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De Silva PR, Perera CN, Bahder BW, Attanayake RN. Nested PCR-Based Rapid Detection of Phytoplasma Leaf Wilt Disease of Coconut in Sri Lanka and Systemic Movement of the Pathogen. Pathogens 2023; 12:pathogens12020294. [PMID: 36839566 PMCID: PMC9966644 DOI: 10.3390/pathogens12020294] [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: 11/02/2022] [Revised: 11/25/2022] [Accepted: 02/03/2023] [Indexed: 02/12/2023] Open
Abstract
Phytoplasmas are associated with many plant diseases. In palms, lethal bronzing disease, Texas Phoenix palm decline, and coconut lethal yellowing decline are some of them. In Sri Lanka, coconut leaf wilt decline has been reported in the Weligama area of the Southern province, and the disease is called Weligama coconut leaf wilt disease (WCLWD). Unlike other phytoplasma diseases of palms, WCLWD shows slow disease progress. Pathogen detection entirely relies on nested polymerase chain reaction (PCR). However, inconsistencies in pathogen detection have been experienced, i.e., symptomatic plants often produce negative results. The objectives of this study were to reconsider the choice of primers and to determine the best sampling tissue types for consistent detection of the pathogen. Among the six universal primer combinations tested, P1/Tint nested with fU5/rU3 produced consistent results. BLASTn searches of the sequences showed 99-100% similarity to sugarcane white leaf disease (SWL) or grassy shoot (SGS) disease-causing phytoplasma. The optimized nested PCR protocol was successful, with the minimum success rating of 88% and 100% specificity. Midribs of milky white bud leaf samples were the best tissue type for rapid detection. Systemic movement of the pathogen and a tentative latent period were also reported. The findings are helpful in the early detection of the disease.
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Affiliation(s)
- Prasad R. De Silva
- Crop Protection Division, Coconut Research Institute, Lunuwila 61150, Sri Lanka
| | - Chandrika N. Perera
- Department of Agricultural Biology, Faculty of Agriculture, University of Peradeniya, Peradeniya 20400, Sri Lanka
| | - Brian W. Bahder
- Department of Entomology and Nematology, FLREC-University of Florida, Davie, FL 33314-7719, USA
| | - Renuka N. Attanayake
- Department of Plant and Molecular Biology, University of Kelaniya, Kelaniya 11600, Sri Lanka
- Correspondence:
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Shreenath YS, Nabi SU, Madhu GS, Kumawat KL, Rao GP. Identification and multilocus gene characterization of phytoplasmas associated with sweet cherry in India. 3 Biotech 2022; 12:291. [PMID: 36276469 PMCID: PMC9509515 DOI: 10.1007/s13205-022-03357-2] [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: 01/13/2022] [Accepted: 09/09/2022] [Indexed: 11/01/2022] Open
Abstract
Symptoms of leaf roll, swollen nodes, flat branch and witches' broom were observed in five cultivars of sweet cherry from Srinagar, Jammu and Kashmir province, India, during 2019-2021. Phytoplasmas association were confirmed by amplifying 16S rRNA, secA, rp, tuf and secY genes with phytoplasma-specific primers in all symptomatic sweet cherry cultivars in nested PCR assays. Pairwise sequence comparison, phylogeny and virtual RFLP (16S rRNA gene) analyses confirmed the presence of 'Candidatus Phytoplasma asteris' and 'Ca. P. trifolii' strains in the sweet cherry samples. The incidence of flat branch and witches' broom symptoms associated with 'Ca. P. trifolii' varied from 5.8 to 25% in cultivars Bigarreau Nepoleon (Double), Bigarreau Noir Grossa and CITH-Cherry-9. However, incidence of leaf rolling, swollen nodes and bud proliferation associated with 'Ca. P. asteris' was recorded 7.5% in cultivar Stella and 10% in Sunburst, respectively, in the surveyed area. The multigene characterization of sweet cherry phytoplasma strains confirmed the validity of these molecular markers for identification of phytoplasmas enclosed in 16SrI and 16SrVI groups. The presence of phytoplasmas in sweet cherry is the first report from India.
