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Keremane M, Singh K, Ramadugu C, Krueger RR, Skaggs TH. Next Generation Sequencing, and Development of a Pipeline as a Tool for the Detection and Discovery of Citrus Pathogens to Facilitate Safer Germplasm Exchange. PLANTS (BASEL, SWITZERLAND) 2024; 13:411. [PMID: 38337944 PMCID: PMC10856814 DOI: 10.3390/plants13030411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024]
Abstract
Citrus is affected by many diseases, and hence, the movement of citrus propagative materials is highly regulated in the USA. Currently used regulatory pathogen detection methods include biological and laboratory-based technologies, which are time-consuming, expensive, and have many limitations. There is an urgent need to develop alternate, rapid, economical, and reliable testing methods for safe germplasm exchange. Citrus huanglongbing (HLB) has devastated citrus industries leading to an increased need for germplasm exchanges between citrus growing regions for evaluating many potentially valuable hybrids for both HLB resistance and multilocational performance. In the present study, Next-Generation Sequencing (NGS) methods were used to sequence the transcriptomes of 21 test samples, including 15 well-characterized pathogen-positive plants. A workflow was designed in the CLC Genomics Workbench software, v 21.0.5 for bioinformatics analysis of the sequence data for the detection of pathogens. NGS was rapid and found to be a valuable technique for the detection of viral and bacterial pathogens, and for the discovery of new citrus viruses, complementary to the existing array of biological and laboratory assays. Using NGS methods, we detected beet western yellows virus, a newly reported citrus virus, and a variant of the citrus yellow vein-associated virus associated with the "fatal yellows" disease.
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Affiliation(s)
- Manjunath Keremane
- USDA ARS, National Clonal Germplasm Repository for Citrus and Dates, Riverside, CA 92507, USA;
| | - Khushwant Singh
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA;
| | - Chandrika Ramadugu
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA;
| | - Robert R. Krueger
- USDA ARS, National Clonal Germplasm Repository for Citrus and Dates, Riverside, CA 92507, USA;
| | - Todd H. Skaggs
- USDA ARS, U.S. Salinity Laboratory, Riverside, CA 92507, USA;
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Villamor DEV, Keller KE, Martin RR, Tzanetakis IE. Comparison of High Throughput Sequencing to Standard Protocols for Virus Detection in Berry Crops. PLANT DISEASE 2022; 106:518-525. [PMID: 34282931 DOI: 10.1094/pdis-05-21-0949-re] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We completed a comprehensive study comparing virus detection between high throughput sequencing (HTS) and standard protocols in 30 berry selections (12 Fragaria, 10 Vaccinium, and eight Rubus) with known virus profiles. The study examined temporal detection of viruses at four sampling times encompassing two growing seasons. Within the standard protocols, reverse transcription (RT) PCR proved better than biological indexing. Detection of known viruses by HTS and RT-PCR nearly mirrored each other. HTS provided superior detection compared with RT-PCR on a wide spectrum of variants and discovery of novel viruses. More importantly, in most cases in which the two protocols showed parallel virus detection, 11 viruses in 16 selections were not consistently detected by both methods at all sampling points. Based on these data, we propose a testing requirement of four sampling times over two growing seasons for berry and potentially other crops, to ensure that no virus remains undetected independent of titer, distribution, or other virus-virus or virus-host interactions.
