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González-Pérez E, Chiquito-Almanza E, Villalobos-Reyes S, Canul-Ku J, Anaya-López JL. Diagnosis and Characterization of Plant Viruses Using HTS to Support Virus Management and Tomato Breeding. Viruses 2024; 16:888. [PMID: 38932180 PMCID: PMC11209215 DOI: 10.3390/v16060888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/20/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
Viral diseases pose a significant threat to tomato crops (Solanum lycopersicum L.), one of the world's most economically important vegetable crops. The limited genetic diversity of cultivated tomatoes contributes to their high susceptibility to viral infections. To address this challenge, tomato breeding programs must harness the genetic resources found in native populations and wild relatives. Breeding efforts may aim to develop broad-spectrum resistance against the virome. To identify the viruses naturally infecting 19 advanced lines, derived from native tomatoes, high-throughput sequencing (HTS) of small RNAs and confirmation with PCR and RT-PCR were used. Single and mixed infections with tomato mosaic virus (ToMV), tomato golden mosaic virus (ToGMoV), and pepper huasteco yellow vein virus (PHYVV) were detected. The complete consensus genomes of three variants of Mexican ToMV isolates were reconstructed, potentially forming a new ToMV clade with a distinct 3' UTR. The absence of reported mutations associated with resistance-breaking to ToMV suggests that the Tm-1, Tm-2, and Tm-22 genes could theoretically be used to confer resistance. However, the high mutation rates and a 63 nucleotide insertion in the 3' UTR, as well as amino acid mutations in the ORFs encoding 126 KDa, 183 KDa, and MP of Mexican ToMV isolates, suggest that it is necessary to evaluate the capacity of these variants to overcome Tm-1, Tm-2, and Tm-22 resistance genes. This evaluation, along with the characterization of advanced lines using molecular markers linked to these resistant genes, will be addressed in future studies as part of the breeding strategy. This study emphasizes the importance of using HTS for accurate identification and characterization of plant viruses that naturally infect tomato germplasm based on the consensus genome sequences. This study provides crucial insights to select appropriate disease management strategies and resistance genes and guide breeding efforts toward the development of virus-resistant tomato varieties.
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Affiliation(s)
| | - Elizabeth Chiquito-Almanza
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Celaya, Guanajuato 38110, Mexico; (E.G.-P.); (S.V.-R.); (J.C.-K.)
| | | | | | - José Luis Anaya-López
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Celaya, Guanajuato 38110, Mexico; (E.G.-P.); (S.V.-R.); (J.C.-K.)
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2
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Hu X, Hurtado-Gonzales OP, Adhikari BN, French-Monar RD, Malapi M, Foster JA, McFarland CD. PhytoPipe: a phytosanitary pipeline for plant pathogen detection and diagnosis using RNA-seq data. BMC Bioinformatics 2023; 24:470. [PMID: 38093207 PMCID: PMC10717670 DOI: 10.1186/s12859-023-05589-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Detection of exotic plant pathogens and preventing their entry and establishment are critical for the protection of agricultural systems while securing the global trading of agricultural commodities. High-throughput sequencing (HTS) has been applied successfully for plant pathogen discovery, leading to its current application in routine pathogen detection. However, the analysis of massive amounts of HTS data has become one of the major challenges for the use of HTS more broadly as a rapid diagnostics tool. Several bioinformatics pipelines have been developed to handle HTS data with a focus on plant virus and viroid detection. However, there is a need for an integrative tool that can simultaneously detect a wider range of other plant pathogens in HTS data, such as bacteria (including phytoplasmas), fungi, and oomycetes, and this tool should also be capable of generating a comprehensive report on the phytosanitary status of the diagnosed specimen. RESULTS We have developed an open-source bioinformatics pipeline called PhytoPipe (Phytosanitary Pipeline) to provide the plant pathology diagnostician community with a user-friendly tool that integrates analysis and visualization of HTS RNA-seq data. PhytoPipe includes quality control of reads, read classification, assembly-based annotation, and reference-based mapping. The final product of the analysis is a comprehensive report for easy interpretation of not only viruses and viroids but also bacteria (including phytoplasma), fungi, and oomycetes. PhytoPipe is implemented in Snakemake workflow with Python 3 and bash scripts in a Linux environment. The source code for PhytoPipe is freely available and distributed under a BSD-3 license. CONCLUSIONS PhytoPipe provides an integrative bioinformatics pipeline that can be used for the analysis of HTS RNA-seq data. PhytoPipe is easily installed on a Linux or Mac system and can be conveniently used with a Docker image, which includes all dependent packages and software related to analyses. It is publicly available on GitHub at https://github.com/healthyPlant/PhytoPipe and on Docker Hub at https://hub.docker.com/r/healthyplant/phytopipe .
