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Biswas KK, Keremane ML, Marais LJ, Ramadugu C, Lee RF. Population dynamics of Citrus tristeza virus (CTV) in single aphid-transmitted sub-isolates of the South African GFMS12 isolate. FRONTIERS IN PLANT SCIENCE 2022; 13:1024556. [PMID: 36388600 PMCID: PMC9650399 DOI: 10.3389/fpls.2022.1024556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Grapefruit trees in South Africa have been cross protected against severe stem pitting genotypes of Citrus tristeza virus (CTV) since the 1920s using a mild strain initially called 'Nartia' but later referred to as grapefruit mild strain 12 (GFMS12). In the current study, the GFMS12 isolate was used as the source for single aphid transmissions (SAT) using Toxoptera citricida, commonly called the brown citrus aphid (BrCA). The BrCA-transmitted CTV sub-isolates were analyzed by the heteroduplex mobility assay (HMA), serological assays, genetic marker analysis (GMA), and selected sub-isolates were biologically indexed. Reverse transcription PCR of genomic regions was conducted using universal primers followed by cloning the PCR products, HMA and sequence analysis; nine genotypes of CTV were identified in the complex of GFMS12, including both severe and mild genotypes. A single BrCA transmitted up to six CTV genotypes simultaneously in one sub-isolate. The HMA was found to be a rapid, reliable tool for the identification of genotypes and can be useful in the development of CTV management strategies and budwood certification programs.
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Affiliation(s)
- K. K. Biswas
- Citrus Research and Education Center (CREC), University of Florida, Lake Alfred, FL, United States
- Plant Protection, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - M. L. Keremane
- Citrus Research and Education Center (CREC), University of Florida, Lake Alfred, FL, United States
- Agricultural Research Service, United States Department of Agriculture (USDA), Riverside, CA, United States
| | - L. J. Marais
- Citrus Research and Education Center (CREC), University of Florida, Lake Alfred, FL, United States
| | - C. Ramadugu
- Botany & Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - R. F. Lee
- Citrus Research and Education Center (CREC), University of Florida, Lake Alfred, FL, United States
- Agricultural Research Service, United States Department of Agriculture (USDA), Riverside, CA, United States
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Pais da Cunha AT, Chiumenti M, Ladeira LC, Abou Kubaa R, Loconsole G, Pantaleo V, Minafra A. High throughput sequencing from Angolan citrus accessions discloses the presence of emerging CTV strains. Virol J 2021; 18:62. [PMID: 33757535 PMCID: PMC7988965 DOI: 10.1186/s12985-021-01535-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/12/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Citrus industry is worldwide dramatically affected by outbreaks of Citrus tristeza virus (CTV). Controls should be applied to nurseries, which could act as diversity hotspots for CTV. Early detection and characterization of dangerous or emerging strains of this virus greatly help to prevent outbreaks of disease. This is particularly relevant in those growing regions where no dedicated certification programs are currently in use. METHODS Double-stranded RNA extracted from Citrus spp. samples, collected in two locations in Angola, were pooled and submitted to a random-primed RNA-seq. This technique was performed to acquire a higher amount of data in the survey, before the amplification and sequencing of genes from single plants. To confirm the CTV infection in individual plants, as suggested by RNA-seq information from the pooled samples, the analysis was integrated with multiple molecular marker amplification (MMM) for the main known CTV strains (T30, T36, VT and T3). RESULTS From the analysis of HTS data, several assembled contigs were identified as CTV and classified according to their similarity to the established strains. By the MMM amplification, only five individual accessions out of the eleven pooled samples, resulted to be infected by CTV. Amplified coat protein genes from the five positive sources were cloned and sequenced and submitted to phylogenetic analysis, while a near-complete CTV genome was also reconstructed by the fusion of three overlapping contigs. CONCLUSION Phylogenetic analysis of the ORF1b and CP genes, retrieved by de novo assembly and RT-PCR, respectively, revealed the presence of a wide array of CTV strains in the surveyed citrus-growing spots in Angola. Importantly, molecular variants among those identified from HTS showed high similarity with known severe strains as well as to recently described and emerging strains in other citrus-growing regions, such as S1 (California) or New Clade (Uruguay).
