Agricultural Research, Indian Institute of Vegetable Research, Varanasi 221 305, Uttar Pradesh, India
| | - Suhas G Karkute
- Indian Council of Agricultural Research, Indian Institute of Vegetable Research, Varanasi 221 305, Uttar Pradesh, India
| | - Nagendran Krishnan
- Indian Council of Agricultural Research, Indian Institute of Vegetable Research, Varanasi 221 305, Uttar Pradesh, India
| | - Tania Seth
- Indian Council of Agricultural Research, Indian Institute of Vegetable Research, Varanasi 221 305, Uttar Pradesh, India
| | - Shweta Kumari
- Indian Council of Agricultural Research, Indian Institute of Vegetable Research, Varanasi 221 305, Uttar Pradesh, India
| | - Bijendra Singh
- Indian Council of Agricultural Research, Indian Institute of Vegetable Research, Varanasi 221 305, Uttar Pradesh, India
| | - Prabhakar M Singh
- Indian Council of Agricultural Research, Indian Institute of Vegetable Research, Varanasi 221 305, Uttar Pradesh, India
| | - Jagdish Singh
- Indian Council of Agricultural Research, Indian Institute of Vegetable Research, Varanasi 221 305, Uttar Pradesh, India
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Jailani AAK, Kumar P, Shilpi S, Tarafdar J, Roy A, Mukherjee SK, Sanan-Mishra N, Mandal B. Genomic properties of allamanda leaf mottle distortion virus, a new begomovirus from golden trumpet (Allamanda cathartica) in India. Arch Virol 2021; 166:2905-2909. [PMID: 34383166 DOI: 10.1007/s00705-021-05179-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 05/31/2021] [Indexed: 11/25/2022]
Abstract
Golden trumpet (Allamanda cathartica) plants were observed to exhibit mottling and distortion symptoms on leaves. The genome of an associated begomovirus (Al-K1) was amplified by rolling-circle amplification, cloned, and sequenced. The viral genome consisted of two circular ssDNA molecules, and the organization of the ORFs was similar to those of DNA-A and DNA-B components of bipartite begomoviruses. The size of DNA-A (KC202818) and DNA-B (MG969497) of the begomovirus was 2772 and 2690 nucleotides, respectively. Sequence analysis revealed that the DNA-A and DNA-B components shared the highest sequence identity with duranta leaf curl virus (MN537564, 87.8%) and cotton leaf curl Alabad virus (MH760452, 81.0%), respectively. Interestingly, the Al-K1 isolate shared significantly less nucleotide sequence identity with allamanda leaf curl virus (EF602306, 71.6%), the only monopartite begomovirus reported previously in golden trumpet from China. Al-K1 shared less than 91% sequence identity with other begomoviruses, and hence, according to the latest ICTV guidelines for species demarcation of begomoviruses, Al-K1 is proposed to be a member of a new species, and we propose the name "allamanda leaf mottle distortion virus" (AllLMoDV-[IN-Al_K1-12]) for this virus. AllLMoDV was detected in various golden trumpet samples from different locations by PCR with specific primers based on the genome sequence determined in this study. Our study provides evidence of the occurrence of a new bipartite begomovirus in a perennial ornamental plant in India.
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Affiliation(s)
- A Abdul Kader Jailani
- 1Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012, India
- Plant RNAi Biology Group, ICGEB, New Delhi, 110067, India
| | - Pradeep Kumar
- 1Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - S Shilpi
- 1Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - J Tarafdar
- Department of Plant Pathology, Bidhan Chandra Krishi Viswa Vidyalaya, Mohanpur, West Bengal, India
| | - Anirban Roy
- 1Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | | | | | - Bikash Mandal
- 1Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012, India.
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Khan A, Imtiaz Y, Tahir M, Briddon RW. Complete genome sequence of hollyhock vein yellowing virus, a novel monopartite begomovirus infecting hollyhock in Pakistan. Arch Virol 2021; 166:2607-2610. [PMID: 34115211 DOI: 10.1007/s00705-021-05134-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/23/2021] [Indexed: 11/26/2022]
Abstract
Hollyhock (Alcea rosea, family Malvaceae) is an ornamental plant grown widely in gardens across South Asia. In a bed of ornamental plants near the village of Chakri (Punjab Province, Pakistan) in 2014, hollyhock plants showing two distinct symptom types were identified: yellow vein mosaic and leaf crumple. PCR amplification with universal primers amplified a begomovirus from separate nucleic acid extracts of single plants of each type but amplified a betasatellite only from the plant with the yellow vein mosaic symptoms. No potential begomovirus DNA B component or alphasatellite could be identified in either sample. After cloning, the genome sequences of two viruses, one from a plant of each symptom type, were determined and shown to share 99.9% nucleotide sequence identity with each other but less than 91% nucleotide sequence identity with all previously characterized begomoviruses, with the highest identity (90%) to an isolate of pedilanthus leaf curl virus (PeLCV). This indicates that the two hollyhock plants were infected with a newly identified begomovirus for which the name "hollyhock vein yellowing virus" (HoVYV) is proposed. HoVYV likely has a recombinant origin. The betasatellite showed the highest nucleotide sequence identity to an isolate of cotton leaf curl Multan betasatellite (CLCuMuB), a betasatellite associated with cotton leaf curl disease across Pakistan and northwestern India. These findings add to the diversity of known begomoviruses in South Asia and again highlight the role of hollyhock as a reservoir of the cotton leaf curl begomovirus betasatellite complex. The results also suggest that the yellow vein mosaic symptoms in hollyhock are due to the betasatellite rather than the virus.