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Affiliation(s)
- Y. S. Shreenath
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Sajad Un Nabi
- ICAR-Central Institute of Temperate Horticulture, Srinagar, J&K 191132 India
| | - G. S. Madhu
- ICAR-Central Institute of Temperate Horticulture, Srinagar, J&K 191132 India
| | - Kishan Lal Kumawat
- ICAR-Central Institute of Arid Horticulture, Bikaner, Rajasthan 334006 India
| | - Govind P. Rao
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012 India
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3
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Zhang H, Zhao X, Cao X, Khan LU, Zhao R, Wang H, Huang X. Transmission of Areca Palm Velarivirus 1 by Mealybugs Causes Yellow Leaf Disease in Betel Palm ( Areca catechu). PHYTOPATHOLOGY 2022; 112:700-707. [PMID: 34491795 DOI: 10.1094/phyto-06-21-0261-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Yellow leaf disease (YLD) is the most destructive disease of betel palm (Areca catechu). A strong association between YLD and areca palm velarivirus 1 (APV1) has been observed. However, the causal relationship between APV1 and disease, and the transmission mode, warrant further investigation. This work showed that APV1 was transmitted by both Ferrisia virgata and Pseudococcus cryptus mealybugs and caused YLD symptoms in betel palm seedlings; therefore, we demonstrate that APV1 is a causal agent of YLD. APV1 was detected in the stylets, foreguts, midguts, and hindguts of the vectors via both immunocapture reverse transcription PCR and immunofluorescence assays. APV1 was not transmitted transovarially from viruliferous female F. virgata to their progeny. In summary, the transmission of APV1 by F. virgata may occur in a noncirculative, semipersistent manner. This study fills important gaps in our knowledge of velarivirus transmission, which is critical for developing YLD management practices.
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Affiliation(s)
- Huaiwen Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, P. R. China
| | - Xue Zhao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, P. R. China
| | - Xianmei Cao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, P. R. China
| | - Latif Ullah Khan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, P. R. China
| | - Ruibai Zhao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, P. R. China
| | - Hongxing Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, P. R. China
| | - Xi Huang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, P. R. China
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Phytoplasma diseases of plants: molecular diagnostics and way forward. World J Microbiol Biotechnol 2021; 37:102. [PMID: 34009500 DOI: 10.1007/s11274-021-03061-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 04/21/2021] [Indexed: 10/21/2022]
Abstract
Phytoplasmas are obligate phytopathogenic bacteria associated with devastating diseases in hundreds of crops across the world. They have been responsible for huge economic losses in many crop plants for decades now. Isolation and establishment of axenic culture of phytoplasma in complex media is a recent progress in phytoplasma research. Earlier methods for phytoplasma disease detection included symptom profiling, microscopy, serology and dodder transmission studies. With advancement in the field of molecular biology, phytoplasma diagnostics and characterisation witnessed radical improvement. Starting from PCR amplification which often necessities a nested PCR on account of low titre of phytoplasmas, to the closed tube quantitative PCR assays and then the ddPCR, an array of diagnostics have been developed for phytoplasma. The isothermal diagnostic platforms are the latest addition to this and the Loop Mediated Isothermal Amplification (LAMP) assay has been applied for the detection of phytoplasma from several hosts. The futuristic approach in phytoplasma detection will be very likely provided by an integration of nanotechnology and molecular diagnostics. Phytoplasma disease management majorly relies on early detection, vector control, use of disease free planting materials and cultivation of resistant varieties. Hence understanding the molecular mechanism of phytoplasma-host interaction is as important as timely and accurate detection, in the management of phytoplasma diseases. Further, the changing climatic scenario and global warming may lead to an upsurge in the phytoplasma diseases spread and severity across the world, making disease management even more challenging.
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Rihne T, Namita, Singh KP, Singh MK, Talukdar A. Improvement in molecular detection of phytoplasma associated with rose by selection of suitable primers and development of a multiplex PCR assay. 3 Biotech 2021; 11:190. [PMID: 33927981 PMCID: PMC7988127 DOI: 10.1007/s13205-021-02713-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/01/2021] [Indexed: 10/21/2022] Open
Abstract
Sensitive and effective phytoplasma DNA amplification in symptomatic rose cultivars is a long unresolved problem. In the present study, improvement in standardization for PCR assay for phytoplasma detection was established with rose samples by selection of various combinations of nested primer pairs of 16S ribosomal gene and secA gene. CTAB DNA extraction method was slightly modified by adding 2% polyvinyl pyrrolidone and increased the isopropanol volume which yielded better quality DNA. Best amplification results were achieved in nested PCR assay employing P1/P7, R16mF2/R16mR2 and R16F2n/R16R2, P1/P7 and R16mF2/R16mR2, and R16mF2/R16mR2 and fU5/rU3 primer pairs. Besides, a multiplex PCR assay was also developed and optimized for consistent identification of phytoplasma in rose samples by employing primer pairs of 16S rRNA and secA genes together in a single PCR reaction by optimizing annealing temperature at 55 °C.
