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Espindola AS, Cardwell K, Martin FN, Hoyt PR, Marek SM, Schneider W, Garzon CD. A Step Towards Validation of High-Throughput Sequencing for the Identification of Plant Pathogenic Oomycetes. PHYTOPATHOLOGY 2022; 112:1859-1866. [PMID: 35345904 DOI: 10.1094/phyto-11-21-0454-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The advancement in high-throughput sequencing (HTS) technology allows the detection of pathogens without the need for isolation or template amplification. Plant regulatory agencies worldwide are adopting HTS as a prescreening tool for plant pathogens in imported plant germplasm. The technique is a multipronged process and, often, the bioinformatic analysis complicates detection. Previously, we developed E-probe diagnostic nucleic acid analysis (EDNA), a bioinformatic tool that detects pathogens in HTS data. EDNA uses custom databases of signature nucleic acid sequences (e-probes) to reduce computational effort and subjectivity when determining pathogen presence in a sample. E-probes of Pythium ultimum and Phytophthora ramorum were previously validated only using simulated HTS data. However, HTS samples generated from infected hosts or pure culture may vary in pathogen concentration, sequencing bias, and data quality, suggesting that each pathosystem requires further validation. Here, we used metagenomic and genomic HTS data generated from infected hosts and pure culture, respectively, to further validate and curate e-probes of Pythium ultimum and Phytophthora ramorum. E-probe length was found to be a determinant of diagnostic sensitivity and specificity; 80-nucleotide e-probes increased the diagnostic specificity to 100%. Curating e-probes to increase specificity affected diagnostic sensitivity only for 80-nucleotide Pythium ultimum e-probes. Comparing e-probes with alternative databases and bioinformatic tools in their speed and ability to find Pythium ultimum and Phytophthora ramorum demonstrated that, although pathogen sequence reads were detected by other methods, they were less specific and slower when compared with e-probes.
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Affiliation(s)
- Andres S Espindola
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078
| | - Kitty Cardwell
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078
| | - Frank N Martin
- U.S. Department of Agriculture-Agriculture Research Service, Salinas, CA
| | - Peter R Hoyt
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078
| | - Stephen M Marek
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078
| | | | - Carla D Garzon
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078
- Department of Plant Science and Landscape Architecture, Delaware Valley University, Doylestown, PA 18901
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2
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Dang T, Espindola A, Vidalakis G, Cardwell K. An In Silico Detection of a Citrus Viroid from Raw High-Throughput Sequencing Data. Methods Mol Biol 2022; 2316:275-283. [PMID: 34845702 DOI: 10.1007/978-1-0716-1464-8_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
E-probe Diagnostic for Nucleic Acid Analysis (EDNA) is a user-friendly bioinformatic tool that has been adapted for the detection and identification of citrus exocortis viroid (CEVd). Here, we describe the procedures for RNA extraction from citrus tissues, library and sequencing preparation, and the utilization of EDNA Mi-Finder online platform on raw high-throughput sequencing (HTS) data.
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Affiliation(s)
- Tyler Dang
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Andres Espindola
- Institute of Biosecurity and Microbial Forensics, Oklahoma State University, Stillwater, OK, USA
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA.
| | - Kitty Cardwell
- Institute of Biosecurity and Microbial Forensics, Oklahoma State University, Stillwater, OK, USA.
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3
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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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4
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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: 165] [Impact Index Per Article: 33.0] [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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5
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Espindola AS, Schneider W, Cardwell KF, Carrillo Y, Hoyt PR, Marek SM, Melouk HA, Garzon CD. Inferring the presence of aflatoxin-producing Aspergillus flavus strains using RNA sequencing and electronic probes as a transcriptomic screening tool. PLoS One 2018; 13:e0198575. [PMID: 30325975 PMCID: PMC6191106 DOI: 10.1371/journal.pone.0198575] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 09/26/2018] [Indexed: 11/24/2022] Open
Abstract
E-probe Diagnostic for Nucleic acid Analysis (EDNA) is a bioinformatic tool originally developed to detect plant pathogens in metagenomic databases. However, enhancements made to EDNA increased its capacity to conduct hypothesis directed detection of specific gene targets present in transcriptomic databases. To target specific pathogenicity factors used by the pathogen to infect its host or other targets of interest, e-probes need to be developed for transcripts related to that function. In this study, EDNA transcriptomics (EDNAtran) was developed to detect the expression of genes related to aflatoxin production at the transcriptomic level. E-probes were designed from genes up-regulated during A. flavus aflatoxin production. EDNAtran detected gene transcripts related to aflatoxin production in a transcriptomic database from corn, where aflatoxin was produced. The results were significantly different from e-probes being used in the transcriptomic database where aflatoxin was not produced (atoxigenic AF36 strain and toxigenic AF70 in Potato Dextrose Broth).