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Affiliation(s)
- Azkia Khan
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Sector H-12, Islamabad, Pakistan
| | - Yaqoot Imtiaz
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Sector H-12, Islamabad, Pakistan
| | - Muhammad Tahir
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Sector H-12, Islamabad, Pakistan.
| | - Rob W Briddon
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
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Complete nucleotide sequence of a begomovirus associated with an alphasatellite and a betasatellite naturally infecting okra in Jordan. Arch Virol 2021; 166:2033-2036. [PMID: 33900467 DOI: 10.1007/s00705-021-05075-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 03/03/2021] [Indexed: 10/21/2022]
Abstract
The complete nucleotide sequences of a monopartite begomovirus and an associated alphasatellite and betasatellite isolated from naturally infected okra (Abelmoschus esculentus) plants originating from Jordan were determined. The sequences of the begomovirus, alphasatellite, and betasatellites were determined to be 2,764, 1,307, and 1,354 nucleotides in length, respectively. Sequence Demarcation Tool (SDT) and phylogenetic analysis revealed that the begomovirus isolate shared the highest (99.5-99.8%) nt sequence identity with isolates of cotton leaf curl Gezira virus (CLCuGeV), a begomovirus found to exclusively infect cotton in Africa, and recently, in Asia and the Middle East. The DNA sequences of the alphasatellite and betasatellite exhibited the highest nt sequence identity (98.7-98.9% and 92.2-95.3%, respectively) to cotton leaf curl Gezira alphasatellite and cotton leaf curl Gezira betasatellite, respectively. This is the first identification of an African begomovirus, associated with DNA satellites, infecting okra in Jordan.
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Complete genome sequence of a previously undescribed monopartite begomovirus and betasatellite infecting Malvastrum coromandelianum in Cambodia. Arch Virol 2021; 166:1789-1793. [PMID: 33811530 DOI: 10.1007/s00705-021-05016-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 01/12/2021] [Indexed: 10/21/2022]
Abstract
A previously undescribed monopartite begomovirus was identified in Kampot province, Cambodia, in Malvastrum coromandelianum plants exhibiting yellow vein symptoms characteristic of begomovirus infections. The apparently full-length viral component was cloned and sequenced following enrichment of circular DNA by rolling-circle amplification and restriction enzyme digestion. The genome of the virus was 2737 nucleotides in length (KP188831) and exhibited an organization like that of other monopartite begomoviruses, sharing the highest nucleotide sequence similarity (87.7% identity) with ageratum yellow vein virus (AM940137). A satellite molecule was amplified from total DNA by PCR amplification, using the betasatellite-specific primer pair β01/β02. The satellite molecule (1346 nt, KP188832) had structural characteristics like those of other betasatellites associated with begomoviruses and shared the highest nucleotide sequence similarity (84.8% identity) with malvastrum yellow vein betasatellite (MN205547). According to the criteria established for species demarcation for classification of begomoviruses (family Geminiviridae) and betasatellites (family Tolecusatellitidae), respectively, the virus isolate from M. coromandelianum in Cambodia is a previously undescribed novel monopartite begomovirus, for which the name "malvastrum yellow vein Cambodia virus" (MaYVCV) is proposed, and the betasatellite is a previously undescribed novel betasatellite, for which the name "malvastrum yellow vein Cambodia betasatellite" (MaYVKHB) is proposed.
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Sangeeta, Ranjan P, Kumar RV, Bhatt BS, Chahwala FD, Yadav BK, Patel S, Singh B, Singh AK. Two distinct monopartite begomovirus-betasatellite complexes in western India cause tomato leaf curl disease. Virus Res 2021; 295:198319. [PMID: 33508355 DOI: 10.1016/j.virusres.2021.198319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/06/2021] [Accepted: 01/18/2021] [Indexed: 10/22/2022]
Abstract
In India, begomovirus infection causing tomato leaf curl disease (ToLCD) is a major constraint for tomato productivity. Here, we have identified two distinct monopartite begomovirus and betasatellite complexes causing ToLCD in the western part of India. A new monopartite begomovirus (Tomato leaf curl Mumbai virus, ToLCMumV) and betasatellite (Tomato leaf curl Mumbai betasatellite, ToLCMumB) were isolated from the Mumbai sample. A distinct Tomato leaf curl Gandhinagar virus (ToLCGanV) and Tomato leaf curl Gandhinagar betasatellite (ToLCGanB) were identified from the Gandhinagar sample. Both of the cloned begomoviruses were recombinants. The demonstration of systemic infection caused by begomovirus (ToLCGanV or ToLCMumV) alone in N. benthamiana and tomato (a virus resistant variety) emphasizes that they were monopartite begomoviruses. Co-inoculation of cognate begomovirus and betasatellite reduces the incubation period and increases symptom severity. Thus, Koch's postulates were satisfied for these virus complexes. Further, an enhanced accumulation of ToLCGanV was detected in the presence of cognate ToLCGanB, however ToLCMumB did not influence the level of ToLCMumV in the agro-inoculated tomato plants. Our results indicate that the cloned viruses form potential virus resistance breaking disease complexes in India. This necessitates to investigate the spread of these disease complexes to major tomato growing regions in the country.
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Affiliation(s)
- Sangeeta
- School of Life Sciences, Central University of Gujarat, Gandhinagar, 382 030, Gujarat, India
| | - Punam Ranjan
- Department of Botany, Patna Science College, Patna University, Patna, 800 005, Bihar, India
| | - R Vinoth Kumar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110 067, India
| | - Bhavin S Bhatt
- School of Life Sciences, Central University of Gujarat, Gandhinagar, 382 030, Gujarat, India
| | - Fenisha D Chahwala
- School of Life Sciences, Central University of Gujarat, Gandhinagar, 382 030, Gujarat, India
| | - Brijesh K Yadav
- School of Life Sciences, Central University of Gujarat, Gandhinagar, 382 030, Gujarat, India
| | - Sunita Patel
- School of Life Sciences, Central University of Gujarat, Gandhinagar, 382 030, Gujarat, India
| | - Bijendra Singh
- Crop Improvement Division, ICAR-Indian Institute of Vegetable Research, Varanasi, 221 305, Uttar Pradesh, India
| | - Achuit K Singh
- Crop Improvement Division, ICAR-Indian Institute of Vegetable Research, Varanasi, 221 305, Uttar Pradesh, India.