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Affiliation(s)
- Aderito Tomàs Pais da Cunha
- Instituto Superior Politécnico do Kuanza Sul (ISPKS), Rua 12 de Novembro, Sumbe, Angola
- Centro Nacional de Investigação Científica (CNIC), 201 Ho Chi Min Avenue, CP 34, Luanda, Angola
| | - Michela Chiumenti
- Institute for Sustainable Plant Protection - Consiglio Nazionale delle Ricerche (CNR), Via Giovanni Amendola 165/A, Bari, Italy
| | | | - Raied Abou Kubaa
- Institute for Sustainable Plant Protection - Consiglio Nazionale delle Ricerche (CNR), Via Giovanni Amendola 165/A, Bari, Italy
| | - Giuliana Loconsole
- Institute for Sustainable Plant Protection - Consiglio Nazionale delle Ricerche (CNR), Via Giovanni Amendola 165/A, Bari, Italy
| | - Vitantonio Pantaleo
- Institute for Sustainable Plant Protection - Consiglio Nazionale delle Ricerche (CNR), Via Giovanni Amendola 165/A, Bari, Italy
| | - Angelantonio Minafra
- Institute for Sustainable Plant Protection - Consiglio Nazionale delle Ricerche (CNR), Via Giovanni Amendola 165/A, Bari, Italy.
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Cook G, Coetzee B, Bester R, Breytenbach JHJ, Steyn C, de Bruyn R, Burger JT, Maree HJ. Citrus Tristeza Virus Isolates of the Same Genotype Differ in Stem Pitting Severity in Grapefruit. PLANT DISEASE 2020; 104:2362-2368. [PMID: 32689882 DOI: 10.1094/pdis-12-19-2586-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Two isolates of the T68 genotype of citrus tristeza virus (CTV) were derived from a common source, GFMS12, by single aphid transmission. These isolates, named GFMS12-8 and GFMS12-1.3, induced stem pitting with differing severity in 'Duncan' grapefruit (Citrus × paradisi [Macfad.]). Full-genome sequencing of these isolates showed only minor nucleotide sequence differences totaling 45 polymorphisms. Numerous nucleotide changes, in relatively close proximity, were detected in the p33 open reading frame (ORF) and the leader protease domains of ORF1a. This is the first report of full-genome characterization of CTV isolates of a single genotype, derived from the same source, but showing differences in pathogenicity. The results demonstrate the development of intragenotype heterogeneity known to occur with single-stranded RNA viruses. Identification of genetic variability between isolates showing different pathogenicity will enable interrogation of specific genome regions for potential stem pitting determinants.
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Affiliation(s)
- Glynnis Cook
- Citrus Research International, Nelspruit, 1200, South Africa
- Department of Genetics, Stellenbosch University, Matieland, 7602, South Africa
| | - Beatrix Coetzee
- Department of Genetics, Stellenbosch University, Matieland, 7602, South Africa
| | - Rachelle Bester
- Department of Genetics, Stellenbosch University, Matieland, 7602, South Africa
| | | | - Chanel Steyn
- Citrus Research International, Nelspruit, 1200, South Africa
| | | | - Johan T Burger
- Department of Genetics, Stellenbosch University, Matieland, 7602, South Africa
| | - Hans J Maree
- Department of Genetics, Stellenbosch University, Matieland, 7602, South Africa
- Citrus Research International, Matieland, 7602, South Africa
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Pechinger K, Chooi KM, MacDiarmid RM, Harper SJ, Ziebell H. A New Era for Mild Strain Cross-Protection. Viruses 2019; 11:E670. [PMID: 31340444 PMCID: PMC6669575 DOI: 10.3390/v11070670] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/12/2019] [Accepted: 07/14/2019] [Indexed: 11/18/2022] Open
Abstract
Societal and environmental pressures demand high-quality and resilient cropping plants and plant-based foods grown with the use of low or no synthetic chemical inputs. Mild strain cross-protection (MSCP), the pre-immunization of a plant using a mild strain of a virus to protect against subsequent infection by a severe strain of the virus, fits with future-proofing of production systems. New examples of MSCP use have occurred recently. New technologies are converging to support the discovery and mechanism(s) of action of MSCP strains thereby accelerating the popularity of their use.