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Affiliation(s)
- Andres S. Espindola
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, Oklahoma, United States of America
- National Institute for Microbial Forensics and Food and Agricultural Biosecurity (NIMFFAB), Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - William Schneider
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - Kitty F. Cardwell
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, Oklahoma, United States of America
- National Institute for Microbial Forensics and Food and Agricultural Biosecurity (NIMFFAB), Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - Yisel Carrillo
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - Peter R. Hoyt
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - Stephen M. Marek
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - Hassan A. Melouk
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - Carla D. Garzon
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, Oklahoma, United States of America
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6
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Pallás V, Sánchez-Navarro JA, James D. Recent Advances on the Multiplex Molecular Detection of Plant Viruses and Viroids. Front Microbiol 2018; 9:2087. [PMID: 30250456 PMCID: PMC6139301 DOI: 10.3389/fmicb.2018.02087] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/15/2018] [Indexed: 12/14/2022] Open
Abstract
Plant viruses are still one of the main contributors to economic losses in agriculture. It has been estimated that plant viruses can cause as much as 50 billion euros loss worldwide, per year. This situation may be worsened by recent climate change events and the associated changes in disease epidemiology. Reliable and early detection methods are still one of the main and most effective actions to develop control strategies for plant viral diseases. During the last years, considerable progress has been made to develop tools with high specificity and low detection limits for use in the detection of these plant pathogens. Time and cost reductions have been some of the main objectives pursued during the last few years as these increase their feasibility for routine use. Among other strategies, these objectives can be achieved by the simultaneous detection and (or) identification of several viruses in a single assay. Nucleic acid-based detection techniques are especially suitable for this purpose. Polyvalent detection has allowed the detection of multiple plant viruses at the genus level. Multiplexing RT polymerase chain reaction (PCR) has been optimized for the simultaneous detection of more than 10 plant viruses/viroids. In this short review, we provide an update on the progress made during the last decade on techniques such as multiplex PCR, polyvalent PCR, non-isotopic molecular hybridization techniques, real-time PCR, and array technologies to allow simultaneous detection of multiple plant viruses. Also, the potential and benefits of the powerful new technique of deep sequencing/next-generation sequencing are described.
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Affiliation(s)
- Vicente Pallás
- Instituto de Biología Molecular y Celular de Plantas, IBMCP, Universitat Politècnica de València – Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Jesus A. Sánchez-Navarro
- Instituto de Biología Molecular y Celular de Plantas, IBMCP, Universitat Politècnica de València – Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Delano James
- Sidney Laboratory, Canadian Food Inspection Agency, Sidney, BC, Canada
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7
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Bronzato Badial A, Sherman D, Stone A, Gopakumar A, Wilson V, Schneider W, King J. Nanopore Sequencing as a Surveillance Tool for Plant Pathogens in Plant and Insect Tissues. PLANT DISEASE 2018; 102:1648-1652. [PMID: 30673417 DOI: 10.1094/pdis-04-17-0488-re] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Plant pathogens are constantly emerging and spreading into new areas and there are often limited postdiagnosis treatment options for infection, making surveillance key to their control. Here we present results from a study testing the efficacy of a portable nanopore-based massively parallel sequencing (MPS) technology for use in the detection of diverse plant pathogens in selected samples. The Oxford MinION device was coupled with whole transcriptome amplification (WTA) to sequence the metatranscriptome of plant and insect tissues infected with either Candidatus Liberibacter asiaticus or plum pox virus. Results showed that this methodology is useful for detecting unsuspected viral and bacterial pathogens in plant and insect tissues. The percentage of generated reads assigned to plum pox virus was 95% from infected tissue and 3% from the viruliferous insect, Myzus persicae. Diaphorina citri sequencing led to 22% of the reads mapping as Ca. L. asiaticus. Plum pox virus and Ca. L. asiaticus were detected in both tissue and insect samples near the beginning of each sequencing run, demonstrating the capability of this methodology to obtain results rapidly. This approach also proved the capability of this system to determine the major components of the insect vector's microbiome and the specific strain of small-genome, high-titer pathogens.
