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Zhao Z, Carey JR, Li Z. The Global Epidemic of Bactrocera Pests: Mixed-Species Invasions and Risk Assessment. ANNUAL REVIEW OF ENTOMOLOGY 2024; 69:219-237. [PMID: 37708416 DOI: 10.1146/annurev-ento-012723-102658] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Throughout the past century, the global spread of Bactrocera pests has continued to pose a significant threat to the commercial fruit and vegetable industry, resulting in substantial costs associated with both control measures and quarantine restrictions. The increasing volume of transcontinental trade has contributed to an escalating rate of Bactrocera pest introductions to new regions. To address the worldwide threat posed by this group of pests, we first provide an overview of Bactrocera. We then describe the global epidemic, including border interceptions, species diagnosis, population genetics, geographical expansion, and invasion tracing of Bactrocera pests. We further consider the literature concerning the invasion co-occurrences, life-history flexibility, risk assessment, bridgehead effects, and ongoing implications of invasion recurrences, as well as a case study of Bactrocera invasions of California. Finally, we call for global collaboration to effectively monitor, prevent, and control the ongoing spread of Bactrocera pests and to share experience and knowledge to combat it.
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Affiliation(s)
- Zihua Zhao
- Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, China, ,
- MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, China Agricultural University, Beijing, China
| | - James R Carey
- Department of Entomology and Nematology, University of California, Davis, California, USA,
| | - Zhihong Li
- Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, China, ,
- MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, China Agricultural University, Beijing, China
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2
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Hong Z, Michel AP, Long EY. Optimizing a rapid LAMP assay for discrimination of Drosophila suzukii (Diptera: Drosophilidae) from common drosophilids captured in monitoring traps from the Midwest, United States. JOURNAL OF ECONOMIC ENTOMOLOGY 2023; 116:1391-1397. [PMID: 37300369 DOI: 10.1093/jee/toad105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/21/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023]
Abstract
Spotted-wing Drosophila, Drosophila suzukii, is an economically important pest of small fruits worldwide. Currently, the timing of management strategies relies on detection of adult flies captured in baited monitoring traps; however, identifying D. suzukii in trap catch based on morphology can be challenging for growers. DNA-based diagnostic methods such as loop-mediated isothermal amplification (LAMP) have the potential to improve D. suzukii detection. This study evaluated a LAMP assay as a diagnostic tool to discriminate between D. suzukii and closely related drosophilid species found commonly in monitoring traps in the Midwestern United States. Targeting the mitochondrial cytochrome oxidase I (COI) gene, we found the LAMP assay accurately detected D. suzukii with as little as 0.1 ng/μl of DNA at 63 °C for 50 min. Under these optimal incubation conditions, D. suzukii could be discriminated from D. affinis and D. simulans consistently, when specimens collected from liquid monitoring traps were tested independently. Compared to other DNA-based diagnostic tools for D. suzukii, LAMP offers unique benefits: DNA extraction is not required, testing occurs at one temperature in less than 1 h, and positive results are visible as a colorimetric change from pink to yellow. The LAMP assay for D. suzukii can reduce reliance on morphological identification, enhance the adoption of monitoring tools, and improve accuracy of detection. Further optimization can be conducted to evaluate the accuracy and sensitivity of results when a mixture of DNA from both D. suzukii and congener flies are tested in a single LAMP reaction.
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Affiliation(s)
- Zihan Hong
- Department of Entomology, Purdue University, West Lafayette, IN 47907, USA
| | - Andrew P Michel
- Department of Entomology, The Ohio State University, Wooster, OH 44691, USA
| | - Elizabeth Y Long
- Department of Entomology, Purdue University, West Lafayette, IN 47907, USA
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3
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Yang W, Su Y, Zeng L, Zhang Y, Ullah F, Wang X, Li X, Feng X, Li Z. LAMP Assay as a Rapid Identification Technique of Chinese Citrus Fly and Japanese Orange Fly (Diptera: Tephritidae). JOURNAL OF ECONOMIC ENTOMOLOGY 2023; 116:956-962. [PMID: 36946506 DOI: 10.1093/jee/toad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Indexed: 06/14/2023]
Abstract
Bactrocera tsuneonis and Bactrocera minax are the most destructive pests that damage citrus in China. These key pests hinder the citrus trade, cause significant financial losses, drastically lower citrus production and quality, and decrease farmer enthusiasm for citrus planting. Bactrocera minax and B. tsuneonis are very similar in all life stages. There are limited morphological characteristics to differentiate the adult species, and it is nearly impossible to differentiate these two species in the egg and larval stages. Loop-mediated isothermal amplification (LAMP) is a rapid and robust diagnostic tool used to identify these two species accurately. We designed two sets of primers to distinguish B. minax and B. tsuneonis using DNA barcoding region of the COI gene. Only 50 min was needed under a constant temperature of 65ºC to determine the species of the two flies. The reaction system has high specificity and sensitivity, in which these two species can be accurately distinguished between different geographical populations and 1.0 ng/μL was the lowest DNA concentration that could be detected. Our primers can quickly identify these key pests without knowing their morphology, which could facilitate plant protection workers at the primary level to solve problems in plant quarantine.
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Affiliation(s)
- Wenzhao Yang
- Department of Plant Biosecurity, College of Plant Protection, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yun Su
- Department of Plant Biosecurity, College of Plant Protection, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Lingyu Zeng
- Department of Plant Biosecurity, College of Plant Protection, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yue Zhang
- Department of Plant Biosecurity, College of Plant Protection, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Farman Ullah
- Department of Plant Biosecurity, College of Plant Protection, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Xiaoliang Wang
- Department of Plant Biosecurity, College of Plant Protection, College of Plant Protection, China Agricultural University, Beijing 100193, China
- National Agro-Tech Extension and Service Center, Beijing 100125, China
| | - Xiaonan Li
- National Agro-Tech Extension and Service Center, Beijing 100125, China
| | - Xiaodong Feng
- National Agro-Tech Extension and Service Center, Beijing 100125, China
| | - Zhihong Li
- Department of Plant Biosecurity, College of Plant Protection, College of Plant Protection, China Agricultural University, Beijing 100193, China
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4
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Shimbori EM, Querino RB, Costa VA, Zucchi RA. Taxonomy and Biological Control: New Challenges in an Old Relationship. NEOTROPICAL ENTOMOLOGY 2023; 52:351-372. [PMID: 36656493 PMCID: PMC9851596 DOI: 10.1007/s13744-023-01025-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 01/03/2023] [Indexed: 05/13/2023]
Abstract
Biological control and taxonomy are continuously developing fields with remarkable impacts on society. At least 80 years of literature have documented this relationship, which remains essentially the same in its mutualistic nature, as well as in its major challenges. From the perspective of Brazilian taxonomists, we discuss the impacts of important scientific and social developments that directly affect research in these areas, posing new challenges for this lasting relationship. The increasing restrictions and concerns regarding the international transit of organisms require improvements in research related to risk assessment for exotic biological control agents and also stimulate prospecting within the native biota. In our view, this is a positive situation that can foster a closer relationship between taxonomists and applied entomologists, as well as local surveys and taxonomic studies that are necessary before new programs and agents can be implemented. We discuss the essential role of molecular biology in this context, as an iconic example of the synergy between applied sciences and natural history. As our society comes to need safer and more sustainable solutions for food security and the biodiversity crisis, scientific progress will build upon this integration, where biological control and taxonomy play an essential role.
