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Ghosh DK, Kokane AD, Kokane SB, Tenzin J, Gubyad MG, Wangdi P, Murkute AA, Sharma AK, Gowda S. Detection and Molecular Characterization of 'C andidatus Liberibacter asiaticus' and Citrus Tristeza Virus Associated with Citrus Decline in Bhutan. PHYTOPATHOLOGY 2021; 111:870-881. [PMID: 33090079 DOI: 10.1094/phyto-07-20-0266-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Citrus, mainly mandarin (Citrus reticulata Blanco), is an economically important fruit crop in Bhutan. Despite having favorable agroclimatic conditions for citrus cultivation, the early decline of fruit-bearing orchards coupled with low crop productivity is a major concern among citrus growers. During a recent survey, an association of 'Candidatus Liberibacter asiaticus' (citrus greening) and citrus tristeza virus (CTV), either singly or as mixed infections in declined citrus trees, was recorded in all four major citrus-growing districts (Tsirang, Dagana, Zhemgang, and Sarpang). Using PCR-based diagnosis, a higher incidence of citrus greening (27.45%) and tristeza (70.58%) was observed in symptomatic field samples. Detection and characterization of 'Ca. L. asiaticus' was performed based on the 16S ribosomal DNA, prophage gene, 50S ribosomal rplA-rplJ gene, and tandem repeats of the CLIBASIA_01645 locus. Similarly, the coat protein, p23, and p18 genes were used as genetic markers for the detection and characterization of Bhutanese CTV. The 'Ca. L. asiaticus' isolates from Bhutan segregated into classes II and III based on the CLIBASIA_01645 locus, analogous to Indian isolates from the northeast region and Term-A based on the CLIBASIA_05610 locus. CTV isolates of Bhutan were observed as closely related to the VT strain, which is considered to be the most devastating. To the best of our knowledge, this is the first study on molecular characterization of 'Ca. L. asiaticus' and CTV isolates and their association with citrus decline in Bhutan.
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Affiliation(s)
- Dilip Kumar Ghosh
- Indian Council of Agricultural Research-Central Citrus Research Institute, Nagpur-440 033, Maharashtra, India
| | - Amol D Kokane
- Indian Council of Agricultural Research-Central Citrus Research Institute, Nagpur-440 033, Maharashtra, India
| | - Sunil B Kokane
- Indian Council of Agricultural Research-Central Citrus Research Institute, Nagpur-440 033, Maharashtra, India
| | - Jigme Tenzin
- National Citrus Program, Department of Agriculture, Royal Government of Bhutan, Thimphu 11001, Bhutan
| | - Mrugendra G Gubyad
- Indian Council of Agricultural Research-Central Citrus Research Institute, Nagpur-440 033, Maharashtra, India
| | - Phuntsho Wangdi
- National Citrus Repository, Department of Agriculture, Royal Government of Bhutan, Tsirang, Bhutan
| | - Ashutosh A Murkute
- Indian Council of Agricultural Research-Central Citrus Research Institute, Nagpur-440 033, Maharashtra, India
| | - Ashwani Kumar Sharma
- Department of Biotechnology, Indian Institute of Technology, Roorkee - 247 667, India
| | - Siddarame Gowda
- University of Florida, Citrus Research and Education Centre, Lake Alfred, FL 33850, U.S.A
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Bester R, Cook G, Maree HJ. Citrus Tristeza Virus Genotype Detection Using High-Throughput Sequencing. Viruses 2021; 13:168. [PMID: 33498597 PMCID: PMC7910887 DOI: 10.3390/v13020168] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/05/2021] [Accepted: 01/11/2021] [Indexed: 12/14/2022] Open
Abstract
The application of high-throughput sequencing (HTS) has successfully been used for virus discovery to resolve disease etiology in many agricultural crops. The greatest advantage of HTS is that it can provide a complete viral status of a plant, including information on mixed infections of viral species or virus variants. This provides insight into the virus population structure, ecology, or evolution and can be used to differentiate among virus variants that may contribute differently toward disease etiology. In this study, the use of HTS for citrus tristeza virus (CTV) genotype detection was evaluated. A bioinformatic pipeline for CTV genotype detection was constructed and evaluated using simulated and real data sets to determine the parameters to discriminate between false positive read mappings and true genotype-specific genome coverage. A 50% genome coverage cut-off was identified for non-target read mappings. HTS with the associated bioinformatic pipeline was validated and proposed as a CTV genotyping assay.