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Affiliation(s)
- Katrin Pechinger
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | - Kar Mun Chooi
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | - Robin M MacDiarmid
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Scott J Harper
- Department of Plant Pathology, Washington, State University, Prosser, WA 99350, USA
| | - Heiko Ziebell
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany.
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Read DA, Pietersen G. Analysis of Genotype Composition of Citrus tristeza virus Populations Using Illumina Miseq Technology. Methods Mol Biol 2019; 2015:179-194. [PMID: 31222704 DOI: 10.1007/978-1-4939-9558-5_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Recent research describing the strain-specific mechanisms underlying experimental CTV superinfection exclusion has far-reaching implications for the manner in which cross-protecting sources should be selected for. The strain composition of both cross-protecting sources and field populations needs to be sufficiently characterized to improve control of severe stem-pitting and decline isolates. Many of the biological, serological, and molecular techniques used in previous studies yield very limited information about the strain composition of populations and the relative titer of their components. In this chapter we describe a protocol for the characterization of CTV populations, based on the use of the next-generation sequencing Illumina MiSeq platform of p33 gene amplicons.
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Affiliation(s)
- David A Read
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
| | - Gerhard Pietersen
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa.
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Ruiz-García AB, Bester R, Olmos A, Maree HJ. Bioinformatic Tools and Genome Analysis of Citrus tristeza virus. Methods Mol Biol 2019; 2015:163-178. [PMID: 31222703 DOI: 10.1007/978-1-4939-9558-5_12] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
High-throughput sequencing (HTS) is a powerful tool employed by plant virologists for the detection of viruses, the characterization of virus genomes and the study of host-pathogen interactions. Virus detection has been an important application of this technology, which has resulted in the discovery of novel viruses or viral strains as well as for the detection of known viruses in a plant sample. Here we describe the entire process that needs to be considered for the genome analysis of Citrus tristeza virus (CTV) by HTS, including the experimental design, sample preparation, nucleic acid purification, HTS library construction, and bioinformatic analysis.
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Affiliation(s)
| | - Rachelle Bester
- Department of Genetics, Stellenbosch University, Matieland, South Africa
- Agricultural Research Council, Infruitec-Nietvoorbij: Institute for Deciduous Fruit, Vines and Wine, Stellenbosch, South Africa
| | - Antonio Olmos
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain.
| | - Hans Jacob Maree
- Department of Genetics, Stellenbosch University, Matieland, South Africa
- Citrus Research International, Nelspruit, Mpumalanga, South Africa
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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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Maliogka VI, Minafra A, Saldarelli P, Ruiz-García AB, Glasa M, Katis N, Olmos A. Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies. Viruses 2018; 10:E436. [PMID: 30126105 PMCID: PMC6116224 DOI: 10.3390/v10080436] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/09/2018] [Accepted: 08/13/2018] [Indexed: 12/21/2022] Open
Abstract
Perennial crops, such as fruit trees, are infected by many viruses, which are transmitted through vegetative propagation and grafting of infected plant material. Some of these pathogens cause severe crop losses and often reduce the productive life of the orchards. Detection and characterization of these agents in fruit trees is challenging, however, during the last years, the wide application of high-throughput sequencing (HTS) technologies has significantly facilitated this task. In this review, we present recent advances in the discovery, detection, and characterization of fruit tree viruses and virus-like agents accomplished by HTS approaches. A high number of new viruses have been described in the last 5 years, some of them exhibiting novel genomic features that have led to the proposal of the creation of new genera, and the revision of the current virus taxonomy status. Interestingly, several of the newly identified viruses belong to virus genera previously unknown to infect fruit tree species (e.g., Fabavirus, Luteovirus) a fact that challenges our perspective of plant viruses in general. Finally, applied methodologies, including the use of different molecules as templates, as well as advantages and disadvantages and future directions of HTS in fruit tree virology are discussed.
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Affiliation(s)
- Varvara I Maliogka
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Angelantonio Minafra
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/D, 70126 Bari, Italy.
| | - Pasquale Saldarelli
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/D, 70126 Bari, Italy.
| | - Ana B Ruiz-García
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113 Moncada, Valencia, Spain.
| | - Miroslav Glasa
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84505 Bratislava, Slovak Republic.
| | - Nikolaos Katis
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Antonio Olmos
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113 Moncada, Valencia, Spain.