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Affiliation(s)
- Eduardo Mitio Shimbori
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ), Universidade de São Paulo (USP), São Paulo Piracicaba, Brazil
| | - Ranyse Barbosa Querino
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Cerrados, Planaltina, Distrito Federal Brazil
| | - Valmir Antonio Costa
- Centro Avançado de Pesquisa e Desenvolvimento em Sanidade Agropecuária, Instituto Biológico, São Paulo Campinas, Brazil
| | - Roberto Antonio Zucchi
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ), Universidade de São Paulo (USP), São Paulo Piracicaba, Brazil
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Pu X, Wu W, Yang D, Zhang Q, Fan X, Du Y, Zu L, Xu Y, Sun C, Zhao K. Rapid, visual and highly sensitive sexing of bovine embryos by recombinase polymerase amplification with CFI staining. Heliyon 2023; 9:e14116. [PMID: 36923860 PMCID: PMC10009442 DOI: 10.1016/j.heliyon.2023.e14116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 02/19/2023] [Accepted: 02/21/2023] [Indexed: 02/27/2023] Open
Abstract
Early bovine embryo sexing both increases the number of offspring of the desired sex, and reduces the subsequent costs of processing unwanted offspring of the opposite sex. The need for cattle of different sexes varies from industry to industry, and a range of tools have been set up to meet this need, but most are energy- and time-consuming, hence it is important to establish a fast and convenient method for bovine embryo determination. Herein, we established a recombinase polymerase amplification (RPA) method combined with CFI dye (RPA-CFI) for sexing of bovine embryos. The assay is highly sensitive, specific, rapid and simple; it can be carried out in only 5 min at 37 °C in a metal bath, and results are visualised using a fluorescent colorimeter. Highly specific male-female common and male-specific primers were designed based on the 1399 bp repeating unit of bovine 1.715 satellite DNA and the male-specific S4 repeating sequence, respectively. The limit of detection (LOD) of RPA-CFI with male-female common primers was 1 pg/μL, and the LOD with male-specific primers was 2 pg/μL. RPA-CFI could determine the sex of bovine embryos from only two cells. This is the first report using RPA-CFI for sex determination of bovine embryos. The assay could be applied to other economically important animals to improve efficiency in livestock industries. Additionally, the assay could relieve pressure on food demand due to human population growth, and contribute to economic development of global stockbreeding.
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Affiliation(s)
- Xinyi Pu
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Wenjing Wu
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Dan Yang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Qi Zhang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xiaorui Fan
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yanan Du
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Liujing Zu
- Shanghai Bio-full Biotech Co., Ltd., Shanghai 201106, China
| | - Yan Xu
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Chuanwen Sun
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Kai Zhao
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
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6
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Agurto-Arteaga A, Vivas-Ruiz DE, Lazo F, Proleón Á, Torrejón D, Electo J, Cayo C, Urra FA, Chávez-Olórtegui C, Sánchez EF, Yarlequé A. Simultaneous identification of three clinically relevant peruvian pit vipers by multiplex loop-mediated isothermal amplification (mLAMP). Toxicon 2023; 223:107022. [PMID: 36621682 DOI: 10.1016/j.toxicon.2023.107022] [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: 10/24/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/07/2023]
Abstract
Previous knowledge about the taxonomic distribution of venomous snake species is very useful for epidemiological aspects of ophidism. Here, we sought to develop an assay for the differential identification of clinically relevant snakes in Peru: Bothrops atrox, Lachesis muta, and Crotalus durissus using a multiplex loop-mediated isothermal amplification (mLAMP) assay. For this, DNA was extracted from the shed snake skins and the mitochondrial genes Cytb, COI, and 12S rRNA were amplified and further sequenced, for the design of mLAMP reaction primers. For each snake species the forward and reverse primers, internal forward and reverse primers, and the loop primers were obtained, bearing the latter different fluorophores for product identification. Finally, the reaction was standardized in the presence of all primer sets, and an optimal amount of low molecular weight polyethyleneimine. The precipitated products were observed in a UV light transilluminator, finding a differential fluorescence according to the DNA used, with a detection limit to the naked eye in the range of 0.2-25 ng of DNA, within 30 min. This study is the first report on the use of mLAMP technology for the identification of venomous snakes.
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Affiliation(s)
- Andres Agurto-Arteaga
- Laboratorio de Biología Molecular-Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima 01, Lima, Peru.
| | - Dan E Vivas-Ruiz
- Laboratorio de Biología Molecular-Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima 01, Lima, Peru.
| | - Fanny Lazo
- Laboratorio de Biología Molecular-Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima 01, Lima, Peru
| | - Álex Proleón
- Laboratorio de Biología Molecular-Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima 01, Lima, Peru
| | - Daniel Torrejón
- Laboratorio de Biología Molecular-Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima 01, Lima, Peru
| | - Jorge Electo
- Laboratorio de Biología Molecular-Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima 01, Lima, Peru
| | - Carmen Cayo
- Laboratorio de Biología Molecular-Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima 01, Lima, Peru
| | - Felix A Urra
- Laboratorio de Plasticidad Metabólica y Bioenergética, Programa de Farmacología Clínica y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, 8380453, Chile
| | - Carlos Chávez-Olórtegui
- Departamento de Bioquímica-Inmunología, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Minas Gerais, Brazil
| | - Eladio F Sánchez
- Research and Development Center, Ezequiel Dias Foundation, 30510-010, Belo Horizonte, MG, Brazil
| | - Armando Yarlequé
- Laboratorio de Biología Molecular-Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima 01, Lima, Peru
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7
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Fan Q, Xie Z, Wei Y, Zhang Y, Xie Z, Xie L, Huang J, Zeng T, Wang S, Luo S, Li M. Development of a visual multiplex fluorescent LAMP assay for the detection of foot-and-mouth disease, vesicular stomatitis and bluetongue viruses. PLoS One 2022; 17:e0278451. [PMID: 36480573 PMCID: PMC9731490 DOI: 10.1371/journal.pone.0278451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is a nucleic acid amplification technique that can be used to amplify target genes at a constant temperature, and it has several advantages, including convenience, specificity and sensitivity. However, due to the special interpretation methods of this technology for reaction results, all the previously reported LAMP detection methods have been restricted to identifying a single target, which limits the application of this technology. In this study, we modified conventional LAMP to include a quencher-fluorophore composite probe complementary to the F1c segment of the inner primer FIP; upon strand separation, a gain in the visible fluorescent signal was observed. The probes could be labeled with different fluorophores, showing different colors at the corresponding wavelengths. Therefore, this multiplex LAMP (mLAMP) assay can simultaneously detect 1-3 target sequences in a single LAMP reaction tube, and the results are more accurate and intuitive. In this study, we comprehensively demonstrated a single-reaction mLAMP assay for the robust detection of three cattle viruses without nonspecific amplification of other related pathogenic cattle viruses. The detection limit of this mLAMP assay was as low as 526-2477 copies/reaction for the recombinant plasmids. It is expected that this mLAMP assay can be widely used in clinical diagnosis.
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Affiliation(s)
- Qing Fan
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Zhixun Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
- * E-mail:
| | - You Wei
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Yanfang Zhang
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Zhiqin Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Liji Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Jiaoling Huang
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Tingting Zeng
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Sheng Wang
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Sisi Luo
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Meng Li
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
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Starkie ML, Fowler EV, Zhu X, Agarwal A, Rako L, Schneider IC, Schutze MK, Royer JE, Gopurenko D, Gillespie P, Blacket MJ. Loop-mediated isothermal amplification (LAMP) assays for detection of the New Guinea fruit fly Bactrocera trivialis (Drew) (Diptera: Tephritidae). Sci Rep 2022; 12:12602. [PMID: 35871253 PMCID: PMC9308764 DOI: 10.1038/s41598-022-16901-0] [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: 03/25/2022] [Accepted: 07/18/2022] [Indexed: 11/09/2022] Open
Abstract
The cue-lure-responding New Guinea fruit fly, Bactroceratrivialis, poses a biosecurity risk to neighbouring countries, e.g., Australia. In trapping programs, lure caught flies are usually morphologically discriminated from non-target species; however, DNA barcoding can be used to confirm similar species where morphology is inconclusive, e.g., Bactrocerabreviaculeus and B.rufofuscula. This can take days—and a laboratory—to resolve. A quicker, simpler, molecular diagnostic assay would facilitate a more rapid detection and potential incursion response. We developed LAMP assays targeting cytochrome c oxidase subunit I (COI) and Eukaryotic Translation Initiation Factor 3 Subunit L (EIF3L); both assays detected B.trivialis within 25 min. The BtrivCOI and BtrivEIF3L assay anneal derivatives were 82.7 ± 0.8 °C and 83.3 ± 1.3 °C, respectively, detecting down to 1 × 101 copies/µL and 1 × 103 copies/µL, respectively. Each assay amplified some non-targets from our test panel; however notably, BtrivCOI eliminated all morphologically similar non-targets, and combined, the assays eliminated all non-targets. Double-stranded DNA gBlocks were developed as positive controls; anneal derivatives for the COI and EIF3L gBlocks were 84.1 ± 0.7 °C and 85.8 ± 0.2 °C, respectively. We recommend the BtrivCOI assay for confirmation of suspect cue-lure-trapped B.trivialis, with BtrivEIF3L used for secondary confirmation when required.