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Affiliation(s)
- Aline Bronzato Badial
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS
| | - Diana Sherman
- USDA-ARS Foreign Disease-Weed Science Research Unit, Fort Detrick, MD
| | - Andrew Stone
- USDA-ARS Foreign Disease-Weed Science Research Unit, Fort Detrick, MD
| | - Anagha Gopakumar
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS
| | - Victoria Wilson
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS
| | - William Schneider
- USDA-ARS Foreign Disease-Weed Science Research Unit, Fort Detrick, MD
| | - Jonas King
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS
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Verchot J, Thapa A, Wijayasekara D, Hoyt PR. Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes. J Vis Exp 2018. [PMID: 30102276 DOI: 10.3791/57855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
This metagenome approach is used to identify plant viruses with circular DNA genomes and their transcripts. Often plant DNA viruses that occur in low titers in their host or cannot be mechanically inoculated to another host are difficult to propagate to achieve a greater titer of infectious material. Infected leaves are ground in a mild buffer with optimal pH and ionic composition recommended for purifying most bacilliform Para retroviruses. Urea is used to break up inclusion bodies that trap virions and to dissolve cellular components. Differential centrifugation provides further separation of virions from plant contaminants. Then proteinase K treatment removes the capsids. Then the viral DNA is concentrated and used for next-generation sequencing (NGS). The NGS data are used to assemble contigs which are submitted to NCBI-BLASTn to identify a subset of virus sequences in the generated dataset. In a parallel pipeline, RNA is isolated from infected leaves using a standard column-based RNA extraction method. Then ribosome depletion is carried out to enrich for a subset of mRNA and virus transcripts. Assembled sequences derived from RNA sequencing (RNA-seq) were submitted to NCBI-BLASTn to identify a subset of virus sequences in this dataset. In our study, we identified two related full-length badnavirus genomes in the two datasets. This method is preferred to another common approach which extracts the aggregate population of small RNA sequences to reconstitute plant virus genomic sequences. This latter metagenomic pipeline recovers virus related sequences that are retro-transcribing elements inserted into the plant genome. This is coupled to biochemical or molecular assays to further discern the actively infectious agents. The approach documented in this study, recovers sequences representative of replicating viruses that likely indicate active virus infection.
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Affiliation(s)
| | - Aastha Thapa
- Noble Research Center, Oklahoma State University
| | - Dulanjani Wijayasekara
- Department of Biology, College of Engineering and Natural Sciences, The University of Tulsa
| | - Peter R Hoyt
- Bioinformatics and Genomics Core Facility, Department of Biochemistry and Molecular Biology, Oklahoma State University
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9
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Jooste TL, Visser M, Cook G, Burger JT, Maree HJ. In Silico Probe-Based Detection of Citrus Viruses in NGS Data. PHYTOPATHOLOGY 2017; 107:988-993. [PMID: 28562184 DOI: 10.1094/phyto-10-16-0379-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The conservation of plant biosecurity relies on the rapid identification of pathogenic organisms, including viruses. With next-generation sequencing (NGS), it is possible to identify multiple viruses within a metagenomic sample. In this study, we explored the use of electronic probes (e-probes) for the simultaneous detection of 11 recognized citrus viruses. E-probes were designed and screened against raw sequencing data to minimize the bioinformatic processing time required. The e-probes were able to accurately detect their cognate viruses in simulated datasets, without any false negatives or positives. The efficiency of the e-probe-based approach was validated with NGS datasets generated from different RNA preparations: double-stranded RNA (dsRNA) from 'Mexican' lime infected with different Citrus tristeza virus (CTV) genotypes, dsRNA from field samples, and small RNA and total RNA from grapefruit infected with the CTV T3 genotype. A set of probes was made available that is able to accurately detect CTV in sequence data regardless of the input dataset or the genotype that plants are infected with.