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Affiliation(s)
- Rachelle Bester
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa;
| | - Glynnis Cook
- Citrus Research International, P.O. Box 28, Nelspruit 1200, South Africa;
| | - Hans J. Maree
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa;
- Citrus Research International, Stellenbosch, P.O. Box 2201, Matieland 7602, South Africa
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Molecular detection and coat protein gene based characterization of Citrus tristeza virus prevalent in Sikkim state of India. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/s42360-019-00180-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Biswas KK, Palchoudhury S, Chakraborty P, Bhattacharyya UK, Ghosh DK, Debnath P, Ramadugu C, Keremane ML, Khetarpal RK, Lee RF. Codon Usage Bias Analysis of Citrus tristeza Virus: Higher Codon Adaptation to Citrus reticulata Host. Viruses 2019; 11:v11040331. [PMID: 30965565 PMCID: PMC6521185 DOI: 10.3390/v11040331] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/25/2019] [Accepted: 04/03/2019] [Indexed: 12/16/2022] Open
Abstract
Citrus tristeza virus (CTV), a member of the aphid-transmitted closterovirus group, is the causal agent of the notorious tristeza disease in several citrus species worldwide. The codon usage patterns of viruses reflect the evolutionary changes for optimization of their survival and adaptation in their fitness to the external environment and the hosts. The codon usage adaptation of CTV to specific citrus hosts remains to be studied; thus, its role in CTV evolution is not clearly comprehended. Therefore, to better explain the host–virus interaction and evolutionary history of CTV, the codon usage patterns of the coat protein (CP) genes of 122 CTV isolates originating from three economically important citrus hosts (55 isolate from Citrus sinensis, 38 from C. reticulata, and 29 from C. aurantifolia) were studied using several codon usage indices and multivariate statistical methods. The present study shows that CTV displays low codon usage bias (CUB) and higher genomic stability. Neutrality plot and relative synonymous codon usage analyses revealed that the overall influence of natural selection was more profound than that of mutation pressure in shaping the CUB of CTV. The contribution of high-frequency codon analysis and codon adaptation index value show that CTV has host-specific codon usage patterns, resulting in higheradaptability of CTV isolates originating from C. reticulata (Cr-CTV), and low adaptability in the isolates originating from C. aurantifolia (Ca-CTV) and C. sinensis (Cs-CTV). The combination of codon analysis of CTV with citrus genealogy suggests that CTV evolved in C. reticulata or other Citrus progenitors. The outcome of the study enhances the understanding of the factors involved in viral adaptation, evolution, and fitness toward their hosts. This information will definitely help devise better management strategies of CTV.
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Affiliation(s)
- Kajal Kumar Biswas
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 11012, India.
| | - Supratik Palchoudhury
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 11012, India.
| | - Prosenjit Chakraborty
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 11012, India.
| | - Utpal K Bhattacharyya
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 11012, India.
| | - Dilip K Ghosh
- ICAR-Central Citrus Research Institute, Nagpur 440033, India.
| | - Palash Debnath
- Department of Plant Pathology, Assam Agricultural University, Jorhat 785013, India.
| | - Chandrika Ramadugu
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92507, USA.
| | - Manjunath L Keremane
- National Clonal Germplasm Repository for Citrus & Dates, United States Department of Agriculture-Agricultural Research Service, Riverside, CA 92507, USA.
| | - Ravi K Khetarpal
- Asia-Pacific Association of Agricultural Research Institutions, Bangkok 10100, Thailand.
| | - Richard F Lee
- National Clonal Germplasm Repository for Citrus & Dates, United States Department of Agriculture-Agricultural Research Service, Riverside, CA 92507, USA.