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A loop-mediated isothermal amplification (LAMP) assay for the detection of Cryptotermes brevis West Indian drywood termite (Blattodea: Kalotermitidae). Sci Rep 2022; 12:15111. [PMID: 36068251 PMCID: PMC9448757 DOI: 10.1038/s41598-022-18582-1] [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: 11/10/2021] [Accepted: 08/16/2022] [Indexed: 11/08/2022] Open
Abstract
Cryptotermes brevis is one of the most destructive invasive termites in the subtropics and tropics and is a common biosecurity intercept at the Australian border. Drywood termite species are cryptic and difficult to identify morphologically in situations when soldiers or imagos are unavailable. We developed a novel DNA based loop-mediated isothermal amplification (LAMP) assay to detect C. brevis and differentiate it from other drywood termites. Validated voucher specimens of 30 different drywood termite species were obtained from several insect collections from which DNA was extracted and amplified. The amplicons containing partial mitochondrial 16S rRNA were sequenced and a DNA database was created from which C. brevis LAMP primers were developed, optimized, and tested. The assay was assessed against a range of target and non-target species and found to be specific, successfully amplifying the target specimens of C. brevis in under 30 min. Amplification success was variable against C. brevis faecal pellets due to minute, unmeasurable or degraded DNA. This LAMP test is a new tool for the rapid detection of C. brevis that will enable faster and less destructive management of drywood termite infestations.
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10
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Kim AY, Koh YH. Development of a Rapid, Accurate, and On-Site Detection Protocol for Red Imported Fire Ants, Solenopsis invicta (Hymenoptera: Formicidae). BIOENGINEERING (BASEL, SWITZERLAND) 2022; 9:bioengineering9090434. [PMID: 36134980 PMCID: PMC9495655 DOI: 10.3390/bioengineering9090434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/12/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022]
Abstract
A rapid, accurate, and on-site molecular diagnostic protocol for red imported fire ants (Solenopsis invicta, Si) was developed using loop-mediated isothermal amplification (LAMP) assays. Si11977 (GenBank accession no. MK986826) was confirmed to be a Si-specific gene. Four-primer Si11977-LAMP (4pSi-LAMP) and six-primer Si11977-LAMP (6pSi-LAMP) assays specifically detected Si. The reaction time of 6pSi-LAMP assays was reduced by 5 min compared with 4pSi-LAMP assays. The optimal amount of polymerase and the detection limit for the 6pSi-LAMP assays were 0.1 unit/μL and 5 fg/μL, respectively. In addition, a method for extracting genomic DNA from ant tissues within 2 to 3 min and a protocol for performing on-site LAMP assays using a car heating mug and a LAMP observation box were described. The on-site Si detection protocol used in this study was possible within 30 min from DNA extraction to species identification.
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Affiliation(s)
- A-Young Kim
- Ilsong Institute of Life Science, Hallym University, Seoul 07247, Korea
| | - Young Ho Koh
- Ilsong Institute of Life Science, Hallym University, Seoul 07247, Korea
- Department of Bio-Medical Gerontology, Hallym University, Chooncheon 24252, Korea
- Correspondence: ; Tel.: +82-10-9979-3703
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11
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Botella JR. Point-of-Care DNA Amplification for Disease Diagnosis and Management. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:1-20. [PMID: 36027938 DOI: 10.1146/annurev-phyto-021621-115027] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Early detection of pests and pathogens is of paramount importance in reducing agricultural losses. One approach to early detection is point-of-care (POC) diagnostics, which can provide early warning and therefore allow fast deployment of preventive measures to slow down the establishment of crop diseases. Among the available diagnostic technologies, nucleic acid amplification-based diagnostics provide the highest sensitivity and specificity, and those technologies that forego the requirement for thermocycling show the most potential for use at POC. In this review, I discuss the progress, advantages, and disadvantages of the established and most promising POC amplification technologies. The success and usefulness of POC amplification are ultimately dependent on the availability of POC-friendly nucleic acid extraction methods and amplification readouts, which are also briefly discussed in the review.
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Affiliation(s)
- José R Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, Australia;
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12
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Choudhary P, Goswami SK, Chakdar H, Verma S, Thapa S, Srivastava AK, Saxena AK. Colorimetric loop-mediated isothermal amplification assay for detection and ecological monitoring of Sarocladium oryzae, an important seed-borne pathogen of rice. FRONTIERS IN PLANT SCIENCE 2022; 13:936766. [PMID: 36061774 PMCID: PMC9434274 DOI: 10.3389/fpls.2022.936766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Accurate and timely disease detection plays a critical role in achieving sustainable crop protection. Globally, rice has been a staple crop for centuries plagued by the diseases that greatly hamper its productivity. Sheath rot, an emerging disease of rice caused by the seed-borne pathogen Sarocladium oryzae, has reportedly caused heavy losses to agricultural produce in recent years. Our study has led to the development and validation of a LAMP assay for early detection of S. oryzae, the causal agent of sheath rot from the live-infected tissues, seeds, weeds, and environmental samples. The assay could detect as low as 1.6 fg/μl of the pathogen in 15 min. The assay was implemented to bio-surveil the presence of this pathogen by testing it on three weed species (Echinochloa colona, Echinochloa crus-galli, and Cyperus teneriffae) growing around the rice fields. The results showed the presence of the pathogen in two of the weed species viz. E. colona and E. crus-galli. The assay was used to test 13 different rice varieties for the presence of S. oryzae in seeds. In total, three of the varieties did not show the presence of S. oryzae in their seeds while the rest were found to harbor the pathogen. The developed assay can effectively be used to detect and screen the presence of S. oryzae in live samples including seeds and field soil.
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Affiliation(s)
- Prassan Choudhary
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Sanjay Kumar Goswami
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Sugarcane Research, Lucknow, India
| | - Hillol Chakdar
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Shaloo Verma
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Shobit Thapa
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Alok Kumar Srivastava
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Anil Kumar Saxena
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
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Next generation biosecurity: Towards genome based identification to prevent spread of agronomic pests and pathogens using nanopore sequencing. PLoS One 2022; 17:e0270897. [PMID: 35877652 PMCID: PMC9312391 DOI: 10.1371/journal.pone.0270897] [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: 02/09/2022] [Accepted: 06/19/2022] [Indexed: 11/19/2022] Open
Abstract
The unintentional movement of agronomic pests and pathogens is steadily increasing due to the intensification of global trade. Being able to identify accurately and rapidly early stages of an invasion is critical for developing successful eradication or management strategies. For most invasive organisms, molecular diagnostics is today the method of choice for species identification. However, the currently implemented tools are often developed for certain taxa and need to be adapted for new species, making them ill-suited to cope with the current constant increase in new invasive species. To alleviate this impediment, we developed a fast and accurate sequencing tool allowing to modularly obtain genetic information at different taxonomical levels. Using whole genome amplification (WGA) followed by Oxford nanopore MinION sequencing, our workflow does not require any a priori knowledge on the investigated species and its classification. While mainly focusing on harmful plant pathogenic insects, we also demonstrate the suitability of our workflow for the molecular identification of bacteria (Erwinia amylovora and Escherichia coli), fungi (Cladosporium herbarum, Colletotrichum salicis, Neofabraea alba) and nematodes (Globodera rostochiensis). On average, the pairwise identity between the generated consensus sequences and best GenBank BLAST matches was 99.6 ± 0.6%. Additionally, assessing the generated insect genomic dataset, the potential power of the workflow to detect pesticide resistance genes, as well as arthropod-infecting viruses and endosymbiotic bacteria is demonstrated.