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Affiliation(s)
- Xiaojun Hu
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA.
| | - Oscar P Hurtado-Gonzales
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA
| | - Bishwo N Adhikari
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA
| | - Ronald D French-Monar
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA
| | - Martha Malapi
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA
- American Seed Trade Association (ASTA), Alexandria, VA, USA
| | - Joseph A Foster
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA
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3
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Rollin J, Rong W, Massart S. Cont-ID: detection of sample cross-contamination in viral metagenomic data. BMC Biol 2023; 21:217. [PMID: 37833740 PMCID: PMC10576407 DOI: 10.1186/s12915-023-01708-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND High-throughput sequencing (HTS) technologies completed by the bioinformatic analysis of the generated data are becoming an important detection technique for virus diagnostics. They have the potential to replace or complement the current PCR-based methods thanks to their improved inclusivity and analytical sensitivity, as well as their overall good repeatability and reproducibility. Cross-contamination is a well-known phenomenon in molecular diagnostics and corresponds to the exchange of genetic material between samples. Cross-contamination management was a key drawback during the development of PCR-based detection and is now adequately monitored in routine diagnostics. HTS technologies are facing similar difficulties due to their very high analytical sensitivity. As a single viral read could be detected in millions of sequencing reads, it is mandatory to fix a detection threshold that will be informed by estimated cross-contamination. Cross-contamination monitoring should therefore be a priority when detecting viruses by HTS technologies. RESULTS We present Cont-ID, a bioinformatic tool designed to check for cross-contamination by analysing the relative abundance of virus sequencing reads identified in sequence metagenomic datasets and their duplication between samples. It can be applied when the samples in a sequencing batch have been processed in parallel in the laboratory and with at least one specific external control called Alien control. Using 273 real datasets, including 68 virus species from different hosts (fruit tree, plant, human) and several library preparation protocols (Ribodepleted total RNA, small RNA and double-stranded RNA), we demonstrated that Cont-ID classifies with high accuracy (91%) viral species detection into (true) infection or (cross) contamination. This classification raises confidence in the detection and facilitates the downstream interpretation and confirmation of the results by prioritising the virus detections that should be confirmed. CONCLUSIONS Cross-contamination between samples when detecting viruses using HTS (Illumina technology) can be monitored and highlighted by Cont-ID (provided an alien control is present). Cont-ID is based on a flexible methodology relying on the output of bioinformatics analyses of the sequencing reads and considering the contamination pattern specific to each batch of samples. The Cont-ID method is adaptable so that each laboratory can optimise it before its validation and routine use.
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Affiliation(s)
- Johan Rollin
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, 5030, Gembloux, Belgium
- DNAVision, 6041, Gosselies, Belgium
| | - Wei Rong
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, 5030, Gembloux, Belgium
| | - Sébastien Massart
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, 5030, Gembloux, Belgium.
