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MacKenzie KJ, Xavier KV, Wen A, Timilsina S, Adkison HM, Dufault NS, Vallad GE. Widespread QoI Fungicide Resistance Revealed Among Corynespora cassiicola Tomato Isolates in Florida. PLANT DISEASE 2020; 104:893-903. [PMID: 31891552 DOI: 10.1094/pdis-03-19-0460-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Target spot of tomato caused by Corynespora cassiicola is one of the most economically destructive diseases of tomato in Florida. A collection of 123 isolates from eight counties in Florida were evaluated for sensitivity to azoxystrobin and fenamidone based on mycelial growth inhibition (MGI), spore germination (SG), detached leaflet assays (DLAs), and sequence-based analysis of the cytochrome b gene (cytb). Cleavage of cytb by restriction enzyme (Fnu4HI) revealed the presence of a mutation conferring a glycine (G) to alanine (A) mutation at amino acid position 143 (G143A) in approximately 90% of the population, correlating with quinone outside inhibitor (QoI) resistance based on MGI (<40% at 5 μg/ml), SG (<50% at 1 and 10 μg/ml), and DLA (<10% severity reduction). The mutation conferring a phenylalanine (F) to leucine (L) substitution at position 129 (F129L) was confirmed in moderately resistant isolates (#9, #19, and #74) based on MGI (40 to 50% at 5 μg/ml), SG (<50% at 1 μg/ml and >50% at 10 μg/ml), and DLA (>10% and <43% severity reduction) for both QoI fungicides, whereas sensitive isolates (#1, #4, #7, #28, #29, #46, #61, #74, #75, #76, #91, #95, and #118) based on MGI (>50% at 5 μg/ml), SG (>50% at 1 μg/ml and 10 μg/ml), and DLA (>50% severity reduction) correlated to non-mutation-containing isolates or those with a silent mutation. This study indicates that QoI resistance among C. cassiicola isolates from tomato is widespread in Florida and validates rapid screening methods using MGI or molecular assays to identify resistant isolates in future studies.
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Affiliation(s)
- Keevan J MacKenzie
- University of Florida, Gulf Coast Research and Education Center, Wimauma, FL 33598
| | - Katia V Xavier
- University of Florida, Gulf Coast Research and Education Center, Wimauma, FL 33598
| | - Aimin Wen
- University of Florida, Gulf Coast Research and Education Center, Wimauma, FL 33598
| | - Sujan Timilsina
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - Heather M Adkison
- University of Florida, Gulf Coast Research and Education Center, Wimauma, FL 33598
| | - Nicholas S Dufault
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - Gary E Vallad
- University of Florida, Gulf Coast Research and Education Center, Wimauma, FL 33598
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Nikitin M, Deych K, Grevtseva I, Girsova N, Kuznetsova M, Pridannikov M, Dzhavakhiya V, Statsyuk N, Golikov A. Preserved Microarrays for Simultaneous Detection and Identification of Six Fungal Potato Pathogens with the Use of Real-Time PCR in Matrix Format. BIOSENSORS 2018; 8:E129. [PMID: 30551630 PMCID: PMC6316111 DOI: 10.3390/bios8040129] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/08/2018] [Accepted: 12/11/2018] [Indexed: 01/11/2023]
Abstract
Fungal diseases of plants are of great economic importance causing 70⁻80% of crop losses associated with microbial plant pathogens. Advanced on-site disease diagnostics is very important to maximize crop productivity. In this study, diagnostic systems have been developed for simultaneous detection and identification of six fungal pathogens using 48-well microarrays (micromatrices) for qPCR. All oligonucleotide sets were tested for their specificity using 59 strains of target and non-target species. Detection limit of the developed test systems varied from 0.6 to 43.5 pg of DNA depending on target species with reproducibility within 0.3-0.7% (standard deviation). Diagnostic efficiency of test systems with stabilized and freeze-dried PCR master-mixes did not significantly differ from that of freshly prepared microarrays, though detection limit increased. Validation of test systems on 30 field samples of potato plants showed perfect correspondence with the results of morphological identification of pathogens. Due to the simplicity of the analysis and the automated data interpretation, the developed microarrays have good potential for on-site use by technician-level personnel, as well as for high-throughput monitoring of fungal potato pathogens.