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Affiliation(s)
- Tasou Rihne
- Division of Floriculture and Landscaping, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Namita
- Division of Floriculture and Landscaping, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Kanwar Pal Singh
- Division of Floriculture and Landscaping, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - M. K. Singh
- Division of Floriculture and Landscaping, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Akshay Talukdar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
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Panda P, Yadav JK, Singh SK, Nigam A, Rao GP. First report on clover proliferation phytoplasma related strain associated with Matthiola incana floral virescence in Uttar Pradesh, India. PLANT DISEASE 2020; 105:1558. [PMID: 33337239 DOI: 10.1094/pdis-10-20-2188-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Matthiola incana R. Br. (Fam: Brassicaceae) is an ornamental, commonly known as hoary stock has an extremely fragrant flowers, which blooms in dense clusters in a large variety of colors. During a survey of flower nurseries in March 2019 at Indian Institute of Sugarcane Research campus, Lucknow, floral virescence (MiV) symptoms (Fig. 1 A, B) were observed in M. incana pots with an incidence of over 40%. Leaf yellows symptoms were also observed on a weed Acalypha indica (AiLY) in Matthiola nursery (Fig. 1 C). Nested PCR assays were carried out to detect and identify the possible association of phytoplasmas with MiV and AiLY symptoms. Three each of symptomatic MiV and AiLY samples and two non-symptomatic samples were collected and processed for DNA extraction from the leaf midrib by CTAB method. Hishimonus phycitis (HP) (Hemiptera: Cicadellidae) leafhopper feeding on MiV symptomatic plants was also collected and DNA was extracted. The DNA of 8 symptomatic and 4 non-symptomatic plants and from the 10 leafhopper was used as a template for PCR assays. Phytoplasma specific 16Sr RNA gene specific primers (P1/P7 and 3Far/3Rev; Schneider et al. 1995; Manimekalai et al. 2010) and multilocus genes' specific primer pairs for secA (SecAfor1/SecArev3;SecAfo5r/SecARev2; Bekele et al. 2011), secY (SecYF1(VI)/SecYR1(VI);SecYF2(VI)/SecYR1(VI); Lee et al. 2010) and rp genes (rpFIC/rp(I)R1A; rp(VI)F2/ rp(VI)R2; Martini et al. 2007) were employed as previously described. Amplified products of ~1.3kb, ~600bp, ~1.7kb and ~1.0kb of 16S rRNA, secA, secY and rp genes of phytoplasma were consistently amplified in all the MiV and AiLY samples and in the HP leafhopper. No amplifications were achieved in any of the asymptomatic plant samples. Amplified products of all the four genes of MiV, AiLY and HP isolates were purified, sequenced and submitted in GenBank. Sequence comparison and phylogeny analysis of the sequences of the four genes of MiV, AiLY and HP isolates revealed 99% - 100% sequence identity and clustering with clover proliferation phytoplasma related strains (16SrVI group)(Fig.2 A,B,C and D). The virtual RFLP analysis of 17 restriction endonucleases corresponding to the 16S rDNA sequence of MiV, AiLY and HP phytoplasma strains by pDraw program, assigned them into a novel phytoplasma subgroup strain under 16SrVI group, since its HpaII restriction profile was different to earlier classified 16SrVI subgroups but was very close to16SrVI-E subgroup (GenBank acc. no. AY270156) (Fig 3). Earlier, peanut witches' broom (16SrII-A) phytoplasma was identified associated with M. incana from Italy (Davino et al. 2007). However, the association of clover proliferation phytoplasma (16SrVI) related strain associated with virescence symptom of M. incana is the first report in world. The weed (A. indica) and HP leafhopper were also reported as additional hosts of 16SrVI subgroup related new strain in India, which needs further investigation. The report of a new host and new subgroup of clover proliferation phytoplasma related strain in India is having an epidemiological significance and warrants attention.
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Affiliation(s)
- Priyam Panda
- Indira Gandhi National Open University, 28827, Discipline of Life Sciences, New Delhi, Delhi, India;
| | - Jay Kumar Yadav
- A.N.D. University of Agriculture and Technology, Kumarganj, Ayodha, Uttar Pradesh, Department of Plant Pathology, Kumarganj, India;
| | - Sushil Kumar Singh
- A.N.D. University of Agriculture and Technology, Kumarganj, Ayodha, Uttar Pradesh, Kumarganj, India;
| | - Amrita Nigam
- Indira Gandhi National Open University, 28827, Discipline of Life Sciences, New Delhi, Delhi, India;
| | - Govind P Rao
- Div Plant Pathology, Indian Agricultural Research Institute, Plant Pathology, IARI, Pusa Campus, New Delhi 110012, New Delhi, Pusa Campus, India, 110012;
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Taloh A, Raju DVS, Banyal N, Kumar G, Panda P, Manimekalai R, Marcone C, Rao GP. Genetic diversity of phytoplasma strains infecting chrysanthemum varieties in India and their possible natural reservoirs. 3 Biotech 2020; 10:411. [PMID: 32904455 PMCID: PMC7455686 DOI: 10.1007/s13205-020-02407-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 08/20/2020] [Indexed: 10/24/2022] Open
Abstract
Symptoms typical of phytoplasma infection such as phyllody, virescence, witches' broom and yellowing were observed in 12 varieties of Chrysanthemum morifolium in floral nurseries and experimental fields at New Delhi, Karnataka, Maharashtra and Andhra Pradesh, India, during surveys made from 2015 to 2017. Disease incidence ranged from 15 to 30%. Phytoplasma presence was confirmed in all symptomatic chrysanthemum varieties by molecular identification assays. Sequence comparison, phylogenetic and in silico RFLP analyses of 16S rDNA sequences allowed the identification of the chrysanthemum infecting phytoplasma strains into different ribosomal groups and subgroups, namely 16SrI, 16SrII-D, 16SrVI-D and 16SrXIV. Detection of phytoplasma strains of 16SrII-D subgroup were also confirmed in symptomatic Chenopodium album and Parthenium hysterophorus plants grown in and around the surveyed chrysanthemum fields at New Delhi, whereas 16SrVI-D phytoplasma strains were detected in symptomatic Cannabis sativa weed and leafhopper Hishimonus phycitis individuals collected from the symptomatic chrysanthemum fields at New Delhi. This is the first report on the presence of 16SrVI and 16SrXIV groups of phytoplasmas in chrysanthemum plants. Studies on genetic diversity of phytoplasmas infecting the major chrysanthemum varieties in India and their epidemiological aspects had previously not been reported. The detection and identification of phytoplasmas in different chrysanthemum varieties could contribute to increase the awareness among farmers in the management of these diseases.