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4
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Gauthier MEA, Abeynayake SW, Lelwala RV, McMaster CA, Eichner R, Morrison J, Elliott CE, Fiorito S, Dinsdale A, Pattemore J, Barrero RA. First detection and complete genome sequence of a new potexvirus naturally infecting Adenium obesum. Arch Virol 2023; 168:244. [PMID: 37676508 PMCID: PMC10484807 DOI: 10.1007/s00705-023-05871-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/06/2023] [Indexed: 09/08/2023]
Abstract
Here, we report the detection and complete genome sequence of a novel potexvirus, tentatively named "Adenium obesum virus X" (AobVX), isolated from Adenium obesum, that was sent for virus screening at Australian Government post-entry quarantine (PEQ) facilities after being imported into Australia from China. The AobVX genome is 6781 nucleotides in length excluding the poly(A) tail and is predicted to encode conserved potexvirus proteins and sequence motifs across five open reading frames. The RNA-dependent RNA polymerase of this virus shares the highest amino acid sequence similarity with that of nerine potexvirus 1 (58.7% identity) and nerine virus X (58.58% identity). This is the first report of a positive-sense single-stranded RNA virus in A. obesum related to members of the genus Potexvirus in the family Alphaflexiviridae.
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Affiliation(s)
- Marie-Emilie A Gauthier
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD, 4000, Australia.
| | - Shamila W Abeynayake
- Department of Agriculture, Forestry and Fisheries, PO Box 858, Canberra, ACT, 2061, Australia
- Department of Animal, Plant and Soil Sciences, Centre for AgriBiosciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Ruvini V Lelwala
- Department of Agriculture, Forestry and Fisheries, PO Box 858, Canberra, ACT, 2061, Australia
| | - Cassie A McMaster
- Department of Agriculture, Forestry and Fisheries, PO Box 858, Canberra, ACT, 2061, Australia
| | - Robin Eichner
- Department of Agriculture, Forestry and Fisheries, PO Box 858, Canberra, ACT, 2061, Australia
| | - Jennifer Morrison
- Department of Agriculture, Forestry and Fisheries, PO Box 858, Canberra, ACT, 2061, Australia
| | - Candace E Elliott
- Department of Agriculture, Forestry and Fisheries, PO Box 858, Canberra, ACT, 2061, Australia
| | - Sonia Fiorito
- Department of Agriculture, Forestry and Fisheries, PO Box 858, Canberra, ACT, 2061, Australia
| | - Adrian Dinsdale
- Department of Agriculture, Forestry and Fisheries, PO Box 858, Canberra, ACT, 2061, Australia
| | - Julie Pattemore
- Department of Agriculture, Forestry and Fisheries, PO Box 858, Canberra, ACT, 2061, Australia
| | - Roberto A Barrero
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD, 4000, Australia
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5
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Roberts JMK, Jooste AEC, Pretorius LS, Geering ADW. Surveillance for Avocado Sunblotch Viroid Utilizing the European Honey Bee ( Apis mellifera). PHYTOPATHOLOGY 2023; 113:559-566. [PMID: 36346373 DOI: 10.1094/phyto-08-22-0295-r] [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: 06/16/2023]
Abstract
Avocado is one of the world's fastest growing tropical fruit industries, and the pathogen avocado sunblotch viroid (ASBVd) is a major threat to both production and access to international export markets. ASBVd is seed transmissible, with infection possible via either the male (pollen) or female gametes. Surveillance for ASBVd across commercial orchards is a major logistical task, particularly when aiming to meet the stringent standards of evidence required for a declaration of pest freedom. As with many fruit crops, insect pollination is important for high avocado yields, and honey bee (Apis mellifera) hives are typically moved into orchards for paid pollination services. Exploiting the foraging behavior of honey bees can provide a complementary strategy to traditional surveillance methods. High-throughput sequencing (HTS) of bee samples for plant viruses shows promise, but this surveillance method has not yet been tested for viroids or in a targeted plant biosecurity context. Here, we tested samples of bees and pollen collected from pollination hives in two ASBVd orchard locations, one in Australia, where only four trees in a block were known to be infected, and a second in South Africa, where the estimated incidence of infection was 10%. Using real-time RT-PCR and HTS (total RNA-seq and small RNA-seq), we demonstrated that ASBVd can be confidently detected in bees and pollen samples from hives within 100 m of infected trees. The potential for using this approach in ASBVd surveillance for improved orchard management and supporting market access is discussed.