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Ahmed N, Amin I, Zaidi SSEA, Rahman SU, Farooq M, Fauquet CM, Mansoor S. Circular DNA enrichment sequencing reveals the viral/satellites genetic diversity associated with the third epidemic of cotton leaf curl disease. Biol Methods Protoc 2021; 6:bpab005. [PMID: 33884305 PMCID: PMC8046901 DOI: 10.1093/biomethods/bpab005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/16/2021] [Accepted: 03/24/2021] [Indexed: 11/13/2022] Open
Abstract
Cotton leaf curl disease (CLCuD) is the most important limiting factor for cotton production in Pakistan. The CLCuD passed through two major epidemics in this region with distinct begomoviruses/satellites complexes. Since 2015 the disease has again started to appear in epidemic form, causing heavy losses to cotton crop, which we termed as the “third epidemic”. We applied CIDER-seq (Circular DNA Enrichment Sequencing), a recently developed sequencing method for PCR-free virus enrichment to produce a full length read of a single circular viral genome coupled with Sanger sequencing to explore the genetic diversity of the disease complex. We identified a highly recombinant strain of Cotton leaf curl Multan virus and a recently evolved strain of Cotton leaf curl Multan betasatellite that are dominant in all major cotton growing regions in the country. Moreover, we also identified multiple species of alphasatellites with one distinct species, Mesta yellow vein mosaic alphasatellite (MeYVMA) for the first time in cotton. Relative abundance of virus and associated satellites was also determined by real-time quantitative PCR. To the best of our knowledge, this is the first study that determined the CLCuD complex associated with its third epidemic.
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Affiliation(s)
- Nasim Ahmed
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan
| | - Syed Shan-E-Ali Zaidi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan
| | - Saleem Ur Rahman
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan
| | - Muhammad Farooq
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan
| | | | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan
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Li P, Ruan T, Meng Q, Li K, Qing L. Identification of a novel pepper-infecting monopartite begomovirus in China. Arch Virol 2021; 166:1751-1754. [PMID: 33743050 DOI: 10.1007/s00705-021-04989-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/21/2020] [Indexed: 11/25/2022]
Abstract
Three full-length monopartite begomovirus sequences were obtained from two field-collected pepper plants exhibiting severe leaf yellowing disease symptoms in Yunnan province of China. The three full-length viral sequences contain 2,748 nucleotides (nt) and share the highest nt sequence similarity (88.2% identity) with that of malvastrum yellow vein Yunnan virus (MYVYNV). The betasatellite molecules of the two viruses share the highest sequence similarity (99.3% identity) with that of malvastrum yellow vein Yunnan betasatellite (MYVYNB). Based on the current species demarcation criteria for the genus Begomovirus, these three newly identified isolates can be considered members of a novel monopartite Begomovirus species, and we have named this virus "pepper yellow leaf curl virus" (PepYLCV). Phylogenetic analysis showed that PepYLCV clustered with pepper leaf curl Yunnan virus (PepLCYNV). Recombination analysis revealed that PepYLCV is likely to have originated through a recombination event between MYVYNV and tomato leaf curl Yunnan virus (TLCYnV).
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Affiliation(s)
- Pengbai Li
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, 400716, People's Republic of China
| | - Tao Ruan
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, 400716, People's Republic of China
| | - Qiyuan Meng
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, 400716, People's Republic of China
| | - Ke Li
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, 400716, People's Republic of China
| | - Ling Qing
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, 400716, People's Republic of China.
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N'cho J, Séka K, Hoareau M, Konan A, Fondio L, Lefeuvre P, Martin T, Coulibaly N, Lett JM. Tomato interveinal yellowing virus: a novel tomato-infecting monopartite begomovirus from Côte d'Ivoire. Arch Virol 2021; 166:1755-1758. [PMID: 33743049 DOI: 10.1007/s00705-021-05019-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/12/2021] [Indexed: 11/26/2022]
Abstract
In this report, we present the first description of the complete genome sequences of a new monopartite begomovirus isolated from tomato with symptoms of interveinal yellowing of leaves collected in the region of Worodougou in the northwest of Côte d'Ivoire and provisionally named "tomato interveinal yellowing virus" (ToIYV). The DNA-A-like nucleotide sequences of ToIYV share the highest nucleotide sequence identity (83%) with tobacco leaf curl Zimbabwe virus (ToLCZWV). Phylogenetic analysis confirmed that ToIYV is related to Old World monopartite begomoviruses. The discovery of a member of a new virus species on diseased tomato plants confirms the high genetic diversity in monopartite begomoviruses in West Africa and stresses the importance of maintaining epidemiological crop surveillance.
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Affiliation(s)
- Jocelin N'cho
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, St Pierre, 97410, La Réunion, France
- Université Nangui Abrogoua, Pôle de Recherche Production Végétale, Abidjan, Côte d'Ivoire
| | - Koutoua Séka
- Université Nangui Abrogoua, Pôle de Recherche Production Végétale, Abidjan, Côte d'Ivoire
| | - Murielle Hoareau
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, St Pierre, 97410, La Réunion, France
| | - Arthur Konan
- Université Félix Houphouët Boigny, Centre d'Excellence Wascal, Abidjan, Côte d'Ivoire
| | - Lassina Fondio
- Centre National de Recherche Agronomique, Programme Cultures Maraîchères et Protéagineuses, Bouaké, Côte d'Ivoire
| | - Pierre Lefeuvre
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, St Pierre, 97410, La Réunion, France
| | - Thibaud Martin
- Université Félix Houphouët Boigny, Centre d'Excellence Wascal, Abidjan, Côte d'Ivoire
- CIRAD, UR Hortsys, Université de Montpellier, Montpellier, France
| | - Noupe Coulibaly
- Centre National de Recherche Agronomique, Programme Cultures Maraîchères et Protéagineuses, Bouaké, Côte d'Ivoire
| | - Jean-Michel Lett
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, St Pierre, 97410, La Réunion, France.