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14
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Jangra S, Ghosh A, Mukherjee S, Baranwal VK, Dietzgen RG. Development of a Polymerase Spiral Reaction-Based Isothermal Assay for Rapid Identification of Thrips palmi. Front Mol Biosci 2022; 9:853339. [PMID: 35586189 PMCID: PMC9108268 DOI: 10.3389/fmolb.2022.853339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/23/2022] [Indexed: 12/03/2022] Open
Abstract
Thrips cause considerable economic losses to a wide range of food, feed, and forest crops. They also transmit several plant viruses. Being cryptic, it is often difficult to distinguish thrips species in crops and large consignments by conventional methods. Melon thrips (Thrips palmi Karny, Thysanoptera: Thripidae) is an invasive insect pest of vegetables, legumes, and ornamentals besides being vector to several viruses. It poses a threat to domestic and international plant biosecurity and can invade and establish in new areas. Here, we report a polymerase spiral reaction (PSR)-based isothermal assay for rapid, sensitive, specific, low-cost, and on-site detection of T. palmi. To the best of our knowledge, this is the first application of PSR in the identification of any insect species. A primer pair designed based on 3′-polymorphism of mtCOIII region can specifically identify T. palmi without any cross-reactivity with predominant thrips species. The assay uses crude lysate of a single thrips saving time and reagents involved in nucleic acid extraction. The presence of T. palmi is visualized by the appearance of bright fluorescence under ultraviolet light or a change in reaction color thus avoiding gel electrophoresis steps. The entire process can be completed in 70 min on-site using only an ordinary water bath. The assay is sensitive to detecting as little as 50 attograms of T. palmi template. The assay was validated with known thrips specimens and found to be efficient in diagnosing T. palmi under natural conditions. The described method will be useful for non-expert personnel to detect an early infestation, accidental introduction to a new area, restrict the spread of diseases and formulate appropriate management strategies.
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Affiliation(s)
- Sumit Jangra
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Amalendu Ghosh
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Amalendu Ghosh, , orcid.org/0000-0001-6634-5771
| | - Sunil Mukherjee
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Virendra Kumar Baranwal
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ralf G. Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Saint Lucia, QLD, Australia
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15
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Agarwal A, Rako L, Schutze MK, Starkie ML, Tay WT, Rodoni BC, Blacket MJ. A diagnostic LAMP assay for rapid identification of an invasive plant pest, fall armyworm Spodoptera frugiperda (Lepidoptera: Noctuidae). Sci Rep 2022; 12:1116. [PMID: 35064176 PMCID: PMC8782856 DOI: 10.1038/s41598-021-04496-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022] Open
Abstract
Fall armyworm (FAW), Spodoptera frugiperda (Lepidoptera: Noctuidae), is a highly polyphagous invasive plant pest that has expanded its global geographic distribution, including recently into much of Australia. Rapid diagnostic tests are required for identification of FAW to assist subsequent management and control. We developed a new loop-mediated isothermal amplification (LAMP) assay based on the mitochondrial cytochrome c oxidase subunit I (COI) gene for accurate and timely diagnosis of FAW in the field. The specificity of the new assay was tested against a broad panel of twenty non-target noctuids, including eight other Spodoptera species. Only S. frugiperda samples produced amplification within 20 min, with an anneal derivative temperature of 78.3 ± 0.3 °C. A gBlock dsDNA fragment was developed and trialled as a synthetic positive control, with a different anneal derivative of 81 °C. The new FAW LAMP assay was able to detect FAW DNA down to 2.4 pg, similar to an existing laboratory-based real-time PCR assay. We also trialled the new FAW assay with a colorimetric master mix and found it could successfully amplify positive FAW samples in half the time compared to an existing FAW colorimetric LAMP assay. Given the high sensitivity and rapid amplification time, we recommend the use of this newly developed FAW LAMP assay in a portable real-time fluorometer for in-field diagnosis of FAW.
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Affiliation(s)
- Arati Agarwal
- Agriculture Victoria, AgriBio, 5 Ring Road, Bundoora, VIC, 3083, Australia
| | - Lea Rako
- Agriculture Victoria, AgriBio, 5 Ring Road, Bundoora, VIC, 3083, Australia
| | - Mark K Schutze
- Biosecurity Queensland, Queensland Department of Agriculture and Fisheries, GPO Box 267, Brisbane, QLD, 4001, Australia
| | - Melissa L Starkie
- Biosecurity Queensland, Queensland Department of Agriculture and Fisheries, GPO Box 267, Brisbane, QLD, 4001, Australia
| | - Wee Tek Tay
- CSIRO, Black Mountain Laboratories, Clunies Ross Street, Canberra, ACT, 2601, Australia.,Applied BioSciences, University of Macquarie, Sydney, NSW, 2109, Australia
| | - Brendan C Rodoni
- Agriculture Victoria, AgriBio, 5 Ring Road, Bundoora, VIC, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Mark J Blacket
- Agriculture Victoria, AgriBio, 5 Ring Road, Bundoora, VIC, 3083, Australia.
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16
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Dermauw W, Van Moerkercke Y, Ebrahimi N, Casteels H, Bonte J, Witters J. A loop-mediated isothermal amplification (LAMP) assay for rapid identification of Ceratitis capitata and related species. CURRENT RESEARCH IN INSECT SCIENCE 2022; 2:100029. [PMID: 36003269 PMCID: PMC9387498 DOI: 10.1016/j.cris.2022.100029] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 05/04/2023]
Abstract
True fruit flies (Tephritidae) are among the most destructive agricultural pests in the world, attacking a wide range of fruits and vegetables. The Mediterranean fruit fly Ceratitis capitata is a highly polyphagous species but, being widely established in the Mediterranean region, is not considered as a EU quarantine pest. Hence, it is important to discriminate Ceratitis capitata from non-EU tephritid species, present in imported fruit and vegetables, as non-EU species have a quarantine status. However, morphological identification of tephritid larvae, the most frequently intercepted stage in non-EU produce, is difficult and an easy-to-use molecular diagnostic tool would be helpful for rapid species identification. Therefore, a loop-mediated isothermal amplification (LAMP) method was developed for C. capitata and non-EU tephritids Ceratitis cosyra group1 and Ceratitis species from the FARQ complex, C. fasciventris, C. anonae, C. rosa and C. quilicii. LAMP assays were run with DNA from ILVO collected specimens and DNA samples collected during previous research surveys. LAMP primers were species-specific, with LAMP amplification occurring within 45 minutes for the targeted species. In addition, LAMP assays were successful for all C. capitata life stages or a limited amount of tissue. To conclude, the LAMP assays developed in this study were able to distinguish C. capitata from non-EU Tephritidae species and could be a useful tool for the rapid identification of C. capitata.
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Affiliation(s)
- Wannes Dermauw
- Corresponding authors: Wannes Dermauw, Johan Witters, Flanders research institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burg. Van Gansberghelaan 96, B-9820 Merelbeke, Belgium.
| | | | | | | | | | - Johan Witters
- Corresponding authors: Wannes Dermauw, Johan Witters, Flanders research institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burg. Van Gansberghelaan 96, B-9820 Merelbeke, Belgium.