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Affiliation(s)
- John M K Roberts
- Commonwealth Scientific and Industrial Research Organisation, Clunies Ross Street, Canberra, Australian Capital Territory 2601, Australia
| | - Anna E C Jooste
- Agricultural Research Council-Tropical and Subtropical Crops, Private Bag X11208, Mbombela 1200, South Africa
| | - Lara-Simone Pretorius
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Andrew D W Geering
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland 4072, Australia
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Delmiglio C, Waite DW, Lilly ST, Yan J, Elliott CE, Pattemore J, Guy PL, Thompson JR. New Virus Diagnostic Approaches to Ensuring the Ongoing Plant Biosecurity of Aotearoa New Zealand. Viruses 2023; 15:v15020418. [PMID: 36851632 PMCID: PMC9964515 DOI: 10.3390/v15020418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
To protect New Zealand's unique ecosystems and primary industries, imported plant materials must be constantly monitored at the border for high-threat pathogens. Techniques adopted for this purpose must be robust, accurate, rapid, and sufficiently agile to respond to new and emerging threats. Polymerase chain reaction (PCR), especially real-time PCR, remains an essential diagnostic tool but it is now being complemented by high-throughput sequencing using both Oxford Nanopore and Illumina technologies, allowing unbiased screening of whole populations. The demand for and value of Point-of-Use (PoU) technologies, which allow for in situ screening, are also increasing. Isothermal PoU molecular diagnostics based on recombinase polymerase amplification (RPA) and loop-mediated amplification (LAMP) do not require expensive equipment and can reach PCR-comparable levels of sensitivity. Recent advances in PoU technologies offer opportunities for increased specificity, accuracy, and sensitivities which makes them suitable for wider utilization by frontline or border staff. National and international activities and initiatives are adopted to improve both the plant virus biosecurity infrastructure and the integration, development, and harmonization of new virus diagnostic technologies.
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Affiliation(s)
- Catia Delmiglio
- Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New Zealand
- Correspondence: (C.D.); (J.R.T.)
| | - David W. Waite
- Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New Zealand
| | - Sonia T. Lilly
- Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New Zealand
| | - Juncong Yan
- Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New Zealand
| | - Candace E. Elliott
- Science and Surveillance Group, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia
| | - Julie Pattemore
- Science and Surveillance Group, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia
| | - Paul L. Guy
- Department of Botany, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Jeremy R. Thompson
- Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New Zealand
- Correspondence: (C.D.); (J.R.T.)
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Moubset O, François S, Maclot F, Palanga E, Julian C, Claude L, Fernandez E, Rott P, Daugrois JH, Antoine-Lorquin A, Bernardo P, Blouin AG, Temple C, Kraberger S, Fontenele RS, Harkins GW, Ma Y, Marais A, Candresse T, Chéhida SB, Lefeuvre P, Lett JM, Varsani A, Massart S, Ogliastro M, Martin DP, Filloux D, Roumagnac P. Virion-Associated Nucleic Acid-Based Metagenomics: A Decade of Advances in Molecular Characterization of Plant Viruses. PHYTOPATHOLOGY 2022; 112:2253-2272. [PMID: 35722889 DOI: 10.1094/phyto-03-22-0096-rvw] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Over the last decade, viral metagenomic studies have resulted in the discovery of thousands of previously unknown viruses. These studies are likely to play a pivotal role in obtaining an accurate and robust understanding of how viruses affect the stability and productivity of ecosystems. Among the metagenomics-based approaches that have been developed since the beginning of the 21st century, shotgun metagenomics applied specifically to virion-associated nucleic acids (VANA) has been used to disentangle the diversity of the viral world. We summarize herein the results of 24 VANA-based studies, focusing on plant and insect samples conducted over the last decade (2010 to 2020). Collectively, viruses from 85 different families were reliably detected in these studies, including capsidless RNA viruses that replicate in fungi, oomycetes, and plants. Finally, strengths and weaknesses of the VANA approach are summarized and perspectives of applications in detection, epidemiological surveillance, environmental monitoring, and ecology of plant viruses are provided. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Oumaima Moubset
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | | | - François Maclot
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Essowè Palanga
- Institut Togolais de Recherche Agronomique (ITRA-CRASS), B.P. 129, Kara, Togo
| | - Charlotte Julian