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Iqbal Z, Sattar MN, Khurshid M. Cotton Leaf Curl Multan Betasatellite as a Tool to Study the Localization of Geminiviruses in Plants. Mol Biol 2021. [DOI: 10.1134/s0026893321010076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Emmanuel CJ, Manohara S, Shaw MW. Molecular characterization of begomovirus-betasatellite-alphasatellite complex associated with okra enation leaf curl disease in Northern Sri Lanka. 3 Biotech 2020; 10:506. [PMID: 33184593 PMCID: PMC7642014 DOI: 10.1007/s13205-020-02502-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/20/2020] [Indexed: 10/23/2022] Open
Abstract
Okra enation leaf curl is a newly emerging disease in commercial okra cultivation fields in Northern Sri Lanka. The present study aimed to identify and characterize the causative begomovirus and associated satellites. Okra plants showing the enation leaf curl disease symptoms were collected from Vavuniya and Jaffna districts of Northern Province. The PCR diagnostic and genome sequencing revealed that the symptomatic okra plants are associated with begomovirus, betasatellite, and alphasatellite complex. The begomovirus isolates shared 98.2-99.7% nucleotide identity with Okra enation leaf curl virus. The betasatellites showed 96-98.8% nucleotide identity with Bhendi yellow vein mosaic betasatellite which is usually associated with Bhendi yellow vein mosaic disease. Two distinct alphasatellite species, Okra leaf curl alphasatellite and Bhendi yellow vein mosaic alphasatellite, were identified in leaf samples with enation leaf curl disease. The disease was transmitted by whiteflies from diseased plants to healthy plants. Hybrid varieties were more susceptible to the disease compared to cultivated varieties.
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Affiliation(s)
| | - Sharmya Manohara
- Department of Botany, Faculty of Science, University of Jaffna, Jaffna, 40000 JA Sri Lanka
| | - Michael Warren Shaw
- School of Agriculture, Policy and Development, University of Reading, Reading, RG6 6BZ UK
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A novel monopartite begomovirus and satellites associated with yellow mosaic disease of Sida spp. in India. Arch Virol 2020; 166:299-302. [PMID: 33068191 DOI: 10.1007/s00705-020-04843-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/04/2020] [Indexed: 01/25/2023]
Abstract
Begomoviruses (family Geminiviridae) cause severe diseases in many economically important crops and non-cultivated plants in the warmer regions of the world. Non-cultivated weeds have been reported to act as natural virus reservoirs. In January 2016, Sida plants with yellow mosaic symptoms were found at the edge of an agricultural field in Gujarat, India. Sequence analysis of the viral genomic components cloned from a diseased Sida plant indicated the presence of a distinct monopartite begomovirus (proposed as sida yellow mosaic Gujarat virus) along with a betasatellite (ludwigia leaf distortion betasatellite) and an alphasatellite (malvastrum yellow mosaic alphasatellite). Our results emphasize that this weed may harbor a begomovirus-alphasatellite-betasatellite complex. This host serves as a potential source of virus inoculum, which can be transmitted by whiteflies to other cultivated crops.
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Mishra M, Verma RK, Marwal A, Sharma P, Gaur RK. Biology and Interaction of the Natural Occurrence of Distinct Monopartite Begomoviruses Associated With Satellites in Capsicum annum From India. Front Microbiol 2020; 11:512957. [PMID: 33117300 PMCID: PMC7575687 DOI: 10.3389/fmicb.2020.512957] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 09/03/2020] [Indexed: 01/29/2023] Open
Abstract
Chili (Capsicum annuum L.) is an important vegetable and spice crop of tropical and sub-tropical regions. Chili plants showing upward leaf curling, leaf crinkling, and leaf yellowing symptoms, collected from Sikar district of Rajasthan, India, were found to be associated with begomovirus and satellite molecules. The presence of virus was confirmed by PCR using virus-specific primer. The full-length genomic DNA-A of three begomovirus (MM-1, CS-1 and RV-1) and two satellites (MM-2 and MM-3) were cloned which was identified from single symptomatic chili plant. The genome organization of isolated three viruses is similar to those of other Old World monopartite begomoviruses. The comparison of the sequences and closest phylogenetic relationships for the begomoviruses, betasatellite and alphasatellite DNAs revealed that MM-1 was designated as DNA-A of Chili leaf curl virus (ChiLCV), CS-1 is considered to be a new distinct species of Tomato leaf curl Gujrat virus (ToLCGV) whereas RV-1 as a new strain of Cotton leaf curl Multan virus (CLCuMuV). The DNA-A component of ChiLCV showed 8.6%, ToLCGV of 16.6% and CLCuMuV of 7.7% average evolutionary divergence, concomitantly, the betasatellite and alphasatellite molecule had 9.9% and 5.9% overall sequence divergence, respectively. Interestingly, most of the begomoviruses were found to be intra-species recombinants. The dN/dS ratio and Tajima D value of all viral DNA-A component and their associated betasatellite showed their selective control on evolutionary relationships. The nucleotide substitution rates were determined for the DNA-A genomes of ChiLCV (7.22 × 10–4 substitutions site–1 year–1), CLCuMuV (1.49 × 10–4 substitutions site–1 year–1), ToLCGV (7.47 × 10–4 substitutions site–1 year–1), the genome of associated ChiLCB (4.20 × 10–4 substitutions site–1 year–1) and CLCuMuA (1.49 × 10–4 substitutions site–1 year–1). Agro-inoculation studies indicate that the presence of DNA betasatellite induce severe symptoms in N. benthamiana and chili, suggesting prerequisite association for typical disease development.