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Affiliation(s)
- Maksim Nikitin
- GenBit LLC, Nauchny pr., 20, Bld. 4, Moscow 117246, Russia.
| | - Ksenia Deych
- GenBit LLC, Nauchny pr., 20, Bld. 4, Moscow 117246, Russia.
| | | | - Natalya Girsova
- All-Russian Research Institute of Phytopathology, Institute Str., 5, Bolshie Vyazemy 143050, Russia.
| | - Maria Kuznetsova
- All-Russian Research Institute of Phytopathology, Institute Str., 5, Bolshie Vyazemy 143050, Russia.
| | - Mikhail Pridannikov
- All-Russian Research Institute of Phytopathology, Institute Str., 5, Bolshie Vyazemy 143050, Russia.
- Centre of Parasitology, Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskii Prospect 33, Moscow 119071, Russia.
| | - Vitaly Dzhavakhiya
- All-Russian Research Institute of Phytopathology, Institute Str., 5, Bolshie Vyazemy 143050, Russia.
| | - Natalia Statsyuk
- All-Russian Research Institute of Phytopathology, Institute Str., 5, Bolshie Vyazemy 143050, Russia.
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Zahariev M, Chen W, Visagie CM, Lévesque CA. Cluster oligonucleotide signatures for rapid identification by sequencing. BMC Bioinformatics 2018; 19:395. [PMID: 30522439 PMCID: PMC6284311 DOI: 10.1186/s12859-018-2363-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Accepted: 09/09/2018] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Oligonucleotide signatures (signatures) have been widely used for studying microbial diversity and function in wet-lab settings, but using them for accurate in silico identification of organisms from high-throughput sequencing (HTS) data is only a proof of concept. Existing signature design programs for sequence signatures (signatures matching exactly one sequence) or clade signatures (signatures matching every sequence in a phylogenetic clade) are not able to identify all possible polymorphic sites for sequences with high similarity and perform poorly when handling large genome sequencing datasets. RESULTS We introduce cluster signatures: subsequences that match perfectly and exclusively any group of sequences in a data set. Cluster signatures provide complete recall for primer/probe design and increased discrimination between sequences beyond that of clade signatures. Using cluster signatures for in silico identification of HTS targets achieves good precision/recall and running time performance. This method has been implemented into an open source tool, the Automated Oligonucleotide Design Pipeline (adop), included in supplementary material and available at: https://bitbucket.org/wenchen_aafc/aodp_v2.0_release . CONCLUSIONS Cluster signatures provide a rapid and universal analysis tool to identify all possible short diagnostic DNA markers and variants from any DNA sequencing dataset. They are particularly useful in discriminating genetic material from closely related organisms and in detecting deleterious mutations in highly or perfectly conserved genomic sites.
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Affiliation(s)
- Manuel Zahariev
- Ottawa R&D Centre, Agriculture & Agri-Food Canada, 960 Carling Ave., Ottawa, ON, K1A 0C6 Canada
| | - Wen Chen
- Skwez Technology Corp, Box 3674, Garibaldi Highlands, BC, V0N 1T0 Canada
| | - Cobus M. Visagie
- The Agricultural Research Counci –PPRI, P/Bag X134, Queenswood, 0121 South Africa
| | - C. André Lévesque
- Sidney Laboratory Project - Science, Canadian Food Inspection Agency, Floor 2E, Room 233, 59 Camelot Drive, Ottawa, ON, K1A 0Y9 Canada
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Shamoun SF, Rioux D, Callan B, James D, Hamelin RC, Bilodeau GJ, Elliott M, Lévesque CA, Becker E, McKenney D, Pedlar J, Bailey K, Brière SC, Niquidet K, Allen E. An Overview of Canadian Research Activities on Diseases Caused by Phytophthora ramorum: Results, Progress, and Challenges. PLANT DISEASE 2018; 102:1218-1233. [PMID: 30673582 DOI: 10.1094/pdis-11-17-1730-fe] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
International trade and travel are the driving forces behind the spread of invasive plant pathogens around the world, and human-mediated movement of plants and plant products is now generally accepted as the primary mode of their introduction, resulting in huge disturbance to ecosystems and severe socio-economic impact. These problems are exacerbated under the present conditions of rapid climatic change. We report an overview of the Canadian research activities on Phytophthora ramorum. Since the first discovery and subsequent eradication of P. ramorum on infected ornamentals in nurseries in Vancouver, British Columbia, in 2003, a research team of Canadian government scientists representing the Canadian Forest Service, Canadian Food Inspection Agency, and Agriculture and Agri-Food Canada worked together over a 10-year period and have significantly contributed to many aspects of research and risk assessment on this pathogen. The overall objectives of the Canadian research efforts were to gain a better understanding of the molecular diagnostics of P. ramorum, its biology, host-pathogen interactions, and management options. With this information, it was possible to develop pest risk assessments and evaluate the environmental and economic impact and future research needs and challenges relevant to P. ramorum and other emerging forest Phytophthora spp.