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Affiliation(s)
- Aido Taloh
- Division of Floriculture and Landscaping, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - D. V. S. Raju
- Directorate of Floricultural Research, ICAR-College of Agriculture Campus Shivajinagar, Pune, 411005 India
| | - Namita Banyal
- Division of Floriculture and Landscaping, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Gunjeet Kumar
- Division of Floriculture and Landscaping, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Priyam Panda
- Discipline of Life Sciences, Indira Gandhi National Open University, New Delhi, 110068 India
| | - R. Manimekalai
- Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 671003 India
| | - Carmine Marcone
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Salerno Italy
| | - G. P. Rao
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
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Rao GP, Mitra S, Johnson JM, Debnath P, Bahadur A, Das SC. Genetic diversity of phytoplasma strains inducing phyllody, flat stem and witches' broom symptoms in Manilkara zapota in India. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1685-1693. [PMID: 32801496 PMCID: PMC7415051 DOI: 10.1007/s12298-020-00854-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 07/13/2020] [Accepted: 07/16/2020] [Indexed: 06/11/2023]
Abstract
During a survey performed in sapota orchards of India, from 2015 to 2018, symptoms of phyllody, little leaf, flat stem and witches' broom were observed in three states: Karnataka, Kerala and Tripura. The association of phytoplasmas was confirmed in all the symptomatic sapota samples by using nested PCR specific primers (P1/P7, R16F2n/R16R2 and 3Far/3Rev) with amplification of fragments of ~ 1.25 kb and ~ 1.3 kb. Association of three phytoplasma groups, aster yellows with flat stem from Tripura (Lembucherra), clover proliferation with phyllody symptoms at Karnataka (Bengaluru) and bermuda grass white leaf with flat stem and little leaf from Kerala (Thiruvananthapuram) and Tripura (Cocotilla) were confirmed by 16S rRNA gene sequence comparison analysis. Virtual RFLP analysis of 16S rRNA gene sequences using pDRAW32 further classified the sapota phytoplasma isolates into 16SrI-B, 16SrVI-D and 16SrXIV-A subgroups. This is the first report on identification of three phytoplasma groups in sapota in world.
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Affiliation(s)
- Govind Pratap Rao
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Surabhi Mitra
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Joy Michal Johnson
- Kerala Agriculture University, Vellanikkara, Thrissur, Kerala 680656 India
| | - Prasenjit Debnath
- College of Agriculture, Tripura, Lembucherra, West Tripura, 799210 India
| | - Amar Bahadur
- College of Agriculture, Tripura, Lembucherra, West Tripura, 799210 India
| | - Sukhen Chandra Das
- College of Agriculture, Tripura, Lembucherra, West Tripura, 799210 India
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Characterization and genetic diversity of phytoplasmas associated with elephant foot yam (Amorphophallus paeoniifolius) in India. 3 Biotech 2020; 10:83. [PMID: 32089978 DOI: 10.1007/s13205-020-2069-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/14/2020] [Indexed: 10/25/2022] Open
Abstract
During the growing season of 2015 and 2016, leaf yellowing, stunting, and declining symptoms were observed on elephant foot yam in three states of India.The 1.3 kb 16S rDNA fragments were amplified from genomic DNA extracted from all the symptomatic elephant foot yam samples in nested PCR assays using primer pairs, P1/P7 followed by 3F/3R. Pair wise sequence comparison, virtual RFLP and phylogenetic analysis of 16S rRNA gene sequences confirmed association of 'Candidatus Phytoplasma trifolii' (16SrVI-D) and 'Candidatus Phytoplasma oryzae' (16SrXI-B) related strains in Uttar Pradesh, Uttarakhand and Tripura states, respectively. To our knowledge, this is the first report of association of 'Ca. P. trifolii' and 'Ca. P. oryzae' related strains in elephant foot yam in world. In the present study, we also reported Datura stramonium showing witches' broom as a natural weed host for 'Ca. P. trifolii' phytoplasma in Gorakhpur and Kushinagar districts of Uttar Pradesh state, India.