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Affiliation(s)
- Megha Mishra
- Department of Biosciences, School of Liberal Arts and Sciences, Mody University of Science and Technology, Sikar, India
| | - Rakesh Kumar Verma
- Department of Biosciences, School of Liberal Arts and Sciences, Mody University of Science and Technology, Sikar, India
| | - Avinash Marwal
- Department of Biotechnology, Mohanlal Sukhadia University, Udaipur, India
| | - Pradeep Sharma
- Biotechnology Unit, ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - R K Gaur
- Department of Biotechnology, D.D.U Gorakhpur University, Gorakhpur, India
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Complete Genome Sequence of a Pepper Yellow Leaf Curl Indonesia Virus Isolated from Tomato in Bali, Indonesia. Microbiol Resour Announc 2020; 9:9/25/e00486-20. [PMID: 32554790 PMCID: PMC7303410 DOI: 10.1128/mra.00486-20] [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] [Indexed: 11/20/2022] Open
Abstract
We report a complete genome sequence of a pepper yellow leaf curl Indonesia virus (PepYLCIV) isolated in Bali, Indonesia. This virus shares around 90% identity with other PepYLCIV DNA-As and 86% identity with DNA-Bs, suggesting that it is a novel isolate of PepYLCIV. We report a complete genome sequence of a pepper yellow leaf curl Indonesia virus (PepYLCIV) isolated in Bali, Indonesia. This virus shares around 90% identity with other PepYLCIV DNA-As and 86% identity with DNA-Bs, suggesting that it is a novel isolate of PepYLCIV.
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Association of a begomovirus-satellite complex with yellow vein and leaf curl disease of hollyhock (Alcea rosea) in India. Arch Virol 2020; 165:2099-2103. [PMID: 32556597 DOI: 10.1007/s00705-020-04696-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/11/2020] [Indexed: 01/01/2023]
Abstract
Geminiviruses cause considerable yield loss in several crop plants worldwide. In 2016, several hollyhock plants displaying yellow mosaic and leaf curling symptoms were noticed in a nursery of Jawaharlal Nehru University, New Delhi, India. Analysis of the collected samples indicated an association of monopartite and bipartite begomoviruses with satellites. Three begomoviruses (including a member of a new begomovirus species), two alphasatellites, and a betasatellite were isolated from yellow-mosaic-disease-affected plants. Similarly, a begomovirus, two alphasatellites, and a betasatellite were found to be associated with leaf curl disease of hollyhock. These begomoviruses and satellites were found to be recombinants. By harboring diverse begomoviruses and satellite DNAs, hollyhock may serve as a potential source of virus inoculum.
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Venkataravanappa V, Ashwathappa KV, Reddy CNL, Shankarappa KS, Reddy MK. Characterization of Tomato leaf curl New Delhi virus associated with leaf curl and yellowing disease of Watermelon and development of LAMP assay for its detection. 3 Biotech 2020; 10:282. [PMID: 32550101 DOI: 10.1007/s13205-020-02245-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 05/04/2020] [Indexed: 12/19/2022] Open
Abstract
Diseases caused by begomoviruses are becoming the major limiting factors for the production of watermelon in India. Survey for the incidence of plants showing symptoms typical to begomovirus infection was conducted in watermelon fields. The study revealed that 40% of the watermelon plants were showing the yellowing and downward curling symptoms. Twenty infected samples were collected from the different farmer's fields to know the association of begomoviruses. The PCR amplification using begomovirus-specific primers resulted in an expected 1.2 kb PCR product indicating the begomovirus association with the watermelon samples. The sequence comparison results of 1.2 kb representing partial genome revealed that all sequences obtained from watermelon samples have a nucleotide (nt) identity of more than 98% among them and are maximum homology with Tomato leaf curl New Delhi virus (ToLCNDV). One watermelon sample (WM1) was selected for complete genome amplification using RCA method (rolling-circle amplification). Amplification of DNA B and no amplification of betasatellites and alphasatellite indicated this virus as bipartite. Sequence Demarcation Tool (SDT) analysis of the DNA A component of the WM1 isolate showed the maximum nt identity of 94.6-97.9% and 85.2-95.8% with ToLCNDV infecting cucurbits. The recombinant analysis showed that the genome was likely to be derived from the recombination of already reported begomoviruses (ToLCNDV, ToLCPalV, and MYMIV) infecting diverse crops. The whitefly cryptic species predominant in the begomovirus-infected watermelon fields were identified as Asia-II-5 group. The LAMP assay developed based on coat protein gene sequence was able to detect the ToLCNDV in the infected samples. Visual detection of the LAMP-amplified products was observed with the hydroxy naphthol blue. LAMP assay was also validated with ToLCNDV infected sponge gourd, spine gourd, ivy gourd, ridge gourd, and cucumber. This is the first report of ToLCNDV association with leaf curl and yellowing disease of watermelon from India and World based on complete genome sequencing.
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Affiliation(s)
- V Venkataravanappa
- ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bangalore, 560089 Karnataka India
- Division of Plant Pathology, Central Horticultural Experiment Station, Chettalli, ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bangalore, India
| | - K V Ashwathappa
- ICAR-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, Bangalore, 560065 Karnataka India
| | - K S Shankarappa
- Department of Plant Pathology, College of Horticulture, Bangaluru, 560065 India
- University of Horticultural Sciences, Bagalkot, Karnataka India
| | - M Krishna Reddy
- ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bangalore, 560089 Karnataka India
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Codiaeum variegatum in Pakistan harbours pedilanthus leaf curl virus and papaya leaf curl virus as well as a newly identified betasatellite. Arch Virol 2020; 165:1877-1881. [PMID: 32447620 DOI: 10.1007/s00705-020-04633-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 02/26/2020] [Indexed: 10/24/2022]
Abstract
Codiaeum variegatum (common name, garden croton) is an ornamental plant grown for its bright yellow variegated leaf morphology. Two C. variegatum plants with upward leaf curling and vein swelling symptoms were collected in Faisalabad, Pakistan. Sequencing of clones obtained by PCR amplification with specific primers showed one plant infected with the monopartite begomoviruses pedilanthus leaf curl virus (PeLCV) and papaya leaf curl virus (PaLCuV) and the other to be infected with only PeLCV. Both plants also harboured a betasatellite that was distinct from all previously identified betasatellites, for which the name "codiaeum leaf curl betasatellite" (CoLCuB) is proposed. This is the first identification of a begomovirus and an associated betasatellite infecting C. variegatum in Pakistan. Both PeLCV and PaLCuV cause problems in a number of crop plants, and C. variegatum may act as a reservoir for these agriculturally important viruses. The precise impact and geographical distribution of the newly identified CoLCuB will be investigated.