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Erkiş-Güngör G, Çevik B. Genetic Diversity and Phylogenetic Analysis of Citrus tristeza virus Isolates from Turkey. Adv Virol 2019; 2019:7163747. [PMID: 30906322 PMCID: PMC6393893 DOI: 10.1155/2019/7163747] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 12/26/2018] [Indexed: 11/17/2022] Open
Abstract
The presence of Citrus tristeza virus (CTV) in Turkey has been known since the 1960s and the virus was detected in all citrus growing regions of the country. Even though serological and biological characteristics of CTV have been studied since the 1980s, molecular characteristics of CTV isolates have not been studied to date in Turkey. In this study, molecular characteristics of 15 CTV isolates collected from different citrus growing regions of Turkey were determined by amplification, cloning, and sequencing of their major coat protein (CP) genes. The sequence analysis showed that the CP genes were highly conserved among Turkish isolates. However, isolates from different regions showed more genetic variation than isolates from the same region. Turkish isolates were clustered into three phylogenetic groups showing no association with geographical origins, host, or symptoms induced in indicator plants. Phylogenetic analysis of Turkish isolates with isolates from different citrus growing regions of the world including well-characterized type isolates of previously established strain specific groups revealed that some Turkish isolates were closely related to severe quick decline or stem pitting isolates. The results demonstrated that although CTV isolates from Turkey are considered biologically mild, majority of them contain severe components potentially causing quick decline or stem pitting.
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Affiliation(s)
- Gözde Erkiş-Güngör
- Applied Sciences University of Isparta, Faculty of Agricultural Sciences and Technologies, Department of Plant Protection, 32260 Isparta, Turkey
- Ministry of Food, Agriculture and Livestock, Antalya Agricultural Quarantine Office, Virology Laboratory, 07260 Antalya, Turkey
| | - Bayram Çevik
- Applied Sciences University of Isparta, Faculty of Agricultural Sciences and Technologies, Department of Plant Protection, 32260 Isparta, Turkey
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Biswas KK, Palchoudhury S, Sharma SK, Saha B, Godara S, Ghosh DK, Keremane ML. Analyses of 3' half genome of citrus tristeza virus reveal existence of distinct virus genotypes in citrus growing regions of India. Virusdisease 2018; 29:308-315. [PMID: 30159365 DOI: 10.1007/s13337-018-0456-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/03/2018] [Indexed: 11/29/2022] Open
Abstract
Citrus tristeza virus (CTV, genus Closterovirus) is one of the most serious pathogens responsible for huge loss of citrus trees worldwide. Four Indian CTV isolates, Kat1 (C. reticulata/Central India), D1 (C. sinensis/North India), B5 (Citrus limettoides/South India) and G28 (C. lemon/Northeast India) collected from different regions of India were characterized based on sequencing of 3' half genome (~ 8.4 kb) comprising 10 open reading frames (ORFs2-11) and 3' UTR and the sequences were submitted to NCBI database as Acc. No KJ914662, HQ912022, HQ912023 and KJ914661, respectively. The present and previously reported Indian isolates Kpg3 and B165 were analyzed and compared with other Asian and international CTV isolates. The Indian CTV isolates had 92-99% nt identities among them. The phylogenetic analysis generated overall ten genogroups/lineages. Of them, all the Asian isolates fell into seven genogroups, whereas the Indian isolates into four. Indian isolates Kat1, D1 and Kpg3 grouped together, termed "Kpg3Gr", along with Florida severe isolate T3. The Indian isolates B5, and G28 were found to be two distinct and separate lineages, indicating that these isolates are two new CTV entities. Based on phylogenetic analysis, Kpg3Gr was identified as "Indian VT" subtype which is distinct from the Asian and the Western VT subtype within diversified VT genotype. The recombination detecting-program, RDP4 detected Indian isolates Kat1, B5, B165 and G28 as recombinants, where G28 as strong recombinant. The present study determined the occurrence of at least four CTV genotypes, B5 (distinct), B165 (T68 type) G28 (distinct) and Kpg3Gr in citrus growing regions of India.