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Abstract
In this paper, we propose a precision agriculture technique to detect various pests in coconut trees with the help of NVIDIA Tegra System on Chip (SoC) along with a camera interfaced drone. The drone flies across the coconut farm and captures the images and processes the data using deep learning algorithm to identify the unhealthy and pest affected trees. The deep learning algorithm uses a set of sample pest database. The Artificial Intelligence (AI) machine learning algorithm is also capable of unsupervised learning from the images that are unstructured. The data is transferred directly to the farmer’s smart phone with the help of wi-fi. This helps in timely treatment of pest infected trees and to improve the yield of the trees.
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Abstract
Phytoplasma detection and identification is primarily based on PCR followed by restriction fragment length polymorphism analysis. This method detects and differentiates phytoplasmas including those not yet identified. The protocol describes the application of this method for identification of phytoplasmas at 16S rRNA (16Sr) group and 16Sr subgroup levels on amplicons and also in silico on the same sequences.
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Gopala, Khasa E, Rao A, Madhupriya, Rao GP. Molecular characterization of 'Clover proliferation' phytoplasma subgroup-D (16SrVI-D) associated with vegetables crops in India. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:203-210. [PMID: 29515315 PMCID: PMC5834985 DOI: 10.1007/s12298-017-0499-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 11/29/2017] [Accepted: 12/26/2017] [Indexed: 06/13/2023]
Abstract
Nine vegetable plants species exhibiting phytoplasma suspected symptoms of white/purple leaf, little leaf, flat stem, witches' broom, phyllody and leaf yellowing were observed in experimental fields at Indian Agricultural Research Institute, New Delhi from December 2015 to July 2016. Total DNA extracted from the three healthy and three symptomatic leaves of all the nine vegetables were subjected to PCR assays using phytoplasma specific primers P1/P7 followed by R16F2n/R16R2 and 3Far/3Rev to amplify the 16S rDNA fragments. No amplifications of DNA were observed in first round PCR assays with primer pair P1/P7 from any of the symptomatic samples. However, phytoplasma DNA specific fragments of ~ 1.3 kb were amplified from Apium graveolens L. (two isolates), Brassica oleracea vr. capitata L. (one isolate) and Solanum melongena L. (one isolate) by using 3Far/3Rev primer pair and 1.2 kb fragment was amplified from Lactuca sativa L. (one isolate) by using R16F2n/R16R2 primer pair. No DNA amplification was seen in other symptomatic vegetable samples of tomato, carrot, cucurbit, bitter gourd and Amaranthus species utilizing either P1/P7 primer pair followed by 3Far/3Rev or R16F2n/R16R2 primer pairs. Out of three leafhopper species collected from the symptomatic vegetable fields, only Hishimonus phycitis was found positive for association of phytoplasma. No DNA amplifications were observed in healthy plant samples and insects collected from non-symptomatic fields. Comparative sequence comparison analyses of 16S rDNA of positive found vegetable phytoplasma strains revealed 100% sequence identities among each other and with phytoplasma strains of 'clover proliferation' (16SrVI) group. Phytoplasma sequences, virtual RFLPs and phylogenetic analyses of 16S rDNA sequence comparison confirmed the identification of 16SrVI subgroup D strain of phytoplasmas in four vegetables and one leafhopper (HP) species. Further virtual RFLP analysis of 16S rDNA sequence of the vegetables phytoplasma strains confirmed their taxonomic classification with strains of 'clover proliferation' subgroup D. Since, H. phycitis feeding on symptomatic vegetable species in the study was also tested positive for the 16SrVI phytoplasma subgroup-D as of vegetables; it may act as potent natural reservoir of 16SrVI-D subgroup of phytoplasmas infecting vegetable and other important agricultural crops.