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Lisa Claude
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Emmanuel Fernandez
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Philippe Rott
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Jean-Heinrich Daugrois
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | | | | | - Arnaud G Blouin
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
- Plant Protection Department, Agroscope, 1260, Nyon, Switzerland
| | - Coline Temple
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, U.S.A
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, U.S.A
| | - Gordon W Harkins
- South African Medical Research Council Capacity Development Unit, South African National Bioinformatics, Institute, University of the Western Cape, South Africa
| | - Yuxin Ma
- Univ. Bordeaux, INRAE, UMR BFP, 33140 Villenave d'Ornon, France
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR BFP, 33140 Villenave d'Ornon, France
| | | | | | | | | | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, U.S.A
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Sébastien Massart
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | | | - Darren P Martin
- Division of Computational Biology, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Denis Filloux
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
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Valenzuela SL, Norambuena T, Morgante V, García F, Jiménez JC, Núñez C, Fuentes I, Pollak B. Viroscope: Plant viral diagnosis from high-throughput sequencing data using biologically-informed genome assembly coverage. Front Microbiol 2022; 13:967021. [PMID: 36338106 PMCID: PMC9634423 DOI: 10.3389/fmicb.2022.967021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/29/2022] [Indexed: 11/25/2022] Open
Abstract
High-throughput sequencing (HTS) methods are transforming our capacity to detect pathogens and perform disease diagnosis. Although sequencing advances have enabled accessible and point-of-care HTS, data analysis pipelines have yet to provide robust tools for precise and certain diagnosis, particularly in cases of low sequencing coverage. Lack of standardized metrics and harmonized detection thresholds confound the problem further, impeding the adoption and implementation of these solutions in real-world applications. In this work, we tackle these issues and propose biologically-informed viral genome assembly coverage as a method to improve diagnostic certainty. We use the identification of viral replicases, an essential function of viral life cycles, to define genome coverage thresholds in which biological functions can be described. We validate the analysis pipeline, Viroscope, using field samples, synthetic and published datasets, and demonstrate that it provides sensitive and specific viral detection. Furthermore, we developed Viroscope.io a web-service to provide on-demand HTS data viral diagnosis to facilitate adoption and implementation by phytosanitary agencies to enable precise viral diagnosis.
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Affiliation(s)
| | | | | | | | | | | | | | - Bernardo Pollak
- Meristem SpA, Santiago, Chile
- Multiplex SpA, Santiago, Chile
- *Correspondence: Bernardo Pollak,
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Waite DW, Liefting L, Delmiglio C, Chernyavtseva A, Ha HJ, Thompson JR. Development and Validation of a Bioinformatic Workflow for the Rapid Detection of Viruses in Biosecurity. Viruses 2022; 14:v14102163. [PMID: 36298719 PMCID: PMC9610911 DOI: 10.3390/v14102163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/25/2022] [Indexed: 11/05/2022] Open
Abstract
The field of biosecurity has greatly benefited from the widespread adoption of high-throughput sequencing technologies, for its ability to deeply query plant and animal samples for pathogens for which no tests exist. However, the bioinformatics analysis tools designed for rapid analysis of these sequencing datasets are not developed with this application in mind, limiting the ability of diagnosticians to standardise their workflows using published tool kits. We sought to assess previously published bioinformatic tools for their ability to identify plant- and animal-infecting viruses while distinguishing from the host genetic material. We discovered that many of the current generation of virus-detection pipelines are not adequate for this task, being outperformed by more generic classification tools. We created synthetic MinION and HiSeq libraries simulating plant and animal infections of economically important viruses and assessed a series of tools for their suitability for rapid and accurate detection of infection, and further tested the top performing tools against the VIROMOCK Challenge dataset to ensure that our findings were reproducible when compared with international standards. Our work demonstrated that several methods provide sensitive and specific detection of agriculturally important viruses in a timely manner and provides a key piece of ground truthing for method development in this space.