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Affiliation(s)
- T L Jooste
- First, second, and fifth authors: Agricultural Research Council, Infruitec-Nietvoorbij (The Fruit, Vine and Wine Institute), Stellenbosch, South Africa; first, second, fourth, and fifth authors: Stellenbosch University, Department of Genetics, Stellenbosch, South Africa; and third author: Citrus Research International, Nelspruit, South Africa
| | - M Visser
- First, second, and fifth authors: Agricultural Research Council, Infruitec-Nietvoorbij (The Fruit, Vine and Wine Institute), Stellenbosch, South Africa; first, second, fourth, and fifth authors: Stellenbosch University, Department of Genetics, Stellenbosch, South Africa; and third author: Citrus Research International, Nelspruit, South Africa
| | - G Cook
- First, second, and fifth authors: Agricultural Research Council, Infruitec-Nietvoorbij (The Fruit, Vine and Wine Institute), Stellenbosch, South Africa; first, second, fourth, and fifth authors: Stellenbosch University, Department of Genetics, Stellenbosch, South Africa; and third author: Citrus Research International, Nelspruit, South Africa
| | - J T Burger
- First, second, and fifth authors: Agricultural Research Council, Infruitec-Nietvoorbij (The Fruit, Vine and Wine Institute), Stellenbosch, South Africa; first, second, fourth, and fifth authors: Stellenbosch University, Department of Genetics, Stellenbosch, South Africa; and third author: Citrus Research International, Nelspruit, South Africa
| | - H J Maree
- First, second, and fifth authors: Agricultural Research Council, Infruitec-Nietvoorbij (The Fruit, Vine and Wine Institute), Stellenbosch, South Africa; first, second, fourth, and fifth authors: Stellenbosch University, Department of Genetics, Stellenbosch, South Africa; and third author: Citrus Research International, Nelspruit, South Africa
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10
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Visser M, Burger JT, Maree HJ. Targeted virus detection in next-generation sequencing data using an automated e-probe based approach. Virology 2016; 495:122-8. [DOI: 10.1016/j.virol.2016.05.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 05/05/2016] [Accepted: 05/12/2016] [Indexed: 11/27/2022]
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11
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Dutta M, Ali A, Melcher U. Detection, discrimination and discovery of a new Tobacco streak virus strain. J Virol Methods 2015; 221:15-21. [PMID: 25907471 DOI: 10.1016/j.jviromet.2015.03.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 03/29/2015] [Indexed: 10/23/2022]
Abstract
Soybean plants that exhibited symptoms of virus infection were sampled from different counties of Oklahoma. These plants were tested serologically for 15 viruses known to infect soybean plants. Fifty-seven samples that exhibited typical virus-like symptoms did not test positive for any of the 15 viruses used in a dot-immunobinding assay (DIBA). Four samples were pooled and used for next generation sequencing using the 454-Roche protocol. Sequence and phylogenetic analysis of the sequences obtained revealed infection with a distinct strain of Tobacco streak virus (TSV). TSV was one of the 15 viruses initially tested for using DIBA and had tested negative. TSV belongs to the genus Ilarvirus and has been reported as a causal agent of bud blight in soybean crops in Brazil and the United States. Out of 10 reported primer pairs for TSV reverse transcription-polymerase chain reaction (RT-PCR), only two had the potential, based on sequence similarity, to amplify part of the genome of the distinct strain of TSV found in Oklahoma and only one was actually able to amplify the region. In this study, a new primer pair, specific to all known TSV and capable of amplifying the Oklahoma strain (TSV-OK), was designed from a highly conserved region of coat protein (CP) sequences and end-point PCR and quantitative RT-PCR detection methods were developed and their sensitivity assayed. This is the first report of specific primers designed from this highly conserved region in the CP of TSV for detection of TSV. Twenty-three of the 57 DIBA soybean samples that initially tested negative were retested with the new specific end-point PCR method and found positive for TSV infection.
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Affiliation(s)
- M Dutta
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078-3035 USA
| | - A Ali
- Department of Biological Science, The University of Tulsa, OK, 74104, USA
| | - U Melcher
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078-3035 USA.