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Affiliation(s)
- Simon Francis Shamoun
- Natural Resources Canada (NRCan), Canadian Forest Service (CFS), Pacific Forestry Centre (PFC), Victoria, BC, V8Z 1M5, Canada
| | - Danny Rioux
- NRCan, CFS, Laurentian Forestry Centre (LFC), P.O. Box 10380, Sainte-Foy, Québec, G1V 4C7, Canada
| | | | - Delano James
- Canadian Food Inspection Agency (CFIA), Sidney Laboratory, Sidney, BC, V8L 1H3, Canada
| | - Richard C Hamelin
- NRCan, CFS, LFC, P.O. Box 10380, Sainte-Foy, Québec, G1V 4C7, Canada
| | | | | | - C André Lévesque
- Agriculture and Agri-Food Canada (AAFC), Ottawa, ON, K1A 0C6, Canada
| | | | - Dan McKenney
- NRCan, CFS, Great Lakes Forestry Centre (GLFC), Sault Ste. Marie, ON, P6A 2E5, Canada
| | - John Pedlar
- NRCan, CFS, Great Lakes Forestry Centre (GLFC), Sault Ste. Marie, ON, P6A 2E5, Canada
| | | | - S C Brière
- CFIA, P.O. Box 11300, Ottawa, ON, K2H 8P9, Canada
| | | | - Eric Allen
- NRCan, CFS, PFC, Victoria, BC, V8Z 1M5, Canada
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DNA Barcoding for Diagnosis and Monitoring of Fungal Plant Pathogens. Fungal Biol 2017. [DOI: 10.1007/978-3-319-34106-4_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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6
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PM 7/129 (1) DNA barcoding as an identification tool for a number of regulated pests. ACTA ACUST UNITED AC 2016. [DOI: 10.1111/epp.12344] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Malapi-Wight M, Demers JE, Veltri D, Marra RE, Crouch JA. LAMP Detection Assays for Boxwood Blight Pathogens: A Comparative Genomics Approach. Sci Rep 2016; 6:26140. [PMID: 27199028 PMCID: PMC4873745 DOI: 10.1038/srep26140] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 04/27/2016] [Indexed: 11/09/2022] Open
Abstract
Rapid and accurate molecular diagnostic tools are critical to efforts to minimize the impact and spread of emergent pathogens. The identification of diagnostic markers for novel pathogens presents several challenges, especially in the absence of information about population diversity and where genetic resources are limited. The objective of this study was to use comparative genomics datasets to find unique target regions suitable for the diagnosis of two fungal species causing a newly emergent blight disease of boxwood. Candidate marker regions for loop-mediated isothermal amplification (LAMP) assays were identified from draft genomes of Calonectria henricotiae and C. pseudonaviculata, as well as three related species not associated with this disease. To increase the probability of identifying unique targets, we used three approaches to mine genome datasets, based on (i) unique regions, (ii) polymorphisms, and (iii) presence/absence of regions across datasets. From a pool of candidate markers, we demonstrate LAMP assay specificity by testing related fungal species, common boxwood pathogens, and environmental samples containing 445 diverse fungal taxa. This comparative-genomics-based approach to the development of LAMP diagnostic assays is the first of its kind for fungi and could be easily applied to diagnostic marker development for other newly emergent plant pathogens.
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Affiliation(s)
- Martha Malapi-Wight
- United States Department of Agriculture, Agricultural Research Service (ARS), Systematic Mycology and Microbiology Laboratory, Beltsville, MD 20705, USA
| | - Jill E. Demers
- United States Department of Agriculture, Agricultural Research Service (ARS), Systematic Mycology and Microbiology Laboratory, Beltsville, MD 20705, USA
| | - Daniel Veltri
- United States Department of Agriculture, Agricultural Research Service (ARS), Systematic Mycology and Microbiology Laboratory, Beltsville, MD 20705, USA
- Oak Ridge Institute for Science and Education, ARS Research Participation Program, Oak Ridge, TN 37831, USA
| | - Robert E. Marra
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT 06504, USA
| | - Jo Anne Crouch
- United States Department of Agriculture, Agricultural Research Service (ARS), Systematic Mycology and Microbiology Laboratory, Beltsville, MD 20705, USA
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Liebe S, Christ DS, Ehricht R, Varrelmann M. Development of a DNA Microarray-Based Assay for the Detection of Sugar Beet Root Rot Pathogens. PHYTOPATHOLOGY 2016; 106:76-86. [PMID: 26524545 DOI: 10.1094/phyto-07-15-0171-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Sugar beet root rot diseases that occur during the cropping season or in storage are accompanied by high yield losses and a severe reduction of processing quality. The vast diversity of microorganism species involved in rot development requires molecular tools allowing simultaneous identification of many different targets. Therefore, a new microarray technology (ArrayTube) was applied in this study to improve diagnosis of sugar beet root rot diseases. Based on three marker genes (internal transcribed spacer, translation elongation factor 1 alpha, and 16S ribosomal DNA), 42 well-performing probes enabled the identification of prevalent field pathogens (e.g., Aphanomyces cochlioides), storage pathogens (e.g., Botrytis cinerea), and ubiquitous spoilage fungi (e.g., Penicillium expansum). All probes were proven for specificity with pure cultures from 73 microorganism species as well as for in planta detection of their target species using inoculated sugar beet tissue. Microarray-based identification of root rot pathogens in diseased field beets was successfully confirmed by classical detection methods. The high discriminatory potential was proven by Fusarium species differentiation based on a single nucleotide polymorphism. The results demonstrate that the ArrayTube constitute an innovative tool allowing a rapid and reliable detection of plant pathogens particularly when multiple microorganism species are present.
