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Olmedo-Velarde A, Ochoa-Corona FM, Larrea-Sarmiento AE, Elbeaino T, Flores F. In-silico prediction of RT-qPCR-high resolution melting for broad detection of emaraviruses. PLoS One 2023; 18:e0272980. [PMID: 37155676 PMCID: PMC10166557 DOI: 10.1371/journal.pone.0272980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 07/30/2022] [Indexed: 05/10/2023] Open
Abstract
Twenty-four species of RNA viruses contain members infecting economically important crops that are classified within the genus Emaravirus, family Fimoviridae. There are at least two other non-classified species that may be added. Some of these viruses are spreading rapidly and cause economically important diseases on several crops, raising a need for a sensitive diagnostic technique for taxonomic and quarantine purposes. High-resolution melting (HRM) has shown to be reliable for the detection, discrimination, and diagnosis of several diseases of plants, animals, and humans. This research aimed to explore the ability to predict HRM outputs coupled to reverse transcription-quantitative polymerase chain reaction (RT-qPCR). To approach this goal a pair of degenerate genus-specific primers were designed for endpoint RT-PCR and RT-qPCR-HRM and the species in the genus Emaravirus were selected to framework the development of the assays. Both nucleic acid amplification methods were able to detect in-vitro several members of seven Emaravirus species with sensitivity up to one fg of cDNA. Specific parameters for in-silico prediction of the melting temperatures of each expected emaravirus amplicon are compared to the data obtained in-vitro. A very distinct isolate of the High Plains wheat mosaic virus was also detected. The high-resolution DNA melting curves of the RT-PCR products predicted in-silico using uMeltSM allowed saving time while designing and developing the RT-qPCR-HRM assay since the approach avoided extensive searching for optimal HRM assay regions and rounds of HRM tests in-vitro for optimization. The resultant assay provides sensitive detection and reliable diagnosis for potentially any emaravirus, including new species or strains.
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Affiliation(s)
- Alejandro Olmedo-Velarde
- Institute for Biosecurity and Microbial Forensics, Oklahoma State University, Stillwater, OK, United States of America
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, United States of America
- Departamento de Ciencias de la Vida y de la Agricultura, Universidad de las Fuerzas Armadas ESPE, Sangolqui, Ecuador
| | - Francisco M Ochoa-Corona
- Institute for Biosecurity and Microbial Forensics, Oklahoma State University, Stillwater, OK, United States of America
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, United States of America
| | - Adriana E Larrea-Sarmiento
- Institute for Biosecurity and Microbial Forensics, Oklahoma State University, Stillwater, OK, United States of America
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, United States of America
| | - Toufic Elbeaino
- Istituto Agronomico Mediterraneo di Bari, Valenzano, BA, Italy
| | - Francisco Flores
- Departamento de Ciencias de la Vida y de la Agricultura, Universidad de las Fuerzas Armadas ESPE, Sangolqui, Ecuador
- Centro de Investigación de Alimentos, CIAL, Facultad de Ciencias de la Ingeniería e Industrias, Universidad UTE, Quito, Ecuador
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Olmedo-Velarde A, Ochoa-Corona FM, Larrea-Sarmiento AE, Elbeaino T, Flores F. Exploring in-silico prediction for the development of a RT-qPCR-high resolution melting assay for the broad detection of emaraviruses. J Virol Methods 2021:114425. [PMID: 34902460 DOI: 10.1016/j.jviromet.2021.114425] [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: 07/13/2020] [Revised: 03/09/2021] [Accepted: 12/09/2021] [Indexed: 01/13/2023]
Abstract
High-resolution melting (HRM) has shown to be reliable for the detection, discrimination, and diagnosis of several diseases of plants, animals, and humans. The aim of this research was to explore the ability to predict HRM outputs when coupled to reverse transcription quantitative polymerase chain reaction (RT-qPCR). This research used the species in the Emaravirus genus as model to framework the development of genus-specific RT-qPCR-HRM assays. A pair of degenerate genus-specific primers were designed for use in endpoint RT-PCR and RT-qPCR-HRM detection of emaraviruses. Eleven species of RNA viruses infecting economically important crops are classified within the genus Emaravirus, family Fimoviridae. There are at least fifteen other non-classified species that may be added. Some of these viruses are spreading rapidly and cause economically important diseases on several crops, raising a need for a sensitive diagnostic technique for taxonomic and quarantine purposes. RT-PCR and RT-qPCR-HRM were able to detect seven emaravirus species in-vitro with sensitivity up to one fg of cDNA. Specific parameters for prediction in-silico of the melting temperatures of each expected emaravirus amplicon are provided and compared to the data obtained in-vitro. A very distinct isolate of the High Plains wheat mosaic virus was also detected. The prediction in-silico of fluorescence of high-resolution DNA melting curves of predicted RT-PCR products using uMeltSM speeded the design and development of RT-qPCR-HRM assay. This approach avoided rounds of HRM tests in-vitro when searching for the optimal regions that provides accurate diagnosis. The resultant assay provided sensitive detection and reliable diagnosis for potentially any emaravirus, including new species or strains.