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Affiliation(s)
- Gopala
- Division of Plant Pathology, Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012 India
| | - Ekta Khasa
- Division of Plant Pathology, Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012 India
| | - Ashutosh Rao
- Division of Plant Pathology, Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012 India
| | - Madhupriya
- Division of Plant Pathology, Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012 India
| | - G. P. Rao
- Division of Plant Pathology, Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012 India
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Yadav A, Thorat V, Deokule S, Shouche Y, Prasad DT. New subgroup 16SrXI-F phytoplasma strain associated with sugarcane grassy shoot (SCGS) disease in India. Int J Syst Evol Microbiol 2017; 67:374-378. [DOI: 10.1099/ijsem.0.001635] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Amit Yadav
- Microbial Culture Collection, National Centre for Cell Science, Pashan, Pune 411 021, India
| | - Vipool Thorat
- Microbial Culture Collection, National Centre for Cell Science, Pashan, Pune 411 021, India
| | - Subhash Deokule
- Department of Botany, University of Pune, Ganeshkhind, Pune 411 007, India
| | - Yogesh Shouche
- Microbial Culture Collection, National Centre for Cell Science, Pashan, Pune 411 021, India
| | - D. Theertha Prasad
- Department of Biotechnology, University of Agriculture Sciences, Gandhi Krishi Vigyan Kendra, Bangalore 560 065, India
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Khasa E, Gopala, Taloh A, Prabha T, Madhupriya, Rao GP. Molecular characterization of phytoplasmas of 'Clover proliferation' group associated with three ornamental plant species in India. 3 Biotech 2016; 6:237. [PMID: 28330309 PMCID: PMC5106402 DOI: 10.1007/s13205-016-0558-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 10/31/2016] [Indexed: 11/25/2022] Open
Abstract
Suspected phytoplasma symptoms of little leaf, yellowing, chlorosis, phyllody, witches' broom, and stunting were observed on ten different ornamental plant species at New Delhi, Andhra Pradesh, Haryana, Bengaluru, and Pune, India, during March to July 2016. To investigate the possibility of phytoplasma etiology, PCR assays were performed using universal primer pairs (P1/P7 followed by 3Far/3Rev) specific to the phytoplasma 16Sr RNA gene. First round PCR amplification with primer pair P1/P7 did not yield expected 1.8 kb product of 16S rRNA region from any of the 17 symptomatic samples. However, 1.3 Kb amplicons were observed in nested PCR assays with 3Far/3Rev primer pair in symptomatic leaf samples of Hibiscus rosa-sinensis L. (Pune isolate), Saponaria officinalis L. (Pune isolate), and Allamanda cathartica L. (Delhi isolate). No amplifications were observed in any of the other tested symptomatic and non-symptomatic plant samples either in first round or second round of nested PCR assays with phytoplasma specific primer pairs. Pairwise sequence comparison of 16S rDNA sequences of the five positive phytoplasma strains of A. catharica, H. rosa-sinensis, and S. officinalis in the present study revealed 99-100% sequence identities with strains of 'clover proliferation' (16SrVI) group. Phylogenetic and virtual RFLP analysis of 16S rDNA sequences of the five identified phytoplasma strains belonging to three ornamental species further confirmed their clustering and grouping with member strains of 'clover proliferation' subgroup D. This is the first record of the phytoplasma association of 'clover proliferation' subgroup D with H. rosa-sinensis, S. officinalis, and A. cathartica in the world.
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Affiliation(s)
- Ekta Khasa
- Division of Plant Pathology, Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - Gopala
- Division of Plant Pathology, Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - Aido Taloh
- Division of Plant Pathology, Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - T Prabha
- Directorate of Floricultural Research College of Agriculture, MPKV, Shivajinagar, Pune, 411005, India
| | - Madhupriya
- Division of Plant Pathology, Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - G P Rao
- Division of Plant Pathology, Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India.
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15
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Gurr GM, Johnson AC, Ash GJ, Wilson BAL, Ero MM, Pilotti CA, Dewhurst CF, You MS. Coconut Lethal Yellowing Diseases: A Phytoplasma Threat to Palms of Global Economic and Social Significance. FRONTIERS IN PLANT SCIENCE 2016; 7:1521. [PMID: 27833616 PMCID: PMC5080360 DOI: 10.3389/fpls.2016.01521] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 09/26/2016] [Indexed: 05/25/2023]
Abstract
The recent discovery of Bogia coconut syndrome in Papua New Guinea (PNG) is the first report of a lethal yellowing disease (LYD) in Oceania. Numerous outbreaks of LYDs of coconut have been recorded in the Caribbean and Africa since the late Nineteenth century and have caused the death of millions of palms across several continents during the Twentieth century. Despite the severity of economic losses, it was only in the 1970s that the causes of LYDs were identified as phytoplasmas, a group of insect-transmitted bacteria associated with diseases in many other economically important crop species. Since the development of polymerase chain reaction (PCR) technology, knowledge of LYDs epidemiology, ecology and vectors has grown rapidly. There is no economically viable treatment for LYDs and vector-based management is hampered by the fact that vectors have been positively identified in very few cases despite many attempted transmission trials. Some varieties and hybrids of coconut palm are known to be less susceptible to LYD but none are completely resistant. Optimal and current management of LYD is through strict quarantine, prompt detection and destruction of symptomatic palms, and replanting with less susceptible varieties or crop species. Advances in technology such as loop mediated isothermal amplification (LAMP) for detection and tracking of phytoplasma DNA in plants and insects, remote sensing for identifying symptomatic palms, and the advent of clustered regularly interspaced short palindromic repeats (CRISPR)-based tools for gene editing and plant breeding are likely to allow rapid progress in taxonomy as well as understanding and managing LYD phytoplasma pathosystems.