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Affiliation(s)
- Sebastian Liebe
- First, second, and fourth authors: Institute of Sugar Beet Research, Holtenser Landstr. 77, 37079 Göttingen, Germany; and third author: Alere Technologies GmbH, Löbstedter Str. 105, 07743 Jena, Germany, and InfectoGnostics Research Campus Jena, Germany
| | - Daniela S Christ
- First, second, and fourth authors: Institute of Sugar Beet Research, Holtenser Landstr. 77, 37079 Göttingen, Germany; and third author: Alere Technologies GmbH, Löbstedter Str. 105, 07743 Jena, Germany, and InfectoGnostics Research Campus Jena, Germany
| | - Ralf Ehricht
- First, second, and fourth authors: Institute of Sugar Beet Research, Holtenser Landstr. 77, 37079 Göttingen, Germany; and third author: Alere Technologies GmbH, Löbstedter Str. 105, 07743 Jena, Germany, and InfectoGnostics Research Campus Jena, Germany
| | - Mark Varrelmann
- First, second, and fourth authors: Institute of Sugar Beet Research, Holtenser Landstr. 77, 37079 Göttingen, Germany; and third author: Alere Technologies GmbH, Löbstedter Str. 105, 07743 Jena, Germany, and InfectoGnostics Research Campus Jena, Germany
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Úrbez-Torres JR, Haag P, Bowen P, Lowery T, O'Gorman DT. Development of a DNA Macroarray for the Detection and Identification of Fungal Pathogens Causing Decline of Young Grapevines. PHYTOPATHOLOGY 2015; 105:1373-1388. [PMID: 25938177 DOI: 10.1094/phyto-03-15-0069-r] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Young vine decline (YVD) is a complex disease caused by at least 51 different fungi and responsible for important economic losses to the grapevine industry worldwide. YVD fungi are known to occur in planting material. Hence, detection prior to planting is critical to assure longevity of newly established vineyards. A DNA macroarray based on reverse dot-blot hybridization containing 102 oligonucleotides complementary to portions of the β-tubulin region was developed for detection of YVD fungi. Specificity of the array was first evaluated against 138 pure fungal cultures representing 72 different taxa from nine genera, including 37 YVD species. In total, 61 species, including 34 YVD pathogens, were detected and identified by the array. The detection limit of the array was below 0.1 pg of genomic DNA. The array was validated against artificially inoculated canes and soil and commercial planting material, with the latter showing a high incidence of YVD fungi in nursery plants otherwise not detected by traditional plating and culturing. This DNA array proved to be a rapid and specific tool to simultaneously detect and identify most YVD fungi in a single test, which has the potential to be used in commercial diagnostics or by the grapevine nursery industry to determine the health status of the planting material.