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Affiliation(s)
- Alejandro Olmedo-Velarde
- Oklahoma State University, Institute for Biosecurity and Microbial Forensics, Stillwater, OK, USA; Oklahoma State University, Department of Entomology and Plant Pathology, Stillwater, OK, USA; Universidad de las Fuerzas Armadas ESPE, Departamento de Ciencias de la Vida y de la Agricultura, Sangolqui, Ecuador
| | - Francisco M Ochoa-Corona
- Oklahoma State University, Institute for Biosecurity and Microbial Forensics, Stillwater, OK, USA; Oklahoma State University, Department of Entomology and Plant Pathology, Stillwater, OK, USA.
| | - Adriana E Larrea-Sarmiento
- Oklahoma State University, Institute for Biosecurity and Microbial Forensics, Stillwater, OK, USA; Oklahoma State University, Department of Entomology and Plant Pathology, Stillwater, OK, USA
| | - Toufic Elbeaino
- Istituto Agronomico Mediterraneo di Bari, Valenzano, BA, Italy
| | - Francisco Flores
- Universidad de las Fuerzas Armadas ESPE, Departamento de Ciencias de la Vida y de la Agricultura, Sangolqui, Ecuador; Universidad UTE, Centro de Investigación de Alimentos, CIAL, Facultad de Ciencias de la Ingeniería e Industrias, Quito, Ecuador
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Nie X, Singh M, Chen D, Gilchrist C, Soqrat Y, Shukla M, Creelman A, Dickison V, Nie B, Lavoie J, Bisht V. Development of High-Resolution DNA Melting Analysis for Simultaneous Detection of Potato Mop-Top Virus and Its Vector, Spongospora subterranea, in Soil. PLANT DISEASE 2021; 105:948-957. [PMID: 32915119 DOI: 10.1094/pdis-06-20-1321-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this study, a set of duplex reverse transcription PCR (RT-PCR)-mediated high-resolution DNA melting (HRM) analyses for simultaneous detection of potato mop-virus (PMTV) and its protist vector, Spongospora subterranea f. sp. subterranea (Sss), was developed. The infestation of soil by PMTV was detected with a tobacco-based baiting system. Total RNA extracted from the soil led to successful RT-PCR gel electrophoresis detection of both PMTV and Sss. To facilitate more efficient detection, newly designed primer pairs for PMTV RNA species (i.e., RNA-Rep, RNA-CP, and RNA-TGB) were analyzed together with the existing Sss primers via real-time RT-PCR. The resulting amplicons exhibited melting profiles that could be readily differentiated. Under duplex RT-PCR format, all PMTV and Sss primer combinations led to successful detection of respective PMTV RNA species and Sss in the samples by HRM analyses. When the duplex HRM assay was applied to soil samples collected from six fields at four different sites in New Brunswick, Canada, positive detection of PMTV or Sss was found in 63 to 100% samples collected from fields in which PMTV-infected tubers had been observed. In contrast, the samples from fields where neither PMTV- nor Sss-infected tubers had been observed resulted in negative detection by the assay. Bait tobacco bioassay for PMTV and Sss produced similar results. Of the soil samples collected from PMTV-infested fields, 63 to 83% and 100% led to PMTV and Sss infections in the bait tobacco plants, respectively, whereas no PMTV- or Sss-infected plants were obtained from soil samples collected from PMTV- and Sss-free fields.