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12
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Budowle B, Connell ND, Bielecka-Oder A, Colwell RR, Corbett CR, Fletcher J, Forsman M, Kadavy DR, Markotic A, Morse SA, Murch RS, Sajantila A, Schmedes SE, Ternus KL, Turner SD, Minot S. Validation of high throughput sequencing and microbial forensics applications. INVESTIGATIVE GENETICS 2014; 5:9. [PMID: 25101166 PMCID: PMC4123828 DOI: 10.1186/2041-2223-5-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 07/09/2014] [Indexed: 01/29/2023]
Abstract
High throughput sequencing (HTS) generates large amounts of high quality sequence data for microbial genomics. The value of HTS for microbial forensics is the speed at which evidence can be collected and the power to characterize microbial-related evidence to solve biocrimes and bioterrorist events. As HTS technologies continue to improve, they provide increasingly powerful sets of tools to support the entire field of microbial forensics. Accurate, credible results allow analysis and interpretation, significantly influencing the course and/or focus of an investigation, and can impact the response of the government to an attack having individual, political, economic or military consequences. Interpretation of the results of microbial forensic analyses relies on understanding the performance and limitations of HTS methods, including analytical processes, assays and data interpretation. The utility of HTS must be defined carefully within established operating conditions and tolerances. Validation is essential in the development and implementation of microbial forensics methods used for formulating investigative leads attribution. HTS strategies vary, requiring guiding principles for HTS system validation. Three initial aspects of HTS, irrespective of chemistry, instrumentation or software are: 1) sample preparation, 2) sequencing, and 3) data analysis. Criteria that should be considered for HTS validation for microbial forensics are presented here. Validation should be defined in terms of specific application and the criteria described here comprise a foundation for investigators to establish, validate and implement HTS as a tool in microbial forensics, enhancing public safety and national security.
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Affiliation(s)
- Bruce Budowle
- Department of Molecular and Medical Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nancy D Connell
- Rutgers New Jersey Medical School, Center for Biodefense, Rutgers University, Newark, New Jersey, USA
| | - Anna Bielecka-Oder
- Department of Epidemiology, The General K. Kaczkowski Military Institute of Hygiene and Epidemiology, Warsaw, Poland
| | - Rita R Colwell
- CosmosID®, 387 Technology Dr, College Park, MD, USA
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD, USA
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Cindi R Corbett
- Bioforensics Assay Development and DiagnosticsSection, Science Technology and Core Services Division, National Microbiology Laboratory, Winnipeg, MB, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
| | - Jacqueline Fletcher
- National Institute for Microbial Forensics & Food and Agricultural Biosecurity, Oklahoma State University, Stillwater, OK, USA
| | - Mats Forsman
- Division of CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden
| | | | - Alemka Markotic
- University Hospital for Infectious Diseases “Fran Mihaljevic” and Medical School University of Rijeka, Zagreb, Croatia
| | - Stephen A Morse
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Antti Sajantila
- Department of Molecular and Medical Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA
- Department of Forensic Medicine, Hjelt Institute, University of Helsinki, Helsinki, Finland
| | - Sarah E Schmedes
- Department of Molecular and Medical Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | | | - Stephen D Turner
- Public Health Sciences, Bioinformatics Core Director, University of Virginia School of Medicine, Charlottesville, VA, USA
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Melcher U, Verma R, Schneider WL. Metagenomic search strategies for interactions among plants and multiple microbes. FRONTIERS IN PLANT SCIENCE 2014; 5:268. [PMID: 24966863 PMCID: PMC4052219 DOI: 10.3389/fpls.2014.00268] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 05/24/2014] [Indexed: 05/22/2023]
Abstract
Plants harbor multiple microbes. Metagenomics can facilitate understanding of the significance, for the plant, of the microbes, and of the interactions among them. However, current approaches to metagenomic analysis of plants are computationally time consuming. Efforts to speed the discovery process include improvement of computational speed, condensing the sequencing reads into smaller datasets before BLAST searches, simplifying the target database of BLAST searches, and flipping the roles of metagenomic and reference datasets. The latter is exemplified by the e-probe diagnostic nucleic acid analysis approach originally devised for improving analysis during plant quarantine.
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Affiliation(s)
- Ulrich Melcher
- Department of Biochemistry and Molecular Biology, Oklahoma State UniversityStillwater, OK, USA
| | - Ruchi Verma
- Department of Biochemistry and Molecular Biology, Oklahoma State UniversityStillwater, OK, USA
| | - William L. Schneider
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture – Agricultural Research ServiceFort Detrick, MD, USA
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