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Affiliation(s)
- Kajal K Biswas
- 1Division of Plant Pathology, Advanced Centre for Plant Virology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Supratik Palchoudhury
- 1Division of Plant Pathology, Advanced Centre for Plant Virology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Susheel K Sharma
- 1Division of Plant Pathology, Advanced Centre for Plant Virology, Indian Agricultural Research Institute, New Delhi, 110012 India.,2ICAR Research Complex for NEH Region, Manipur Centre, Lamphelpat, Imphal, 795004 India
| | - Bikram Saha
- 1Division of Plant Pathology, Advanced Centre for Plant Virology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Shruti Godara
- 1Division of Plant Pathology, Advanced Centre for Plant Virology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Dilip K Ghosh
- ICAR-Central Citrus Research Institute, Nagpur, 440033 India
| | - Manjunath L Keremane
- 4USDA-ARS, National Clonal Germplasm Repository for Citrus and Dates, Riverside, CA 92507 USA
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Development of a simple and rapid reverse transcription-loop mediated isothermal amplification (RT-LAMP) assay for sensitive detection of Citrus tristeza virus. J Virol Methods 2017; 250:6-10. [DOI: 10.1016/j.jviromet.2017.09.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/21/2017] [Accepted: 09/05/2017] [Indexed: 11/18/2022]
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Minor Coat and Heat Shock Proteins Are Involved in the Binding of Citrus Tristeza Virus to the Foregut of Its Aphid Vector, Toxoptera citricida. Appl Environ Microbiol 2016; 82:6294-6302. [PMID: 27520823 DOI: 10.1128/aem.01914-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/10/2016] [Indexed: 02/06/2023] Open
Abstract
Vector transmission is a critical stage in the viral life cycle, yet for most plant viruses how they interact with their vector is unknown or is explained by analogy with previously described relatives. Here we examined the mechanism underlying the transmission of citrus tristeza virus (CTV) by its aphid vector, Toxoptera citricida, with the objective of identifying what virus-encoded proteins it uses to interact with the vector. Using fluorescently labeled virions, we demonstrated that CTV binds specifically to the lining of the cibarium of the aphid. Through in vitro competitive binding assays between fluorescent virions and free viral proteins, we determined that the minor coat protein is involved in vector interaction. We also found that the presence of two heat shock-like proteins, p61 and p65, reduces virion binding in vitro Additionally, treating the dissected mouthparts with proteases did not affect the binding of CTV virions. In contrast, chitinase treatment reduced CTV binding to the foregut. Finally, competition with glucose, N-acetyl-β-d-glucosamine, chitobiose, and chitotriose reduced the binding. These findings together suggest that CTV binds to the sugar moieties of the cuticular surface of the aphid cibarium, and the binding involves the concerted activity of three virus-encoded proteins. IMPORTANCE Limited information is known about the specific interactions between citrus tristeza virus and its aphid vectors. These interactions are important for the process of successful transmission. In this study, we localized the CTV retention site as the cibarium of the aphid foregut. Moreover, we demonstrated that the nature of these interactions is protein-carbohydrate binding. The viral proteins, including the minor coat protein and two heat shock proteins, bind to sugar moieties on the surface of the foregut. These findings will help in understanding the transmission mechanism of CTV by the aphid vector and may help in developing control strategies which interfere with the CTV binding to its insect vector to block the transmission.