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Affiliation(s)
- Xianzhou Nie
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
| | - Mathuresh Singh
- Agricultural Certification Services, Fredericton, NB E3B 8B7, Canada
| | - Dahu Chen
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
| | - Cassandra Gilchrist
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Yasmine Soqrat
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
- Biology Program, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Manisha Shukla
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
| | - Alexa Creelman
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
| | - Virginia Dickison
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
| | - Bihua Nie
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Jacques Lavoie
- New Brunswick Department of Agriculture, Aquaculture and Fisheries, Potato Development Centre, Wicklow, NB E7L 3S4, Canada
| | - Vikram Bisht
- Manitoba Agriculture, Carman, MB R0G 0J0, Canada
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Worasilchai N, Permpalung N, Chindamporn A. High-resolution melting analysis: A novel approach for clade differentiation in Pythium insidiosum and pythiosis. Med Mycol 2018; 56:868-876. [PMID: 29228389 DOI: 10.1093/mmy/myx123] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/12/2017] [Indexed: 01/02/2023] Open
Abstract
Pythium insidiosum causes life-threatening human pythiosis. Based on phylogenetic analysis using internal transcribed spacer (ITS) region, mitochondrial cytochrome C oxidase II (COX2) gene, intergenic spacer (IGS) region and exo-1,3-β-glucanase gene (exo1), P. insidiosum is classified into clade ATH, BTH, and CTH related to geographic distribution. At present, polymerase chain reaction in any of these specific regions with DNA sequencing is the only technique to provide clade diagnosis. In this study, P. insidiosum-specific primers targeting COX2 gene were designed and used in real-time quantitative polymerase chain reaction (qPCR) with subsequent high-resolution melting (HRM) to provide rapid identification as well as clade classification for P. insidiosum. Based on the qPCR-HRM method, 15 P. insidiosum isolates could be differentiated from 28 related organisms with 100% specificity and 1 pg limit of detection. This technique was, in addition, directly tested on clinical samples from proved human pythiosis cases: nine corneal scrapes and six arterial clots. The qPCR-HRM results of all nine corneal samples were a 100% match with the results from the conventional PCR at clade level. However, the qPCR-HRM results of arterial clot samples were only matched with the nucleotide sequencing results from the conventional PCR at species level. In conclusion, the qPCR-HRM is a simple one closed tube, inexpensive and user-friendly method to identify P. insidiosum into clade level.
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Affiliation(s)
- Navaporn Worasilchai
- Interdisciplinary Program, Medical Microbiology, Chulalongkorn University, Bangkok, Thailand
| | - Nitipong Permpalung
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina, USA
| | - Ariya Chindamporn
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
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di Rienzo V, Bubici G, Montemurro C, Cillo F. Rapid identification of tomato Sw-5 resistance-breaking isolates of Tomato spotted wilt virus using high resolution melting and TaqMan SNP Genotyping assays as allelic discrimination techniques. PLoS One 2018; 13:e0196738. [PMID: 29709020 PMCID: PMC5927427 DOI: 10.1371/journal.pone.0196738] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/18/2018] [Indexed: 12/11/2022] Open
Abstract
In tomato, resistance to Tomato spotted wilt virus (TSWV) is conferred by the dominant gene, designated Sw-5. Virulent Sw-5 resistance breaking (SRB) mutants of TSWV have been reported on Sw-5 tomato cultivars. Two different PCR-based allelic discrimination techniques, namely Custom TaqMan™ SNP Genotyping and high-resolution melting (HRM) assays, were developed and compared for their ability to distinguish between avirulent (Sw-5 non-infecting, SNI) and SRB biotypes. TaqMan assays proved to be more sensitive (threshold of detection in a range of 50–70 TSWV RNA copies) and more reliable than HRM, assigning 25 TSWV isolates to their correct genotype with an accuracy of 100%. Moreover, the TaqMan SNP assays were further improved developing a rapid and simple protocol that included crude leaf extraction for RNA template preparations. On the other hand, HRM assays showed higher levels of sensitivity than TaqMan when used to co-detect both biotypes in different artificial mixtures. These diagnostic assays contributed to gain preliminary information on the epidemiology of TSWV isolates in open field conditions. In fact, the presented data suggest that SRB isolates are present as stable populations established year round, persisting on both winter (globe artichoke) and summer (tomato) crops, in the same cultivated areas of Southern Italy.