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17
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Dia NC, Van Vaerenbergh J, Van Malderghem C, Blom J, Smits THM, Cottyn B, Pothier JF. Xanthomonas hydrangeae sp. nov., a novel plant pathogen isolated from Hydrangea arborescens. Int J Syst Evol Microbiol 2021; 71. [PMID: 34913859 DOI: 10.1099/ijsem.0.005163] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This paper describes a novel species isolated in 2011 and 2012 from nursery-grown Hydrangea arborescens cultivars in Flanders, Belgium. After 4 days at 28 °C, the strains yielded yellow, round, convex and mucoid colonies. Pathogenicity of the strains was confirmed on its isolation host, as well as on Hydrangea quercifolia. Analysis using MALDI-TOF MS identified the Hydrangea strains as belonging to the genus Xanthomonas but excluded them from the species Xanthomonas hortorum. A phylogenetic tree based on gyrB confirmed the close relation to X. hortorum. Three fatty acids were dominant in the Hydrangea isolates: anteiso-C15 : 0, iso-C15 : 0 and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c). Unlike X. hortorum pathovars, the Hydrangea strains were unable to grow in the presence of lithium chloride and could only weakly utilize d-fructose-6-PO4 and glucuronamide. Phylogenetic characterization based on multilocus sequence analysis and phylogenomic characterization revealed that the strains are close to, yet distinct from, X. hortorum. The genome sequences of the strains had average nucleotide identity values ranging from 94.35-95.19 % and in silico DNA-DNA hybridization values ranging from 55.70 to 59.40 % to genomes of the X. hortorum pathovars. A genomics-based loop-mediated isothermal amplification assay was developed which was specific to the Hydrangea strains for its early detection. A novel species, Xanthomonas hydrangeae sp. nov., is proposed with strain LMG 31884T (=CCOS 1956T) as the type strain.
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Affiliation(s)
- Nay C Dia
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland.,Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Johan Van Vaerenbergh
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Cinzia Van Malderghem
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig University Giessen, Giessen, Germany
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Bart Cottyn
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Joël F Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
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18
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Alien Invasive Pathogens and Pests Harming Trees, Forests, and Plantations: Pathways, Global Consequences and Management. FORESTS 2021. [DOI: 10.3390/f12101364] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Forest health worldwide is impacted by many invasive alien pathogens and pests (IAPPs) that cause significant harm, with severe economic losses and environmental alterations. Destructive tree pathogens and pests have in the past devastated our forests, natural landscapes and cityscapes and still continue to represent a serious threat. The main driver of pathogen and pest invasions is human activities, above all global trade, which allows these invasive species to overstep their natural distribution ranges. While natural transport occurs according to a regular, expected colonization pattern (based on the dispersive capacity of the organism), human-mediated transport takes place on a larger, unpredictable scale. In order for a pathogen or pest species to become invasive in a new territory it must overcome distinct stages (barriers) that strongly affect the outcome of the invasion. Early detection is crucial to enabling successful eradication and containment. Although sophisticated diagnostic techniques are now available for disease and pest surveillance and monitoring, few control and mitigation options are usable in forestry; of these, biological control is one of the most frequently adopted. Since invasion by pathogens and pests is an economic and ecological problem of supranational relevance, governments should endorse all necessary preventive and corrective actions. To this end, establishing and harmonizing measures among countries is essential, both for preventing new introductions and for diminishing the eventual range expansion of IAPPs present at a local scale. Research is fundamental for: (i) developing effective and rapid diagnostic tools; (ii) investigating the epidemiology and ecology of IAPPs in newly introduced areas; and (iii) supporting policymakers in the implementation of quarantine regulations.
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Kim J, Nam HY, Kwon M, Kim HJ, Yi HJ, Haenniger S, Unbehend M, Heckel DG. Development of a simple and accurate molecular tool for Spodoptera frugiperda species identification using LAMP. PEST MANAGEMENT SCIENCE 2021; 77:3145-3153. [PMID: 33644961 DOI: 10.1002/ps.6350] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/28/2020] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The fall armyworm, Spodoptera frugiperda is a native species of the Americas. First detected in western and central Africa in early 2016, it has become one of the most serious invasive lepidopteran pests in many African and Asian countries. S. frugiperda has spread very quickly; however, there are no molecular-based, simple and accurate diagnostic tools for identification of this species in the field. Methods to identify invasive S. frugiperda are urgently needed because farmers and agricultural managers have no prior experience with this pest. RESULTS Based on mitochondrial genome sequence alignment, a S. frugiperda-specific sequence region was identified in the transfer RNA-coding region between NADH dehydrogenase, ND3, and ND5. Using this unique region, species-diagnostic primers were designed and applied in a loop-mediated isothermal amplification (LAMP) assay and a conventional polymerase chain reaction to identify field-collected samples of S. frugiperda. The optimal incubation conditions for the LAMP assay were 61°C for 90 min with four LAMP primers; an additional loop primer increased the amplification efficiency. A response was obtained for a wide range of DNA concentrations in the LAMP assay and the minimum detectable DNA concentration was 10 pg. CONCLUSIONS We developed a new LAMP-based molecular diagnostic method that it is easy to use and accurate. The LAMP assay was used with a DNA-releasing technique for larval and adult samples, without a DNA extraction step, by incubating the tissue sample at 95°C for 5 min. This method can be applied in intensive field monitoring of S. frugiperda and its ecological studies. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Juil Kim
- Program of Applied Biology, Division of Bio-resource Sciences, College of Agriculture and Life Science, Kangwon National University, Chuncheon, Republic of Korea
- Highland Agriculture Research Institute, National Institute of Crop Science, RDA, Pyeongchang, Republic of Korea
| | - Hwa Y Nam
- Program of Applied Biology, Division of Bio-resource Sciences, College of Agriculture and Life Science, Kangwon National University, Chuncheon, Republic of Korea
- Highland Agriculture Research Institute, National Institute of Crop Science, RDA, Pyeongchang, Republic of Korea
| | - Min Kwon
- Highland Agriculture Research Institute, National Institute of Crop Science, RDA, Pyeongchang, Republic of Korea
| | - Hyun J Kim
- Crop foundation Division, National Institute of Crop Science, RDA, Wanju, Republic of Korea
| | - Hwi J Yi
- Crop Production Technology Research Division, National Institute of Crop Science, RDA, Miryang, Republic of Korea
| | - Sabine Haenniger
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Melanie Unbehend
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - David G Heckel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
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20
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TaqMan probe assays on different biological samples for the identification of three ambrosia beetle species, Xylosandrus compactus (Eichoff) , X. crassiusculus (Motschulsky) and X. germanus (Blandford) (Coleoptera Curculionidae Scolytinae). 3 Biotech 2021; 11:259. [PMID: 33996371 PMCID: PMC8110672 DOI: 10.1007/s13205-021-02786-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/08/2021] [Indexed: 12/03/2022] Open
Abstract
Molecular assays based on qPCR TaqMan Probes were developed to identify three species of the genus Xylosandrus, X. compactus, X. crassiusculus and X. germanus (Coleoptera Curculionidae Scolytinae). These ambrosia beetles are xylophagous species alien to Europe, causing damages to many ornamental and fruiting trees as well as shrubs. DNA extraction was carried out from adults, larvae and biological samples derived from insect damages on infested plants. For X. compactus, segments of galleries in thin infested twigs were cut and processed; in the case of X. crassiusculus, raw frass extruded from exit holes was used, while DNA of X. germanus was extracted from small wood chips removed around insect exit holes. The assays were inclusive for the target species and exclusive for all the non-target species tested. The LoD was 3.2 pg/µL for the frass of X. crassiusculus and 0.016 ng/µL for the woody matrices of the other two species. Both repeatability and reproducibility were estimated on adults and woody samples, showing very low values ranging between 0.00 and 4.11. Thus, the proposed diagnostic assays resulted to be very efficient also on the woody matrices used for DNA extraction, demonstrating the applicability of the protocol in the absence of dead specimens or living stages.