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Affiliation(s)
- Geoff M. Gurr
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujain Agriculture and Forestry UniversityFuzhou, China
- Institute of Applied Ecology, College of Plant Protection, Fujian Agriculture and Forestry UniversityFuzhou, China
- Graham Centre of Agricultural Innovation, Charles Sturt UniversityOrange, NSW, Australia
| | - Anne C. Johnson
- Graham Centre of Agricultural Innovation, Charles Sturt UniversityOrange, NSW, Australia
| | - Gavin J. Ash
- Research and Innovation Division, Centre for Crop Health, Institute for Agriculture and the Environment, University of Southern QueenslandToowoomba, QLD, Australia
| | - Bree A. L. Wilson
- Research and Innovation Division, Centre for Crop Health, Institute for Agriculture and the Environment, University of Southern QueenslandToowoomba, QLD, Australia
| | - Mark M. Ero
- PNG Oil Palm Research AssociationKimbe, Papua New Guinea
| | | | - Charles F. Dewhurst
- Formerly affiliated with the PNG Oil Palm Research AssociationKimbe, Papua New Guinea
| | - Minsheng S. You
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujain Agriculture and Forestry UniversityFuzhou, China
- Institute of Applied Ecology, College of Plant Protection, Fujian Agriculture and Forestry UniversityFuzhou, China
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16
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Abeysinghe S, Abeysinghe PD, Kanatiwela-de Silva C, Udagama P, Warawichanee K, Aljafar N, Kawicha P, Dickinson M. Refinement of the Taxonomic Structure of 16SrXI and 16SrXIV Phytoplasmas of Gramineous Plants using Multilocus Sequence Typing. PLANT DISEASE 2016; 100:2001-2010. [PMID: 30683016 DOI: 10.1094/pdis-02-16-0244-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Phytoplasmas that infect gramineous plants, including Napier grass stunt, sugarcane whiteleaf, sugarcane grassy shoot, and Bermuda grass whiteleaf, have been classified into two closely related groups, 16SrXI and 16SrXIV, based on the 16S ribosomal RNA (rRNA) gene. Subsequently, phytoplasmas associated with coconut and Areca palm in southern India and Sri Lanka have been added into the 16SrXI group. However, the 16S rRNA gene gives relatively poor resolution between these phytoplasmas. In this study, a new set of universal phytoplasma primers that amplify approximately 1 kb of the leucyl transfer RNA synthetase (leuS) gene have been validated on a broad range of phytoplasma taxonomic groups. These have been used along with partial sequences of the secA gene to clarify the taxonomic classification of 16SrXI and 16SrXIV phytoplasmas. Based on this data, the sugarcane whiteleaf and grassy shoot phytoplasmas appear to be the same phytoplasma. The Napier grass stunt phytoplasma forms a distinct group from the Bermuda grass whiteleaf and sugarcane phytoplasmas, suggesting that Napier grass stunt should be in its own 'Candidatus Phytoplasma sp.'. The phytoplasmas associated with coconut and arecanut in southern India and Sri Lanka, which are in the same 16SrXI group, appear in different groups based on secA analysis.
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Affiliation(s)
- Saman Abeysinghe
- Department of Botany, Faculty of Science, University of Ruhuna, Matara, Sri Lanka
| | | | | | - Preethi Udagama
- Department of Zoology, Faculty of Science, University of Colombo, Colombo 03, Sri Lanka
| | - Kanjana Warawichanee
- Plant Virology Section, Department of Agriculture, Chatuchak, Bangkok, 10900, Thailand
| | - Naofel Aljafar
- School of Biosciences, Sutton Bonington Campus, University of Nottingham, LE12 5RD, UK
| | - Praphat Kawicha
- School of Biosciences, Sutton Bonington Campus, University of Nottingham, LE12 5RD, UK
| | - Matt Dickinson
- School of Biosciences, Sutton Bonington Campus, University of Nottingham, LE12 5RD, UK
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17
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Nair S, Manimekalai R, Ganga Raj P, Hegde V. Loop mediated isothermal amplification (LAMP) assay for detection of coconut root wilt disease and arecanut yellow leaf disease phytoplasma. World J Microbiol Biotechnol 2016; 32:108. [PMID: 27263003 DOI: 10.1007/s11274-016-2078-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 04/27/2016] [Indexed: 11/28/2022]
Abstract
The coconut root wilt disease (RWD) and the arecanut yellow leaf disease (YLD) are two major phytoplasma associated diseases affecting palms in South India. Greatly debilitating the palm health, these diseases cause substantial yield reduction and economic loss to farmers. A rapid and robust diagnostic technique is crucial in efficient disease management. We established phytoplasma 16S rDNA targeted loop mediated isothermal amplification (LAMP) and real time LAMP based diagnostics for coconut RWD and arecanut YLD. The LAMP reaction was set at 65 °C and end point detection made using hydroxynaphthol blue (HNB) and agarose gel electrophoresis. Molecular typing of LAMP products were made with restriction enzyme HpyCH4 V. Conventional PCR with LAMP external primers and sequencing of amplicons was carried out. Real time LAMP was performed on the Genei II platform (Optigene Ltd., UK). An annealing curve analysis was programmed at the end of the incubation to check the fidelity of the amplicons. The phytoplasma positive samples produced typical ladder like bands on agarose gel, showed colour change from violet to blue with HNB and produced unique annealing peak at 85 ± 0.5 °C in the real time detection. Restriction digestion produced predicted size fragments. Sequencing and BLASTN analysis confirmed that the amplification corresponded to phytoplasma 16S rRNA gene. LAMP method devised here was found to be more robust compared to conventional nested PCR and hence has potential applications in detection of phytoplasma from symptomatic palm samples and in rapid screening of healthy seedlings.