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Affiliation(s)
| | - Giovanni Bubici
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Cinzia Montemurro
- Spin off SINAGRI s.r.l., Bari, Italy
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Fabrizio Cillo
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
- * E-mail:
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Ferro AM, Ramos P, Guerreiro O, Jerónimo E, Pires I, Capel C, Capel J, Lozano R, Duarte MF, Oliveira MM, Gonçalves S. Impact of novel SNPs identified in Cynara cardunculus genes on functionality of proteins regulating phenylpropanoid pathway and their association with biological activities. BMC Genomics 2017; 18:183. [PMID: 28212611 PMCID: PMC5314637 DOI: 10.1186/s12864-017-3534-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 02/02/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cynara cardunculus L. offers a natural source of phenolic compounds with the predominant molecule being chlorogenic acid. Chlorogenic acid is gaining interest due to its involvement in various biological properties such as, antibacterial, antifungal, antioxidant, hepatoprotective, and anticarcinogenic activities. RESULTS In this work we screened a Cynara cardunculus collection for new allelic variants in key genes involved in the chlorogenic acid biosynthesis pathway. The target genes encode p-coumaroyl ester 3'-hydroxylase (C3'H) and hydroxycinnamoyl-CoA: quinate hydroxycinnamoyl transferase (HQT), both participating in the synthesis of chlorogenic acid. Using high-resolution melting, the C3'H gene proved to be highly conserved with only 4 haplotypes while, for HQT, 17 haplotypes were identified de novo. The putative influence of the identified polymorphisms in C3'H and HQT proteins was further evaluated using bioinformatics tools. We could identify some polymorphisms that may lead to protein conformational changes. Chlorogenic acid content, antioxidant and antithrombin activities were also evaluated in Cc leaf extracts and an association analysis was performed to assess a putative correlation between these traits and the identified polymorphisms. CONCLUSION In this work we identified allelic variants with putative impact on C3'H and HQT proteins which are significantly associated with chlorogenic acid content and antioxidant activity. Further study of these alleles should be explored to assess putative relevance as genetic markers correlating with Cynara cardunculus biological properties with further confirmation by functional analysis.
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Affiliation(s)
- Ana Margarida Ferro
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Rua Pedro Soares, 7801-908 Beja, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2781-901 Oeiras, Portugal
| | - Patrícia Ramos
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Rua Pedro Soares, 7801-908 Beja, Portugal
- Centre for Research in Ceramics and Composite Materials (CICECO) and Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Olinda Guerreiro
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Rua Pedro Soares, 7801-908 Beja, Portugal
- Centro de Investigação Interdisciplinar em Sanidade Animal (CIISA), Faculdade de Medicina Veterinária, University of Lisbon, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Eliana Jerónimo
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Rua Pedro Soares, 7801-908 Beja, Portugal
| | - Inês Pires
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2781-901 Oeiras, Portugal
| | - Carmen Capel
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, 04120 Almeria, Spain
| | - Juan Capel
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, 04120 Almeria, Spain
| | - Rafael Lozano
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, 04120 Almeria, Spain
| | - Maria F. Duarte
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Rua Pedro Soares, 7801-908 Beja, Portugal
| | - M. Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2781-901 Oeiras, Portugal
| | - Sónia Gonçalves
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Rua Pedro Soares, 7801-908 Beja, Portugal
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB101SA Cambridge, UK
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Wang HB, Mo QH, Wang Q, Wu BM, Feng ZL, Lin JC, Yang Z. Probe-free and sensitive detection of diarrhea-causing pathogens using RT-PCR combined high resolution melting analysis. Biologicals 2016; 44:360-6. [DOI: 10.1016/j.biologicals.2016.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 06/24/2016] [Accepted: 06/29/2016] [Indexed: 11/29/2022] Open
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