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Yokomi R, Selvaraj V, Maheshwari Y, Chiumenti M, Saponari M, Giampetruzzi A, Weng Z, Xiong Z, Hajeri S. Molecular and biological characterization of a novel mild strain of citrus tristeza virus in California. Arch Virol 2018; 163:1795-1804. [PMID: 29550931 DOI: 10.1007/s00705-018-3799-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 02/28/2018] [Indexed: 10/17/2022]
Abstract
Strain differentiating marker profiles of citrus tristeza virus (CTV) isolates from California have shown the presence of multiple genotypes. To better define the genetic diversity involved, full-length genome sequences from four California CTV isolates were determined by small-interfering RNA sequencing. Phylogenetic analysis and nucleotide sequence comparisons differentiated these isolates into the genotypes VT (CA-VT-AT39), T30 (CA-T30-AT4), and a new strain called S1 (CA-S1-L and CA-S1-L65). S1 isolates had three common recombination events within portions of genes from VT, T36 and RB strains and were transmissible by Aphis gossypii. Virus indexing showed that CA-VT-AT39 could be classified as a severe strain, whereas CA-T30-AT4, CA-S1-L and CA-S1-L65 were mild. CA-VT-AT39, CA-S1-L, and CA-S1-L65 reacted with monoclonal antibody MCA13, whereas CA-T30-AT4 did not. RT-PCR and RT-qPCR detection assays for the S1 strain were developed and used to screen MCA13-reactive isolates in a CTV collection from central California collected from 1968 to 2011. Forty-two isolates were found to contain the S1 strain, alone or in combinations with other genotypes. BLAST and phylogenetic analysis of the S1 p25 gene region with other extant CTV sequences from the NCBI database suggested that putative S1-like isolates might occur elsewhere (e.g., China, South Korea, Turkey, Bosnia and Croatia). This information is important for CTV evolution, detection of specific strains, and cross-protection.
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Affiliation(s)
- Raymond Yokomi
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA, 93648-9757, USA.
| | - Vijayanandraj Selvaraj
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA, 93648-9757, USA
| | - Yogita Maheshwari
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA, 93648-9757, USA
| | - Michela Chiumenti
- Institute for Sustainable Plant Protection, Italian National Research Council, Sezione di Bari, Via Amendola 122/D, 70126, Bari, Italy
| | - Maria Saponari
- Institute for Sustainable Plant Protection, Italian National Research Council, Sezione di Bari, Via Amendola 122/D, 70126, Bari, Italy
| | - Annalisa Giampetruzzi
- Department of Soil Plant and Food Science, University of Bari Aldo Moro, Via Amendola 165/A, 70126, Bari, Italy
| | - Ziming Weng
- School of Plant Sciences and BIO5 Institute, University of Arizona, Tucson, AZ, 85721-7186, USA
| | - Zhongguo Xiong
- School of Plant Sciences and BIO5 Institute, University of Arizona, Tucson, AZ, 85721-7186, USA
| | - Subhas Hajeri
- Citrus Pest Detection Program, Central California Tristeza Eradication Agency, 22847 Road 140, Tulare, CA, 93274-9367, USA
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Cook G, van Vuuren SP, Breytenbach JHJ, Steyn C, Burger JT, Maree HJ. Characterization of Citrus tristeza virus Single-Variant Sources in Grapefruit in Greenhouse and Field Trials. PLANT DISEASE 2016; 100:2251-2256. [PMID: 30682917 DOI: 10.1094/pdis-03-16-0391-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Citrus tristeza virus (CTV) is endemic to southern Africa and the stem pitting syndrome that it causes was a limiting factor in grapefruit production prior to the introduction of cross-protection in the Citrus Improvement Scheme. This disease mitigation strategy, using various field-derived CTV sources, has significantly extended the productive lifespan of grapefruit orchards in South Africa. CTV commonly occurs as a population of various strains, masking the phenotypic effect of individual strains. Likewise, current South African CTV cross-protection sources are strain mixtures, obscuring an understanding of which strains are influencing cross-protection. The severity of various CTV strains has mostly been assessed on sensitive indicator hosts, but their effect on commercial varieties has seldom been investigated. Single-variant CTV isolates were used to investigate the phenotypic expression of CTV strains in commercial grapefruit varieties as well as CTV indicator hosts. They were biologically characterized for their ability to cause stem pitting and their rate of translocation and titer in the different hosts, monitored by enzyme-linked immunosorbent assay. Complete genome sequences for three CTV strain variants were generated. Isolates of CTV strains VT, T68, RB, and HA16-5 did not induce severe stem pitting in four grapefruit hosts in a glasshouse trial. Viral titers of the strains differed in the grapefruit hosts, but the RB isolate reached a higher titer in the grapefruit hosts compared with the VT, T68, and HA16-5 isolates. Additionally, horticultural assessment of two grapefruit varieties inoculated with the RB isolate in two field trials demonstrated that mild stem pitting did not negatively influence the horticultural performance of the grapefruit trees over an eight-year assessment period. 'Star Ruby' trees containing the CTV source GFMS35 showed less stem pitting than trees inoculated with the RB isolate, but had smaller canopy volumes and lower yields than trees containing the RB isolate. This suggests that the influence of CTV sources on tree performance is not limited to the effect of stem pitting.