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Sahu AK, Sanan-Mishra N. Complete genome sequence of a new bipartite begomovirus associated with leaf curl disease of Capsicum annum. 3 Biotech 2020; 10:235. [PMID: 32399385 DOI: 10.1007/s13205-020-02220-6] [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: 03/14/2019] [Accepted: 04/24/2020] [Indexed: 11/25/2022] Open
Abstract
The complete bipartite genome, consisting of DNA-A and DNA-B, of a novel begomovirus isolate associated with apical leaf curling and crinkled leaf disease of Chili (Capsicum annum) from New Delhi, India was cloned and sequenced. The sequence of DNA-A (2737 nt) and DNA-B (2692 nt) of the virus was submitted to NCBI, USA under the accessions MK069591 & MG597211, respectively. Sequence identity of the common region (CR) and presence of identical iterons (GAGTG) between the DNA-A and DNA-B clones indicate that they constitute a related pair. The virus corresponds to a novel species of tomato leaf curl virus and sequence analysis has ruled out the involvement of recombination events in its evolution. Therefore, we report the complete nucleotide sequence of a new bipartite begomovirus infecting Capsicum annum, a vegetable crop communally cultivated throughout India.
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Affiliation(s)
- Anurag Kumar Sahu
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067 India
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067 India
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Mishra M, Verma RK, Gaur RK. Identification of Chilli leaf curl virus and associated betasatellite infecting Osteospermum fruticosum in Rajasthan, India. 3 Biotech 2020; 10:169. [PMID: 32206503 DOI: 10.1007/s13205-020-2159-9] [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: 05/15/2019] [Accepted: 02/28/2020] [Indexed: 10/24/2022] Open
Abstract
A monopartite begomovirus associated with betasatellite was identified from Osteospermum fruticosum (Cape Daisy) showing severe yellowing vein net symptoms in Rajasthan, India through molecular characterization. The DNA-A shared the highest nucleotide (96.61%) identity to Chilli leaf curl Ahmedabad virus (KM880103), while the betasatellite depicted the highest sequence similarity (99.28%) to Chilli leaf curl betasatellite (JF706231, 99.28%). Based on the sequence identity with other begomoviruses known to date, they were recognized as Chilli leaf curl virus (CDI, MH355641) and Chilli leaf curl betasatellite (CDB1, MH355642), respectively. Phylogenetic analysis showed that DNA-A (CD1) clustered with ChiLCV Goa (KP235539), whereas the betasatellite (CDB1) clustered with ChiLCB Jodhapur (JF70623). Recombination events were observed among the clades of ChiLCV, showing intragenic recombination in Rep (C1) and coat protein (V1/AV1) regions. To our knowledge, this is the first report of ChiLC begomovirus strain affecting O. fruticosum.
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Affiliation(s)
- Megha Mishra
- 1Department of Biosciences, School of Sciences, Mody University of Science and Technology, Lakshmangarh, Sikar, Rajasthan 332311 India
| | - Rakesh Kumar Verma
- 1Department of Biosciences, School of Sciences, Mody University of Science and Technology, Lakshmangarh, Sikar, Rajasthan 332311 India
| | - R K Gaur
- 2Department of Biotechnology, DDU Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
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Zaidi SS, Naqvi RZ, Asif M, Strickler S, Shakir S, Shafiq M, Khan AM, Amin I, Mishra B, Mukhtar MS, Scheffler BE, Scheffler JA, Mueller LA, Mansoor S. Molecular insight into cotton leaf curl geminivirus disease resistance in cultivated cotton (Gossypium hirsutum). PLANT BIOTECHNOLOGY JOURNAL 2020; 18:691-706. [PMID: 31448544 PMCID: PMC7004920 DOI: 10.1111/pbi.13236] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/01/2019] [Accepted: 08/15/2019] [Indexed: 05/21/2023]
Abstract
Cultivated cotton (Gossypium hirsutum) is the most important fibre crop in the world. Cotton leaf curl disease (CLCuD) is the major limiting factor and a threat to textile industry in India and Pakistan. All the local cotton cultivars exhibit moderate to no resistance against CLCuD. In this study, we evaluated an exotic cotton accession Mac7 as a resistance source to CLCuD by challenging it with viruliferous whiteflies and performing qPCR to evaluate the presence/absence and relative titre of CLCuD-associated geminiviruses/betasatellites. The results indicated that replication of pathogenicity determinant betasatellite is significantly attenuated in Mac7 and probably responsible for resistance phenotype. Afterwards, to decipher the genetic basis of CLCuD resistance in Mac7, we performed RNA sequencing on CLCuD-infested Mac7 and validated RNA-Seq data with qPCR on 24 independent genes. We performed co-expression network and pathway analysis for regulation of geminivirus/betasatellite-interacting genes. We identified nine novel modules with 52 hubs of highly connected genes in network topology within the co-expression network. Analysis of these hubs indicated the differential regulation of auxin stimulus and cellular localization pathways in response to CLCuD. We also analysed the differential regulation of geminivirus/betasatellite-interacting genes in Mac7. We further performed the functional validation of selected candidate genes via virus-induced gene silencing (VIGS). Finally, we evaluated the genomic context of resistance responsive genes and found that these genes are not specific to A or D sub-genomes of G. hirsutum. These results have important implications in understanding CLCuD resistance mechanism and developing a durable resistance in cultivated cotton.