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Rubio L, Guerri J, Moreno P. Genetic variability and evolutionary dynamics of viruses of the family Closteroviridae. Front Microbiol 2013; 4:151. [PMID: 23805130 PMCID: PMC3693128 DOI: 10.3389/fmicb.2013.00151] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 05/29/2013] [Indexed: 11/15/2022] Open
Abstract
RNA viruses have a great potential for genetic variation, rapid evolution and adaptation. Characterization of the genetic variation of viral populations provides relevant information on the processes involved in virus evolution and epidemiology and it is crucial for designing reliable diagnostic tools and developing efficient and durable disease control strategies. Here we performed an updated analysis of sequences available in Genbank and reviewed present knowledge on the genetic variability and evolutionary processes of viruses of the family Closteroviridae. Several factors have shaped the genetic structure and diversity of closteroviruses. (I) A strong negative selection seems to be responsible for the high genetic stability in space and time for some viruses. (2) Long distance migration, probably by human transport of infected propagative plant material, have caused that genetically similar virus isolates are found in distant geographical regions. (3) Recombination between divergent sequence variants have generated new genotypes and plays an important role for the evolution of some viruses of the family Closteroviridae. (4) Interaction between virus strains or between different viruses in mixed infections may alter accumulation of certain strains. (5) Host change or virus transmission by insect vectors induced changes in the viral population structure due to positive selection of sequence variants with higher fitness for host-virus or vector-virus interaction (adaptation) or by genetic drift due to random selection of sequence variants during the population bottleneck associated to the transmission process.
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Affiliation(s)
- Luis Rubio
- Instituto Valenciano de Investigaciones AgrariasMoncada, Valencia, Spain
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Singh JK, Tarafdar A, Sharma SK, Biswas KK. Evidence of Recombinant Citrus tristeza virus Isolate Occurring in Acid Lime cv. Pant Lemon Orchard in Uttarakhand Terai Region of Northern Himalaya in India. INDIAN JOURNAL OF VIROLOGY : AN OFFICIAL ORGAN OF INDIAN VIROLOGICAL SOCIETY 2012; 24:35-41. [PMID: 24426255 DOI: 10.1007/s13337-012-0118-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 10/15/2012] [Indexed: 10/27/2022]
Abstract
The present study for the first time describes biological and molecular characterization of Citrus tristeza virus (CTV) occurring in the Terai area of Uttarakhand State in Northern Himalaya region of India. Direct antigen coated-ELISA and reverse transcriptase-polymerase chain reaction (RT-PCR) detected the CTV infection in Acid lime cv. Pant lemon (Citrus aurantifolia) orchards of Pantnagar with an estimated disease incidence of 16.6-20.5 %. To know the biological and genetic properties, an isolate, CTV Pant 4 was characterized. Isolate Pant 4 could be graft transmitted to Kinnow, Nagpur and Darjeeling mandarins, Mosambi sweet orange, Kagzi lime, Sweet lime, Sour orange but not to Rough lemon. The sequence analyses of the 5'ORF1a (3038 nucleotides) of LPro domain and 3'end (2058 nt) covering ORF7-ORF10 regions of the CTV genome revealed that Pant 4 was closely related to the previously reported Indian CTV isolate, Kpg3 from Northeastern Himalaya region with 97 and 98 % sequence identity, respectively. Whereas, it differed from the previously reported CTV isolate B165 from Southern India with 79 and 92 % identity, respectively for 5'ORF1a and 3' end regions. Recombination and SplitsTree decomposition analyses indicated that CTV isolate Pant 4 was a recombinant isolate originating from Kpg3 as a major and B165 as a minor donor.
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Affiliation(s)
- Jaywant Kumar Singh
- Plant Virology Unit, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Avijit Tarafdar
- Plant Virology Unit, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Susheel Kumar Sharma
- Plant Virology Unit, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Kajal Kumar Biswas
- Plant Virology Unit, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012 India
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