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Affiliation(s)
- J R Úrbez-Torres
- Agriculture and Agri-Food Canada, Science & Technology Branch, Pacific Agri-Food Research Centre, Summerland, British Columbia V0H 1Z0, Canada
| | - P Haag
- Agriculture and Agri-Food Canada, Science & Technology Branch, Pacific Agri-Food Research Centre, Summerland, British Columbia V0H 1Z0, Canada
| | - P Bowen
- Agriculture and Agri-Food Canada, Science & Technology Branch, Pacific Agri-Food Research Centre, Summerland, British Columbia V0H 1Z0, Canada
| | - T Lowery
- Agriculture and Agri-Food Canada, Science & Technology Branch, Pacific Agri-Food Research Centre, Summerland, British Columbia V0H 1Z0, Canada
| | - D T O'Gorman
- Agriculture and Agri-Food Canada, Science & Technology Branch, Pacific Agri-Food Research Centre, Summerland, British Columbia V0H 1Z0, Canada
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Català S, Pérez-Sierra A, Abad-Campos P. The use of genus-specific amplicon pyrosequencing to assess phytophthora species diversity using eDNA from soil and water in Northern Spain. PLoS One 2015; 10:e0119311. [PMID: 25775250 PMCID: PMC4361056 DOI: 10.1371/journal.pone.0119311] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 01/12/2015] [Indexed: 11/18/2022] Open
Abstract
Phytophthora is one of the most important and aggressive plant pathogenic genera in agriculture and forestry. Early detection and identification of its pathways of infection and spread are of high importance to minimize the threat they pose to natural ecosystems. eDNA was extracted from soil and water from forests and plantations in the north of Spain. Phytophthora-specific primers were adapted for use in high-throughput Sequencing (HTS). Primers were tested in a control reaction containing eight Phytophthora species and applied to water and soil eDNA samples from northern Spain. Different score coverage threshold values were tested for optimal Phytophthora species separation in a custom-curated database and in the control reaction. Clustering at 99% was the optimal criteria to separate most of the Phytophthora species. Multiple Molecular Operational Taxonomic Units (MOTUs) corresponding to 36 distinct Phytophthora species were amplified in the environmental samples. Pyrosequencing of amplicons from soil samples revealed low Phytophthora diversity (13 species) in comparison with the 35 species detected in water samples. Thirteen of the MOTUs detected in rivers and streams showed no close match to sequences in international sequence databases, revealing that eDNA pyrosequencing is a useful strategy to assess Phytophthora species diversity in natural ecosystems.
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Affiliation(s)
- Santiago Català
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Camino de Vera s/n, Valencia, Spain
| | - Ana Pérez-Sierra
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Camino de Vera s/n, Valencia, Spain
- Forest Research, Alice Holt Lodge, Farnham, Surrey, United Kingdom
| | - Paloma Abad-Campos
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Camino de Vera s/n, Valencia, Spain
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Bilodeau GJ, Martin FN, Coffey MD, Blomquist CL. Development of a multiplex assay for genus- and species-specific detection of Phytophthora based on differences in mitochondrial gene order. PHYTOPATHOLOGY 2014; 104:733-748. [PMID: 24915428 DOI: 10.1094/phyto-09-13-0263-r] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A molecular diagnostic assay for Phytophthora spp. that is specific, sensitive, has both genus- and species-specific detection capabilities multiplexed, and can be used to systematically develop markers for detection of a wide range of species would facilitate research and regulatory efforts. To address this need, a marker system was developed based on the high copy sequences of the mitochondrial DNA utilizing gene orders that were highly conserved in the genus Phytophthora but different in the related genus Pythium and plants to reduce the importance of highly controlled annealing temperatures for specificity. An amplification primer pair designed from conserved regions of the atp9 and nad9 genes produced an amplicon of ≈340 bp specific for the Phytophthora spp. tested. The TaqMan probe for the genus-specific Phytophthora test was designed from a conserved portion of the atp9 gene whereas variable intergenic spacer sequences were used for designing the species-specific TaqMan probes. Specific probes were developed for 13 species and the P. citricola species complex. In silico analysis suggests that species-specific probes could be developed for at least 70 additional described and provisional species; the use of locked nucleic acids in TaqMan probes should expand this list. A second locus spanning three tRNAs (trnM-trnP-trnM) was also evaluated for genus-specific detection capabilities. At 206 bp, it was not as useful for systematic development of a broad range of species-specific probes as the larger 340-bp amplicon. All markers were validated against a test panel that included 87 Phytophthora spp., 14 provisional Phytophthora spp., 29 Pythium spp., 1 Phytopythium sp., and 39 plant species. Species-specific probes were validated further against a range of geographically diverse isolates to ensure uniformity of detection at an intraspecific level, as well as with other species having high levels of sequence similarity to ensure specificity. Both diagnostic assays were also validated against 130 environmental samples from a range of hosts. The only limitation observed was that primers for the 340 bp atp9-nad9 locus did not amplify Phytophthora bisheria or P. frigida. The identification of species present in a sample can be determined without the need for culturing by sequencing the genus-specific amplicon and comparing that with a reference sequence database of known Phytophthora spp.
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On-site detection of Phytophthora spp.—single-stranded target DNA as the limiting factor to improve on-chip hybridization. Mikrochim Acta 2013. [DOI: 10.1007/s00604-013-1107-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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