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Affiliation(s)
- Syed Shan‐e‐Ali Zaidi
- National Institute for Biotechnology and Genetic EngineeringFaisalabadPakistan
- Boyce Thompson InstituteIthacaNYUSA
- Plant Genetics LabTERRA Teaching and Research CenterGembloux Agro-Bio TechUniversity of LiègeGemblouxBelgium
| | - Rubab Zahra Naqvi
- National Institute for Biotechnology and Genetic EngineeringFaisalabadPakistan
- Boyce Thompson InstituteIthacaNYUSA
| | - Muhammad Asif
- National Institute for Biotechnology and Genetic EngineeringFaisalabadPakistan
| | | | - Sara Shakir
- National Institute for Biotechnology and Genetic EngineeringFaisalabadPakistan
- Boyce Thompson InstituteIthacaNYUSA
- Plant Genetics LabTERRA Teaching and Research CenterGembloux Agro-Bio TechUniversity of LiègeGemblouxBelgium
| | - Muhammad Shafiq
- National Institute for Biotechnology and Genetic EngineeringFaisalabadPakistan
- Present address:
Department of BiotechnologyUniversity of OkaraOkaraPakistan
| | - Abdul Manan Khan
- National Institute for Biotechnology and Genetic EngineeringFaisalabadPakistan
| | - Imran Amin
- National Institute for Biotechnology and Genetic EngineeringFaisalabadPakistan
| | - Bharat Mishra
- Department of BiologyUniversity of Alabama at BirminghamBirminghamALUSA
| | - M. Shahid Mukhtar
- Department of BiologyUniversity of Alabama at BirminghamBirminghamALUSA
| | - Brian E. Scheffler
- Genomics and Bioinformatics Research UnitUnited States Department of Agriculture‐Agricultural Research Service (USDA‐ARS)StonevilleMSUSA
| | - Jodi A. Scheffler
- Crop Genetics Research UnitUnited States Department of Agriculture‐Agricultural Research Service (USDA‐ARS)StonevilleMSUSA
| | | | - Shahid Mansoor
- National Institute for Biotechnology and Genetic EngineeringFaisalabadPakistan
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Leke WN, Kvarnheden A, Avelar S, Brown JK. Molecular characterization of two previously undescribed begomovirus-associated alphasatellite molecules infecting malvaceous species in Cameroon. Arch Virol 2020; 165:775-779. [PMID: 31919592 DOI: 10.1007/s00705-020-04523-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 12/10/2019] [Indexed: 11/29/2022]
Abstract
Two begomovirus-associated alphasatellites were isolated from okra and a malvastrum plant (Malvaceae) in Cameroon. The complete nucleotide sequences of the okra- and malvastrum-infecting alphasatellites were 1375 and 1416-1418 nucleotides, respectively, and both exhibited features characteristic of other alphasatellites. Based on pairwise sequence comparisons, these previously undescribed alphasatellites are members of distinct species in the genera Colecusatellite and Gosmusatellite and have been tentatively named "pepper yellow vein Mali alphasatellite" and "cotton leaf curl Gezira alphasatellite3", respectively. Taken together with previous studies, alphasatellites endemic to Cameroon appear to be more diverse and infect plants of many more species and families than currently recognized.
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Affiliation(s)
- W N Leke
- Institute of Agricultural Research for Development (IRAD), Ekona, P.O. Box 83, Buea, Cameroon. .,Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural, Sciences and Linnean Center of Plant Biology in Uppsala, P.O. Box 7080, 750 07, Uppsala, Sweden.
| | - A Kvarnheden
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural, Sciences and Linnean Center of Plant Biology in Uppsala, P.O. Box 7080, 750 07, Uppsala, Sweden
| | - S Avelar
- School of Plant Sciences, The University of Arizona, Tucson, AZ, 85721, USA
| | - J K Brown
- School of Plant Sciences, The University of Arizona, Tucson, AZ, 85721, USA
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Tharmila CJ, Emmanuel CJ, Devika MDC, Michael WS. Detection and absolute quantification of betasatellites associated with okra yellow vein mosaic disease by qPCR. J Virol Methods 2019; 276:113789. [PMID: 31778677 DOI: 10.1016/j.jviromet.2019.113789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 11/01/2019] [Accepted: 11/22/2019] [Indexed: 12/13/2022]
Abstract
Okra yellow vein mosaic disease (OYVMD) causes serious loss in okra production in Sri Lanka. Therefore, screening of resistant okra verities is an essential need to control the disease. As the available qualitative and semi-quantitative methods failed to detect latent infection the present study aimed to develop a quantitative PCR (qPCR) assay to detect and quantify one of the OYVMD causing agent, symptom modulating satellite molecules. A pair of primers targeting a portion of βC1 gene of BYVMBs was designed and used to quantify of BYVMBs by absolute quantification method using SYBR Green I chemistry. Standard curves were prepared using series of dilutions of known copy number plasmids carrying target sequence. The mean amplification efficiency was 95% and the coefficient of determination was 0.994. The method was tested to find out the relation between symptoms and betasatellite titre in range of severity of OYVMD symptoms; the betasatellite titre increased with increasing severity. Interestingly, the method was able to detect BYVMBs present in apparently healthy plants growing in an infected field at a concentration which was not able to detect in end point PCR. Betasatellite titre was also measured in different ages of leaves and different positions. On average, the betasatellite titre in younger leaves was higher than in mature leaves and there were no significant variations in betasatellite titre in different position in each leaf. The assay was also tested as a tool to screen for resistant okra varieties; among the eight varieties tested no BYVMBs were detected in variety Maha F1. Varieties TV8 and MI5 had significantly higher copy number than rest of the varieties. The qPCR protocol described in this study is a useful method to detect and quantify BYVMBs in okra, especially for plant samples with betasatellite titre lower than the detection limit of conventional methods.