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21
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Rizzo D, Moricca S, Bracalini M, Benigno A, Bernardo U, Luchi N, Da Lio D, Nugnes F, Cappellini G, Salemi C, Cacciola SO, Panzavolta T. Rapid Detection of Pityophthorus juglandis (Blackman) (Coleoptera, Curculionidae) with the Loop-Mediated Isothermal Amplification (LAMP) Method. PLANTS 2021; 10:plants10061048. [PMID: 34067342 PMCID: PMC8224600 DOI: 10.3390/plants10061048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/14/2021] [Accepted: 05/20/2021] [Indexed: 11/16/2022]
Abstract
The walnut twig beetle Pityophthorus juglandis is a phloem-boring bark beetle responsible, in association with the ascomycete Geosmithia morbida, for the Thousand Cankers Disease (TCD) of walnut trees. The recent finding of TCD in Europe prompted the development of effective diagnostic protocols for the early detection of members of this insect/fungus complex. Here we report the development of a highly efficient, low-cost, and rapid method for detecting the beetle, or even just its biological traces, from environmental samples: the loop-mediated isothermal amplification (LAMP) assay. The method, designed on the 28S ribosomal RNA gene, showed high specificity and sensitivity, with no cross reactivity to other bark beetles and wood-boring insects. The test was successful even with very small amounts of the target insect’s nucleic acid, with limit values of 0.64 pg/µL and 3.2 pg/µL for WTB adults and frass, respectively. A comparison of the method (both in real time and visual) with conventional PCR did not display significant differences in terms of LoD. This LAMP protocol will enable quick, low-cost, and early detection of P. juglandis in areas with new infestations and for phytosanitary inspections at vulnerable sites (e.g., seaports, airports, loading stations, storage facilities, and wood processing companies).
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Affiliation(s)
- Domenico Rizzo
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Via Ciliegiole 99, 51100 Pistoia, Italy; (D.R.); (G.C.)
| | - Salvatore Moricca
- Department of Agricultural, Food, Environmental and Forestry Science and Technology (DAGRI), Plant Pathology and Entomology Section, University of Florence, Piazzale delle Cascine 28, 50144 Florence, Italy; (M.B.); (A.B.); (T.P.)
- Correspondence:
| | - Matteo Bracalini
- Department of Agricultural, Food, Environmental and Forestry Science and Technology (DAGRI), Plant Pathology and Entomology Section, University of Florence, Piazzale delle Cascine 28, 50144 Florence, Italy; (M.B.); (A.B.); (T.P.)
| | - Alessandra Benigno
- Department of Agricultural, Food, Environmental and Forestry Science and Technology (DAGRI), Plant Pathology and Entomology Section, University of Florence, Piazzale delle Cascine 28, 50144 Florence, Italy; (M.B.); (A.B.); (T.P.)
| | - Umberto Bernardo
- Portici Unit, Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), P. le Enrico Fermi 1, 80055 Portici, Italy; (U.B.); (F.N.)
| | - Nicola Luchi
- Florence Unit, Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy;
| | - Daniele Da Lio
- Department of Agricultural, Food and Agro-Environmental Sciences, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy; (D.D.L.); (C.S.)
| | - Francesco Nugnes
- Portici Unit, Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), P. le Enrico Fermi 1, 80055 Portici, Italy; (U.B.); (F.N.)
| | - Giovanni Cappellini
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Via Ciliegiole 99, 51100 Pistoia, Italy; (D.R.); (G.C.)
| | - Chiara Salemi
- Department of Agricultural, Food and Agro-Environmental Sciences, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy; (D.D.L.); (C.S.)
| | - Santa Olga Cacciola
- Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy;
| | - Tiziana Panzavolta
- Department of Agricultural, Food, Environmental and Forestry Science and Technology (DAGRI), Plant Pathology and Entomology Section, University of Florence, Piazzale delle Cascine 28, 50144 Florence, Italy; (M.B.); (A.B.); (T.P.)
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Catara V, Cubero J, Pothier JF, Bosis E, Bragard C, Đermić E, Holeva MC, Jacques MA, Petter F, Pruvost O, Robène I, Studholme DJ, Tavares F, Vicente JG, Koebnik R, Costa J. Trends in Molecular Diagnosis and Diversity Studies for Phytosanitary Regulated Xanthomonas. Microorganisms 2021; 9:862. [PMID: 33923763 PMCID: PMC8073235 DOI: 10.3390/microorganisms9040862] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 11/17/2022] Open
Abstract
Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence of phylogenetically close strains, but drastically different in their phenotype, poses an added challenge to diagnosis. Data on future climate change scenarios predict an increase in the severity of epidemics and a geographical expansion of pathogens, increasing pressure on plant health services. In this context, the effectiveness of integrated disease management strategies strongly depends on the availability of rapid, sensitive, and specific diagnostic methods. The accumulation of genomic information in recent years has facilitated the identification of new DNA markers, a cornerstone for the development of more sensitive and specific methods. Nevertheless, the challenges that the taxonomic complexity of this genus represents in terms of diagnosis together with the fact that within the same bacterial species, groups of strains may interact with distinct host species demonstrate that there is still a long way to go. In this review, we describe and discuss the current molecular-based methods for the diagnosis and detection of regulated Xanthomonas, taxonomic and diversity studies in Xanthomonas and genomic approaches for molecular diagnosis.
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Affiliation(s)
- Vittoria Catara
- Department of Agriculture, Food and Environment, University of Catania, 95125 Catania, Italy
| | - Jaime Cubero
- National Institute for Agricultural and Food Research and Technology (INIA), 28002 Madrid, Spain;
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), 8820 Wädenswil, Switzerland;
| | - Eran Bosis
- Department of Biotechnology Engineering, ORT Braude College of Engineering, Karmiel 2161002, Israel;
| | - Claude Bragard
- UCLouvain, Earth & Life Institute, Applied Microbiology, 1348 Louvain-la-Neuve, Belgium;
| | - Edyta Đermić
- Department of Plant Pathology, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia;
| | - Maria C. Holeva
- Benaki Phytopathological Institute, Scientific Directorate of Phytopathology, Laboratory of Bacteriology, GR-14561 Kifissia, Greece;
| | - Marie-Agnès Jacques
- IRHS, INRA, AGROCAMPUS-Ouest, Univ Angers, SFR 4207 QUASAV, 49071 Beaucouzé, France;
| | - Francoise Petter
- European and Mediterranean Plant Protection Organization (EPPO/OEPP), 75011 Paris, France;
| | - Olivier Pruvost
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France; (O.P.); (I.R.)
| | - Isabelle Robène
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France; (O.P.); (I.R.)
| | | | - Fernando Tavares
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal; or
- FCUP-Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | | | - Ralf Koebnik
- Plant Health Institute of Montpellier (PHIM), Univ Montpellier, Cirad, INRAe, Institut Agro, IRD, 34398 Montpellier, France;
| | - Joana Costa
- Centre for Functional Ecology-Science for People & the Planet, Department of Life Sciences, University of Coimbra, 300-456 Coimbra, Portugal
- Laboratory for Phytopathology, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
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Barr NB, Garza D, Ledezma LA, Salinas DA. Using the rDNA Internal Transcribed Spacer 1 to Identify the Invasive Pest Rhagoletis cerasi (Diptera: Tephritidae) in North America. JOURNAL OF ECONOMIC ENTOMOLOGY 2021; 114:360-370. [PMID: 33367677 DOI: 10.1093/jee/toaa281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Indexed: 06/12/2023]
Abstract
The cherry-infesting fruit fly Rhagoletis cerasi Loew is a significant commercial pest in Europe that has recently invaded North America. To date, it has been trapped only in Canada and northwestern counties of New York. It has the potential to spread further and threaten production and movement of cherry commodities. Timely diagnosis of the pest will facilitate surveys and quick response to new detections. Adult morphology of the pest is distinct from other flies in North America. However, when flies are significantly damaged on traps or the immature life stages are found in fruits, molecular methods of identification are important to confirm presence and host-use records. Other than DNA sequencing of genes from flies which takes over a day to complete, there are no timely methods of molecular identification for this pest. In this study, we report the first sequence record of the internal transcribed spacer 1 (ITS1) from R. cerasi and develop two diagnostic tests for the pest based on ITS1 differences among species in North America. The tests use loop-mediated isothermal amplification (LAMP) and multiplex, conventional polymerase chain reaction (mcPCR) technologies that target the same region of the R. cerasi ITS1 sequence. Both tests performed well when tested against collections of R. cerasi from North America and Europe, generating Diagnostic Sensitivity estimates of 98.4-99.5%. Likewise, the tests had relatively high estimates of Diagnostic Specificity (97.8-100%) when tested against Rhagoletis Loew species present in North America that also use cherry as a developmental host.