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Affiliation(s)
- Smita Nair
- Central Plantation Crops Research Institute, Indian Council of Agricultural Research (ICAR), Kudlu P.O, Kasaragod, 671124, Kerala, India
| | - Ramaswamy Manimekalai
- Department of Biotechnology, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, 641007, Tamil Nadu, India.
| | - Palliyath Ganga Raj
- Central Plantation Crops Research Institute, Indian Council of Agricultural Research (ICAR), Kudlu P.O, Kasaragod, 671124, Kerala, India
| | - Vinayaka Hegde
- Central Plantation Crops Research Institute, Indian Council of Agricultural Research (ICAR), Kudlu P.O, Kasaragod, 671124, Kerala, India
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18
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Ramaswamy M, Nair S, Soumya VP, Thomas GV. Phylogenetic analysis identifies a ‘Candidatus
Phytoplasma oryzae
’-related strain associated with yellow leaf disease of areca palm (Areca catechu L.) in India. Int J Syst Evol Microbiol 2013; 63:1376-1382. [DOI: 10.1099/ijs.0.043315-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Yellow leaf disease (YLD) with phytoplasmal aetiology is a serious disease of arecanut palm in India. The present study was undertaken to characterize the 16S rRNA and secA gene sequences of the Indian arecanut YLD phytoplasma for ‘Candidatus
Phytoplasma
’ species assignment and 16Sr group/subgroup classification. Phytoplasma 16S rRNA genes were amplified using three sets of semi-nested/nested primers, 1F7/7R3–1F7/7R2, 4Fwd/3Rev–4Fwd/5Rev and P1/P7–R16F2n/R16R2, producing amplicons of 491, 1150 and 1250 bp, respectively, from diseased samples. The amplicons were cloned and sequenced. A blast search showed that the sequences had 99 % similarity with sugar cane white leaf phytoplasma (16SrXI) and Napier grass stunt phytoplasma (16SrXI). Phylogenetic analysis based on the 16S rRNA gene revealed the clustering of YLD phytoplasma with the rice yellow dwarf and Bermuda grass white leaf groups. The YLD phytoplasma F2nR2 sequence shared 97.5 % identity with that of ‘Candidatus
Phytoplasma oryzae
’ and 97.8 % identity with that of ‘Candidatus
Phytoplasma cynodontis
’. Hence, for finer differentiation, we examined the secA gene-based phylogeny, where the YLD phytoplasma clustered with Napier grass stunt and sugar cane grassy shoot phytoplasmas, both belonging to the rice yellow dwarf group. Hence, we are assigning the Indian arecanut YLD phytoplasma as a ‘Candidatus
Phytoplasma oryzae
’-related strain. Virtual RFLP analysis of a 1.2 kb fragment of the 16S rRNA gene (F2nR2 region) identified the Indian arecanut YLD phytoplasma as a member of 16SrXI-B subgroup. We name the phytoplasma Indian yellow leaf disease phytoplasma, to differentiate it from the Hainan YLD phytoplasma, which belongs to group 16SrI.
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Affiliation(s)
- Manimekalai Ramaswamy
- Molecular Biology Laboratory, Central Plantation Crops Research Institute, Kasaragod, Kerala, India
| | - Smita Nair
- Molecular Biology Laboratory, Central Plantation Crops Research Institute, Kasaragod, Kerala, India
| | - V. P. Soumya
- Molecular Biology Laboratory, Central Plantation Crops Research Institute, Kasaragod, Kerala, India
| | - George V. Thomas
- Molecular Biology Laboratory, Central Plantation Crops Research Institute, Kasaragod, Kerala, India
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19
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Rao G, Mall S, Raj S, Snehi S. Review article: Phytoplasma diseases affecting various plant species in India. ACTA ACUST UNITED AC 2011. [DOI: 10.1556/aphyt.46.2011.1.7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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