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Affiliation(s)
- Christy Jeyaseelan Tharmila
- Department of Botany, Faculty of Science, University of Jaffna, Jaffna, JA, 40000, Sri Lanka; Plant Protection Board of Study, Postgraduate Institute of Agriculture, University of Peradeniya, Peradeniya, KY, 20400, Sri Lanka.
| | | | - M De Costa Devika
- Department of Agricultural Biology, Faculty of Agriculture, University of Peradeniya, Peradeniya, KY, 20400, Sri Lanka; Plant Protection Board of Study, Postgraduate Institute of Agriculture, University of Peradeniya, Peradeniya, KY, 20400, Sri Lanka
| | - Warren Shaw Michael
- School of Agriculture, Policy and Development, University of Reading, Reading, RG6 6BZ, United Kingdom
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Mubin M, Ijaz S, Nahid N, Hassan M, Younus A, Qazi J, Nawaz-Ul-Rehman MS. Journey of begomovirus betasatellite molecules: from satellites to indispensable partners. Virus Genes 2019; 56:16-26. [PMID: 31773493 DOI: 10.1007/s11262-019-01716-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 11/17/2019] [Indexed: 12/21/2022]
Abstract
Betasatellites are a group of circular, single-stranded DNA molecules that are frequently found to be associated with monopartite begomoviruses of the family Geminiviridae. Betasatellites require their helper viruses for replication, movement, and encapsidation and they are often essential for induction of typical disease symptoms. The βC1 protein encoded by betasatellites is multifunctional that participates in diverse cellular events. It interferes with several cellular processes like normal development, chloroplasts, and innate immune system of plants. Recent research has indicated βC1 protein interaction with cellular proteins and its involvement in modulation of the host's cell cycle and symptom determination. This article focuses on the functional mechanisms of βC1 and its interactions with other viral and host proteins.
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Affiliation(s)
- Muhammad Mubin
- Virology Lab, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Sehrish Ijaz
- Virology Lab, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Nazia Nahid
- Department of Bioinformatics and Biotechnology, GC University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Hassan
- Virology Lab, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Ayesha Younus
- Laser Matter Interaction and Nano-sciences Lab, Department of Physics, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Javaria Qazi
- Department of Biotechnology, Quaid e Azam University, Islamabad, Pakistan
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Frequent occurrence of Mungbean yellow mosaic India virus in tomato leaf curl disease affected tomato in Oman. Sci Rep 2019; 9:16634. [PMID: 31719590 PMCID: PMC6851148 DOI: 10.1038/s41598-019-53106-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 10/23/2019] [Indexed: 11/20/2022] Open
Abstract
Next generation sequencing (NGS) of DNAs amplified by rolling circle amplification from 6 tomato (Solanum lycopersicum) plants with leaf curl symptoms identified a number of monopartite begomoviruses, including Tomato yellow leaf curl virus (TYLCV), and a betasatellite (Tomato leaf curl betasatellite [ToLCB]). Both TYLCV and ToLCB have previously been identified infecting tomato in Oman. Surprisingly the NGS results also suggested the presence of the bipartite, legume-adapted begomovirus Mungbean yellow mosaic Indian virus (MYMIV). The presence of MYMIV was confirmed by cloning and Sanger sequencing from four of the six plants. A wider analysis by PCR showed MYMIV infection of tomato in Oman to be widespread. Inoculation of plants with full-length clones showed the host range of MYMIV not to extend to Nicotiana benthamiana or tomato. Inoculation to N. benthamiana showed TYLCV to be capable of maintaining MYMIV in both the presence and absence of the betasatellite. In tomato MYMIV was only maintained by TYLCV in the presence of the betasatellite and then only at low titre and efficiency. This is the first identification of TYLCV with ToLCB and the legume adapted bipartite begomovirus MYMIV co-infecting tomato. This finding has far reaching implications. TYLCV has spread around the World from its origins in the Mediterranean/Middle East, in some instances, in live tomato planting material. The results here may suggest that begomoviruses which do not commonly infect tomato, such as MYMIV, could be spread as a passenger of TYLCV in tomato.
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Sohrab SS. Genetic diversity of begomoviruses infecting tomato plant in Saudi Arabia. Saudi J Biol Sci 2019; 27:222-228. [PMID: 31889840 PMCID: PMC6933193 DOI: 10.1016/j.sjbs.2019.08.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 11/25/2022] Open
Abstract
Tomato is known as a highly valuable crop and grown worldwide for various uses. The cultivation and tomato production severely affected globally by several diseases caused by various pathogens. Begomoviruses causes yellow mosaic and leaf curl disease of tomato in the tropical, subtropical, temperate, and semi-arid regions. In Saudi Arabia, the tomato production adversely affected by disease caused by begomoviruses known as TYLCV and ToLCSDV. In this study, the pathogen was identified by Polymerase Chain Reaction using virus-specific primers and transmitted by whiteflies to healthy tomato seedlings. In a field survey, the tomato plants were exhibiting symptoms like viral infection. The infected leaf was randomly collected from various fields of tomato growing areas like Jeddah, Makkah, Tabuk, and Hail. The full-length viral genome was amplified by Rolling Circle Amplification technology (RCA) while betasatellites were amplified by PCR using universal betasatellites primers. The full-length viral genome (∼2.7 kb) and betasatellites (∼1.4 kb) were cloned and sequenced bi-directionally. The generated sequences were assembled and analyzed to find out the genetic variability by using bioinformatics tools and the genetic variability and phylogenetic relationships with selected begomoviruses were analyzed. The sequences showed the highest identity with an isolate of ToLCSDV and TYLCV. The nucleotide similarity and phylogenetic relationship showed the closest cluster with ToLCSDV and TYLCV. The data generated in this study elucidate that the causal organism is a variant of either TYLCV or ToLCSDV. The provided information from this study will be highly valuable for researchers and vegetable growers not only in Saudi Arabia but also in Arabian Peninsula.
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Affiliation(s)
- Sayed Sartaj Sohrab
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Post Box No: 80216, Jeddah 21589, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Saudi Arabia
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Yasin S, Yasmin A. Standardization of a genotype independent combination of growth regulators for axenic shoot tip culture of cotton. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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