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Affiliation(s)
- Norman B Barr
- USDA APHIS PPQ Science & Technology Mission Laboratory, Edinburg, TX
| | - Daniel Garza
- USDA APHIS PPQ Science & Technology Mission Laboratory, Edinburg, TX
| | - Lisa A Ledezma
- USDA APHIS PPQ Science & Technology Mission Laboratory, Edinburg, TX
| | - David A Salinas
- USDA APHIS PPQ Science & Technology Mission Laboratory, Edinburg, TX
- Department of Biology, University of Texas Rio Grande Valley, Edinburg, TX
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Rizzo D, Luchi N, Da Lio D, Bartolini L, Nugnes F, Cappellini G, Bruscoli T, Salemi C, Griffo RV, Garonna AP, Rossi E. Development of a loop-mediated isothermal amplification (LAMP) assay for the identification of the invasive wood borer Aromia bungii (Coleoptera: Cerambycidae) from frass. 3 Biotech 2021; 11:85. [PMID: 33500873 PMCID: PMC7815857 DOI: 10.1007/s13205-020-02602-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 12/17/2020] [Indexed: 11/24/2022] Open
Abstract
The red-necked longhorn beetle Aromia bungii (Faldermann, 1835) (Coleoptera: Cerambycidae) is native to east Asia, where it is a major pest of cultivated and ornamental species of the genus Prunus. Morphological or molecular discrimination of adults or larval specimens is required to identify this invasive wood borer. However, recovering larval stages of the pest from trunks and branches causes extensive damage to plants and is timewasting. An alternative approach consists in applying non-invasive molecular diagnostic tools to biological traces (i.e., fecal pellets, frass). In this way, infestations in host plants can be detected without destructive methods. This paper presents a protocol based on both real-time and visual loop-mediated isothermal amplification (LAMP), using DNA of A. bungii extracted from fecal particles in larval frass. Laboratory validations demonstrated the robustness of the protocols adopted and their reliability was confirmed performing an inter-lab blind panel. The LAMP assay and the qPCR SYBR Green method using the F3/B3 LAMP external primers were equally sensitive, and both were more sensitive than the conventional PCR (sensitivity > 103 to the same starting matrix). The visual LAMP protocol, due to the relatively easy performance of the method, could be a useful tool to apply in rapid monitoring of A. bungii and in the management of its outbreaks.
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Affiliation(s)
- Domenico Rizzo
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Via Ciliegiole 99, 51100 Pistoia, Italy
| | - Nicola Luchi
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano 10, Sesto Fiorentino, 50019 Florence, Italy
| | - Daniele Da Lio
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Linda Bartolini
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Via Ciliegiole 99, 51100 Pistoia, Italy
| | - Francesco Nugnes
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), P.le Enrico Fermi 1, 80055 Portici, Italy
| | - Giovanni Cappellini
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Via Ciliegiole 99, 51100 Pistoia, Italy
| | - Tommaso Bruscoli
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Via Ciliegiole 99, 51100 Pistoia, Italy
| | - Chiara Salemi
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Raffaele V. Griffo
- Plant Protection Service of Campania, Centro Direzionale, Isola A6, 80124 Naples, Italy
| | - Antonio P. Garonna
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Elisabetta Rossi
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
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25
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Rizzo D, Taddei A, Da Lio D, Bruscoli T, Cappellini G, Bartolini L, Salemi C, Luchi N, Pennacchio F, Rossi E. Molecular Identification of Anoplophora glabripennis (Coleoptera: Cerambycidae) From Frass by Loop-Mediated Isothermal Amplification. JOURNAL OF ECONOMIC ENTOMOLOGY 2020; 113:2911-2919. [PMID: 32949143 DOI: 10.1093/jee/toaa206] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Indexed: 06/11/2023]
Abstract
Anoplophora glabripennis (Motschulsky, 1853), native to eastern Asia, is a destructive woodborer of many ornamental species, leading to the decline and the death of the attacked trees. In outbreak areas as Europe or North America, this pest is usually identified using morphological or molecular analyses of adult or larval specimens. However, the procedures for collecting A. glabripennis specimens from infested plants are too expensive and time consuming for routine screening. A noninvasive diagnostic tool based on frass discrimination is therefore crucial for the rapid identification of A. glabripennis at different development stages in the host. This article describes a rapid diagnostic protocol based on loop-mediated isothermal amplification (LAMP). DNA extracted from A. glabripennis frass was amplified with both visual and real-time LAMP and compared with those of nontarget species. The results show that the method is reliable and accurate and therefore could be a promising diagnostic tool in phytosanitary surveys.
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Affiliation(s)
- Domenico Rizzo
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Via Ciliegiole, Pistoia, Italy
| | - Andrea Taddei
- Plant Health Laboratory ANSES, Avenue du Campus, Agropolis, Montferrier sur Lez, France
| | - Daniele Da Lio
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto, Pisa, Italy
| | - Tommaso Bruscoli
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Via Ciliegiole, Pistoia, Italy
| | - Giovanni Cappellini
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Via Ciliegiole, Pistoia, Italy
| | - Linda Bartolini
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Via Ciliegiole, Pistoia, Italy
| | - Chiara Salemi
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto, Pisa, Italy
| | - Nicola Luchi
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano, Sesto Fiorentino, Florence, Italy
| | - Fabrizio Pennacchio
- CREA-Research Centre for Plant Protection and Certification, via Lanciola, Florence, Italy
| | - Elisabetta Rossi
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto, Pisa, Italy
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26
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Nam HY, Kwon M, Kim HJ, Kim J. Development of a Species Diagnostic Molecular Tool for an Invasive Pest, Mythimna loreyi, Using LAMP. INSECTS 2020; 11:E817. [PMID: 33228220 PMCID: PMC7699485 DOI: 10.3390/insects11110817] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/15/2020] [Accepted: 11/17/2020] [Indexed: 11/17/2022]
Abstract
The Mythimna loreyi (Duponchel) is one of the well-known invasive noctuid pests in Africa, Australia, and many Asian countries. However, it is difficult to identify the invasive and morphologically similar species, Mythimna separate, which occur at the cornfield in the larvae stage. Currently, the molecular biology method for diagnosing M. loreyi species is only using the mtCO1 universal primer (LCO1490, HCO2198), which requires a lot of time and effort, such as DNA extraction, PCR, electrophoresis, and sequencing. In this study, the LAMP assay was developed for rapid, simple, effective species identification. By analyzing the mitochondrial genome, the species-specific sequence was found at the coding region of the NADH dehydrogenase subunit 5 gene. Based on this unique sequence, four LAMP primers and two loop primers were designed. The F3 and B3 primers were able to diagnose species-specific, in general, and multiplex PCR and specifically reacted within the inner primers in LAMP assay. The optimal incubation condition of the LAMP assay was 61 °C for 60 min with four LAMP primers, though additional loop primers, BF and LF, did not significantly shorten the amplification time. The broad range of DNA concentration was workable in LAMP assay, in which the minimum detectable DNA concentration was 100 pg. DNA releasing method was applied, which took five minutes of incubation at 95 °C without the DNA extraction process. Only some pieces of tissue of larvae and adult samples were needed to extract DNA. The incidence of invasive pests is gradually diversifying. Therefore, this simple and accurate LAMP assay is possibly applied in the intensive field monitoring for invasive pests and integrated management of Mythimna loreyi.