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Affiliation(s)
- D E V Villamor
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - K E Keller
- U.S. Department of Agriculture Agricultural Research Service, Corvallis, OR 97330
| | - R R Martin
- U.S. Department of Agriculture Agricultural Research Service, Corvallis, OR 97330
| | - I E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
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Bester R, Cook G, Breytenbach JHJ, Steyn C, De Bruyn R, Maree HJ. Towards the validation of high-throughput sequencing (HTS) for routine plant virus diagnostics: measurement of variation linked to HTS detection of citrus viruses and viroids. Virol J 2021; 18:61. [PMID: 33752714 PMCID: PMC7986492 DOI: 10.1186/s12985-021-01523-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/02/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND High-throughput sequencing (HTS) has been applied successfully for virus and viroid discovery in many agricultural crops leading to the current drive to apply this technology in routine pathogen detection. The validation of HTS-based pathogen detection is therefore paramount. METHODS Plant infections were established by graft inoculating a suite of viruses and viroids from established sources for further study. Four plants (one healthy plant and three infected) were sampled in triplicate and total RNA was extracted using two different methods (CTAB extraction protocol and the Zymo Research Quick-RNA Plant Miniprep Kit) and sent for Illumina HTS. One replicate sample of each plant for each RNA extraction method was also sent for HTS on an Ion Torrent platform. The data were evaluated for biological and technical variation focussing on RNA extraction method, platform used and bioinformatic analysis. RESULTS The study evaluated the influence of different HTS protocols on the sensitivity, specificity and repeatability of HTS as a detection tool. Both extraction methods and sequencing platforms resulted in significant differences between the data sets. Using a de novo assembly approach, complemented with read mapping, the Illumina data allowed a greater proportion of the expected pathogen scaffolds to be inferred, and an accurate virome profile was constructed. The complete virome profile was also constructed using the Ion Torrent data but analyses showed that more sequencing depth is required to be comparative to the Illumina protocol and produce consistent results. The CTAB extraction protocol lowered the proportion of viroid sequences recovered with HTS, and the Zymo Research kit resulted in more variation in the read counts obtained per pathogen sequence. The expression profiles of reference genes were also investigated to assess the suitability of these genes as internal controls to allow for the comparison between samples across different protocols. CONCLUSIONS This study highlights the need to measure the level of variation that can arise from the different variables of an HTS protocol, from sample preparation to data analysis. HTS is more comprehensive than any assay previously used, but with the necessary validations and standard operating procedures, the implementation of HTS as part of routine pathogen screening practices is possible.
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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
| | | | - Chanel Steyn
- Citrus Research International, P.O. Box 28, Nelspruit, 1200, South Africa
- Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Rochelle De Bruyn
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
- 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, P.O. Box 2201, Matieland, 7602, South Africa.
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Belabess Z, Sagouti T, Rhallabi N, Tahiri A, Massart S, Tahzima R, Lahlali R, Jijakli MH. Citrus Psorosis Virus: Current Insights on a Still Poorly Understood Ophiovirus. Microorganisms 2020; 8:microorganisms8081197. [PMID: 32781662 PMCID: PMC7465697 DOI: 10.3390/microorganisms8081197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/27/2020] [Accepted: 08/03/2020] [Indexed: 01/11/2023] Open
Abstract
Citrus psorosis was reported for the first time in Florida in 1896 and was confirmed as a graft-transmissible disease in 1934. Citrus psorosis virus (CPsV) is the presumed causal agent of this disease. It is considered as a type species of the genus Ophiovirus, within the family Aspiviridae. CPsV genome is a negative single-stranded RNA (-ssRNA) with three segments. It has a coat protein (CP) of 48 kDa and its particles are non-enveloped with naked filamentous nucleocapsids existing as either circular open structures or collapsed pseudo-linear forms. Numerous rapid and sensitive immuno-enzymatic and molecular-based detection methods specific to CPsV are available. CPsV occurrence in key citrus growing regions across the world has been spurred the establishment of the earliest eradication and virus-free budwood programs. Despite these efforts, CPsV remains a common and serious challenge in several countries and causes a range of symptoms depending on the isolate, the cultivar, and the environment. CPsV can be transmitted mechanically to some herbaceous hosts and back to citrus. Although CPsV was confirmed to be seedborne, the seed transmission is not efficient. CPsV natural spread has been increasing based on both CPsV surveys detection and specific CPsV symptoms monitoring. However, trials to ensure its transmission by a soil-inhabiting fungus and one aphid species have been unsuccessful. Psorosis disease control is achieved using CPsV-free buds for new plantations, launching budwood certification and indexing programs, and establishing a quarantine system for the introduction of new varieties. The use of natural resistance to control CPsV is very challenging. Transgenic resistance to at least some CPsV isolates is now possible in at least some sweet orange varieties and constitutes a promising biotechnological alternative to control CPsV. This paper provides an overview of the most remarkable achievements in CPsV research that could improve the understanding of the disease and lead the development of better control strategies.
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Affiliation(s)
- Zineb Belabess
- Plant Protection Laboratory. INRA, Centre Régional de la Recherche Agronomique (CRRA), Oujda 60000, Qualipole de Berkane, 63300 Berkane, Morocco;
| | - Tourya Sagouti
- Faculté des Sciences et Techniques de Mohammedia, Laboratoire de Virologie, Microbiologie et Qualité/Ecotoxicologie et Biodiversité, 20650 Mohammedia, Morocco; (T.S.); (N.R.)
| | - Naima Rhallabi
- Faculté des Sciences et Techniques de Mohammedia, Laboratoire de Virologie, Microbiologie et Qualité/Ecotoxicologie et Biodiversité, 20650 Mohammedia, Morocco; (T.S.); (N.R.)