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Affiliation(s)
- David W. Waite
- Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New Zealand
- Correspondence:
| | - Lia Liefting
- Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New Zealand
| | - Catia Delmiglio
- Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New Zealand
| | | | - Hye Jeong Ha
- Animal Health Laboratory, Ministry for Primary Industries, Upper Hutt 5018, New Zealand
| | - Jeremy R. Thompson
- Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New Zealand
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10
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Lelwala RV, LeBlanc Z, Gauthier MEA, Elliott CE, Constable FE, Murphy G, Tyle C, Dinsdale A, Whattam M, Pattemore J, Barrero RA. Implementation of GA-VirReport, a Web-Based Bioinformatics Toolkit for Post-Entry Quarantine Screening of Virus and Viroids in Plants. Viruses 2022; 14:v14071480. [PMID: 35891459 PMCID: PMC9317486 DOI: 10.3390/v14071480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/29/2022] [Accepted: 06/29/2022] [Indexed: 02/01/2023] Open
Abstract
High-throughput sequencing (HTS) of host plant small RNA (sRNA) is a popular approach for plant virus and viroid detection. The major bottlenecks for implementing this approach in routine virus screening of plants in quarantine include lack of computational resources and/or expertise in command-line environments and limited availability of curated plant virus and viroid databases. We developed: (1) virus and viroid report web-based bioinformatics workflows on Galaxy Australia called GA-VirReport and GA-VirReport-Stats for detecting viruses and viroids from host plant sRNA extracts and (2) a curated higher plant virus and viroid database (PVirDB). We implemented sRNA sequencing with unique dual indexing on a set of plants with known viruses. Sequencing data were analyzed using GA-VirReport and PVirDB to validate these resources. We detected all known viruses in this pilot study with no cross-sample contamination. We then conducted a large-scale diagnosis of 105 imported plants processed at the post-entry quarantine facility (PEQ), Australia. We detected various pathogens in 14 imported plants and discovered that de novo assembly using 21–22 nt sRNA fraction and the megablast algorithm yielded better sensitivity and specificity. This study reports the successful, large-scale implementation of HTS and a user-friendly bioinformatics workflow for virus and viroid screening of imported plants at the PEQ.
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Affiliation(s)
- Ruvini V. Lelwala
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD 4001, Australia; (R.V.L.); (Z.L.); (M.-E.A.G.)
- Science and Surveillance Group, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia; (C.E.E.); (J.P.)
| | - Zacharie LeBlanc
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD 4001, Australia; (R.V.L.); (Z.L.); (M.-E.A.G.)
| | - Marie-Emilie A. Gauthier
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD 4001, Australia; (R.V.L.); (Z.L.); (M.-E.A.G.)
| | - Candace E. Elliott
- Science and Surveillance Group, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia; (C.E.E.); (J.P.)
| | - Fiona E. Constable
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia;
| | - Greg Murphy
- Technology Infrastructure Branch, Information Services Division, Department of Agriculture, Fisheries and Forestry, Canberra, ACT 2601, Australia; (G.M.); (C.T.)
| | - Callum Tyle
- Technology Infrastructure Branch, Information Services Division, Department of Agriculture, Fisheries and Forestry, Canberra, ACT 2601, Australia; (G.M.); (C.T.)
| | - Adrian Dinsdale
- Plant Innovation Centre, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia; (A.D.); (M.W.)
| | - Mark Whattam
- Plant Innovation Centre, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia; (A.D.); (M.W.)
| | - Julie Pattemore
- Science and Surveillance Group, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia; (C.E.E.); (J.P.)
| | - Roberto A. Barrero
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD 4001, Australia; (R.V.L.); (Z.L.); (M.-E.A.G.)
- Correspondence:
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