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Affiliation(s)
- Glynnis Cook
- Citrus Research International, Nelspruit, 1200, South Africa
| | | | | | - Chanel Steyn
- Citrus Research International, Nelspruit, 1200, South Africa
| | - Johan T Burger
- Department of Genetics, Stellenbosch University, Matieland, 7602, South Africa
| | - Hans J Maree
- Agricultural Research Council, Infruitec-Nietvoorbij: Institute for Deciduous Fruit, Vines and Wine, Stellenbosch, 7599, South Africa, and Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
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11
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Comparison of multiple viral population characterization methods on a candidate cross-protection Citrus tristeza virus (CTV) source. J Virol Methods 2016; 237:92-100. [PMID: 27599410 DOI: 10.1016/j.jviromet.2016.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 09/01/2016] [Accepted: 09/02/2016] [Indexed: 11/21/2022]
Abstract
Citrus tristeza virus (CTV) is the most economically important virus found on citrus and influences production worldwide. The 3' half of the RNA genome is generally conserved amongst sources, whereas the 5' portion is more divergent, allowing for the classification of the virus into a number of genotypes based on sequence diversity. The acknowledged genotypes of CTV are continually being expanded, and thus far include T36, T30, T3, VT, B165, HA16-5, T68 and RB. The genotype composition of the CTV populations of a potential cross protection source in Mexican lime was studied whilst comparing different techniques of viral population characterization. Cloning and sequencing of an ORF 1a fragment, genotype specific RT-PCRs and Illumina sequencing of the p33 gene as well as RNA template enrichment through immuno-capture was done. Primers used in the cloning and sequencing proved to be biased towards detection of the VT genotype. RT-PCR and Illumina sequencing using the two different templates provided relatively comparable results, even though the immuno-captured enriched template provided less than expected CTV specific data, while the RT-PCRs and p33 sequencing cannot be used to make inferences about the rest of the genome; which may vary due to recombination. The source was found to contain multiple genotypes, including RB and VT. When choosing a characterization method, the features of the virus under study should be considered. It was found that Illumina sequencing offers an opportunity to gain a large amount of information regarding the entire viral genome, but challenges encountered are discussed.
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12
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Wu Q, Ding SW, Zhang Y, Zhu S. Identification of viruses and viroids by next-generation sequencing and homology-dependent and homology-independent algorithms. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:425-44. [PMID: 26047558 DOI: 10.1146/annurev-phyto-080614-120030] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
A fast, accurate, and full indexing of viruses and viroids in a sample for the inspection and quarantine services and disease management is desirable but was unrealistic until recently. This article reviews the rapid and exciting recent progress in the use of next-generation sequencing (NGS) technologies for the identification of viruses and viroids in plants. A total of four viroids/viroid-like RNAs and 49 new plant RNA and DNA viruses from 18 known or unassigned virus families have been identified from plants since 2009. A comparison of enrichment strategies reveals that full indexing of RNA and DNA viruses as well as viroids in a plant sample at single-nucleotide resolution is made possible by one NGS run of total small RNAs, followed by data mining with homology-dependent and homology-independent computational algorithms. Major challenges in the application of NGS technologies to pathogen discovery are discussed.
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Affiliation(s)
- Qingfa Wu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 China;
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