| | - Abdessalem Tahiri
- Phytopathology Unit, Department of Plant Protection, Ecole Nationale d’Agriculture de Meknès, 50001 Meknes, Morocco;
| | - Sébastien Massart
- Integrated and Urban Plant Pathology Laboratory, Gembloux Agro BioTech, University of Liege, 25030 Gembloux, Belgium; (S.M.); (R.T.); (M.H.J.)
| | - Rachid Tahzima
- Integrated and Urban Plant Pathology Laboratory, Gembloux Agro BioTech, University of Liege, 25030 Gembloux, Belgium; (S.M.); (R.T.); (M.H.J.)
| | - Rachid Lahlali
- Phytopathology Unit, Department of Plant Protection, Ecole Nationale d’Agriculture de Meknès, 50001 Meknes, Morocco;
- Correspondence: ; Tel.: +212-55-30-02-39
| | - M. Haissam Jijakli
- Integrated and Urban Plant Pathology Laboratory, Gembloux Agro BioTech, University of Liege, 25030 Gembloux, Belgium; (S.M.); (R.T.); (M.H.J.)
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Villamor DEV, Ho T, Al Rwahnih M, Martin RR, Tzanetakis IE. High Throughput Sequencing For Plant Virus Detection and Discovery. PHYTOPATHOLOGY 2019; 109:716-725. [PMID: 30801236 DOI: 10.1094/phyto-07-18-0257-rvw] [Citation(s) in RCA: 162] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Over the last decade, virologists have discovered an unprecedented number of viruses using high throughput sequencing (HTS), which led to the advancement of our knowledge on the diversity of viruses in nature, particularly unraveling the virome of many agricultural crops. However, these new virus discoveries have often widened the gaps in our understanding of virus biology; the forefront of which is the actual role of a new virus in disease, if any. Yet, when used critically in etiological studies, HTS is a powerful tool to establish disease causality between the virus and its host. Conversely, with globalization, movement of plant material is increasingly more common and often a point of dispute between countries. HTS could potentially resolve these issues given its capacity to detect and discover. Although many pipelines are available for plant virus discovery, all share a common backbone. A description of the process of plant virus detection and discovery from HTS data are presented, providing a summary of the different pipelines available for scientists' utility in their research.
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Affiliation(s)
- D E V Villamor
- 1 Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - T Ho
- 1 Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - M Al Rwahnih
- 2 Department of Plant Pathology, University of California, Davis 95616; and
| | - R R Martin
- 3 Horticulture Crops Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330
| | - I E Tzanetakis
- 1 Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
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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: 61] [Impact Index Per Article: 10.2] [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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Visser M, Cook G, Burger JT, Maree HJ. In silico analysis of the grapefruit sRNAome, transcriptome and gene regulation in response to CTV-CDVd co-infection. Virol J 2017; 14:200. [PMID: 29058618 PMCID: PMC5651572 DOI: 10.1186/s12985-017-0871-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 10/16/2017] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Small RNA (sRNA) associated gene regulation has been shown to play a significant role during plant-pathogen interaction. In commercial citrus orchards co-infection of Citrus tristeza virus (CTV) and viroids occur naturally. METHODS A next-generation sequencing-based approach was used to study the sRNA and transcriptional response in grapefruit to the co-infection of CTV and Citrus dwarfing viroid. RESULTS The co-infection resulted in a difference in the expression of a number of sRNA species when comparing healthy and infected plants; the majority of these were derived from transcripts processed in a phased manner. Several RNA transcripts were also differentially expressed, including transcripts derived from two genes, predicted to be under the regulation of sRNAs. These genes are involved in plant hormone systems; one in the abscisic acid, and the other in the cytokinin regulatory pathway. Additional analysis of virus- and viroid-derived small-interfering RNAs (siRNAs) showed areas on the pathogen genomes associated with increased siRNA synthesis. Most interestingly, the starting position of the p23 silencing suppressor's sub-genomic RNA generated a siRNA hotspot on the CTV genome. CONCLUSIONS This study showed the involvement of various genes, as well as endogenous and exogenous RNA-derived sRNA species in the plant-defence response. The results highlighted the role of sRNA-directed plant hormone regulation during biotic stress, as well as a counter-response of plants to virus suppressors of RNA-silencing.
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Affiliation(s)
- Marike Visser
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Glynnis Cook
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
- Citrus Research International, Nelspruit, South Africa
| | - Johan T. Burger
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Hans J. Maree
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
- Agricultural Research Council, Infruitec-Nietvoorbij: Institute for Deciduous Fruit, Vines and Wine, Stellenbosch, South Africa
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