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Affiliation(s)
- Hwa Yeun Nam
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang 25342, Korea; (H.Y.N.); (M.K.)
| | - Min Kwon
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang 25342, Korea; (H.Y.N.); (M.K.)
| | - Hyun Ju Kim
- Crop foundation Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea;
| | - Juil Kim
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang 25342, Korea; (H.Y.N.); (M.K.)
- Program of Applied Biology, Division of Bio-resource Sciences, College of Agriculture and Life Science, Kangwon National University, Chuncheon 24341, Korea
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27
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Rizzo D, Da Lio D, Bartolini L, Cappellini G, Bruscoli T, Bracalini M, Benigno A, Salemi C, Del Nista D, Aronadio A, Panzavolta T, Moricca S. A duplex real-time PCR with probe for simultaneous detection of Geosmithia morbida and its vector Pityophthorus juglandis. PLoS One 2020; 15:e0241109. [PMID: 33095845 PMCID: PMC7584228 DOI: 10.1371/journal.pone.0241109] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 10/09/2020] [Indexed: 11/26/2022] Open
Abstract
The cultivation of walnuts (Juglans sp.) in Europe retains high economic, social, and environmental value. The recent reporting of the Thousand Cankers Disease (TCD) fungus, Geosmithia morbida, and of its vector, Pityophthorus juglandis, in walnut trees in Italy is alarming the whole of Europe. Although Italy is at present the only foothold of the disease outside North America, given the difficulties inherent in traditional identification of both members of this beetle/fungus complex, a rapid and effective protocol for the early detection and identification of TCD organisms is an absolute priority for Europe. Here we report the development of an effective and sensitive molecular tool based on simplex/duplex qPCR assays for the rapid, accurate and highly specific detection of both the bionectriaceous fungal pathogen and its bark-beetle vector. Our assay performed excellently, detecting minute amounts of target DNA without any non-specific amplification. Detection limits from various and heterogeneous matrices were lower than other reported assays. Our molecular protocol could assist in TCD organism interception at entry points, territory monitoring for the early identification and eradication of outbreaks, delineation of quarantine areas, and tracing back TCD entry and dispersal pathways.
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Affiliation(s)
- Domenico Rizzo
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Pistoia, Italy
| | - Daniele Da Lio
- Department of Agricultural, Food and Agro-Environmental Sciences, University of Pisa, Pisa, Italy
| | - Linda Bartolini
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Pistoia, Italy
| | - Giovanni Cappellini
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Pistoia, Italy
| | - Tommaso Bruscoli
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Pistoia, Italy
| | - Matteo Bracalini
- Department of Agriculture, Food, Environment, and Forestry (DAGRI), Plant Pathology and Entomology Division, University of Florence, Florence, Italy
| | - Alessandra Benigno
- Department of Agriculture, Food, Environment, and Forestry (DAGRI), Plant Pathology and Entomology Division, University of Florence, Florence, Italy
| | - Chiara Salemi
- Department of Agricultural, Food and Agro-Environmental Sciences, University of Pisa, Pisa, Italy
| | - Dalia Del Nista
- Plant Protection Service of Tuscany, c/o Interporto Toscano "Amerigo Vespucci", Collesalvetti, Livorno, Italy
| | - Antonio Aronadio
- Plant Protection Service of Tuscany, c/o Interporto Toscano "Amerigo Vespucci", Collesalvetti, Livorno, Italy
| | - Tiziana Panzavolta
- Department of Agriculture, Food, Environment, and Forestry (DAGRI), Plant Pathology and Entomology Division, University of Florence, Florence, Italy
- * E-mail:
| | - Salvatore Moricca
- Department of Agriculture, Food, Environment, and Forestry (DAGRI), Plant Pathology and Entomology Division, University of Florence, Florence, Italy
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28
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Identification of the Red-Necked Longhorn Beetle Aromia bungii (Faldermann, 1835) (Coleoptera: Cerambycidae) with Real-Time PCR on Frass. SUSTAINABILITY 2020. [DOI: 10.3390/su12156041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Aromia bungii (Faldermann, 1835) (Coleoptera: Cerambycidae), the red-necked longhorn beetle is native to eastern Asia, where it is an important wood-borer of fruit and ornamental species of the genus Prunus. A. bungii is a quarantine pest in the European Union, following its accidental introduction and establishment in Germany and Italy, and is currently included in the list of priority pests. To confirm its infestations in outbreak areas, adult or larval specimens are needed to perform morphological or molecular analyses. The presence of A. bungii larvae inside the attacked trees makes the collection of specimens particularly difficult. Thus, we present two diagnostic protocols based on frass analysis with real-time PCR (probe and SYBR Green). The results obtained show that a non-invasive approach for detecting the presence of this harmful invasive pest can be a reliable and accurate alternative diagnostic tool in phytosanitary surveys, as well as to outline a sustainable pest management strategy.
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29
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Blacket MJ, Agarwal A, Zheng L, Cunningham JP, Britton D, Schneider I, Rodoni BC. A LAMP assay for the detection of Bactrocera tryoni Queensland fruit fly (Diptera: Tephritidae). Sci Rep 2020; 10:9554. [PMID: 32533005 PMCID: PMC7293347 DOI: 10.1038/s41598-020-65715-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/29/2020] [Indexed: 11/30/2022] Open
Abstract
LAMP assays are targeted molecular tests for the rapid detection of species in the laboratory and field. We developed a LAMP assay for an economically important fruit fly species, Queensland fruit fly, Bactrocera tryoni. This assay was assessed against a broad panel of target and non-target species and found to be specific, only amplifying the target species and closest relatives, in a portable real-time fluorometer (Genie III) in under 15 minutes with an anneal derivative temperature of 82.5 oC. The assay is sensitive to low levels of target DNA (>0.016 ng/µl), performing equally to the existing qPCR test. To enable retention of a physical voucher specimen, for potential morphological confirmation of LAMP results, a novel whole-specimen non-destructive DNA extraction method was developed, suitable for LAMP in the field. The stability of DNA extraction and LAMP reagents was tested under simulated and actual field conditions and shown to be robust. Our new assay now provides a portable molecular tool for the detection of this significant tephritid fruit fly pest species of biosecurity/quarantine concern. This has already proven invaluable for in-field diagnostics, providing real-time support influencing immediate actions, with negative results allowing the release of fruit produce, and positive results initiating fruit fly control measures.
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Affiliation(s)
- Mark J Blacket
- Agriculture Victoria Research, AgriBio, 5 Ring Road, Bundoora, Victoria, 3083, Australia.
| | - Arati Agarwal
- Agriculture Victoria Research, AgriBio, 5 Ring Road, Bundoora, Victoria, 3083, Australia
| | - Linda Zheng
- Agriculture Victoria Research, AgriBio, 5 Ring Road, Bundoora, Victoria, 3083, Australia
| | - J Paul Cunningham
- Agriculture Victoria Research, AgriBio, 5 Ring Road, Bundoora, Victoria, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3083, Australia
| | - David Britton
- Department of Agriculture, Water and the Environment, Northern Australian Quarantine Strategy (NAQS), Cairns, Queensland, 4870, Australia
| | - Isarena Schneider
- Department of Agriculture, Water and the Environment, Northern Australian Quarantine Strategy (NAQS), Cairns, Queensland, 4870, Australia
| | - Brendan C Rodoni
- Agriculture Victoria Research, AgriBio, 5 Ring Road, Bundoora, Victoria, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3083, Australia
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30
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Amano T, Nomura M. A Diagnostic Loop-Mediated Isothermal Amplification Method to Distinguish Helicoverpa armigera (Lepidoptera: Noctuidae) From Other Related Species in the New World. JOURNAL OF INSECT SCIENCE (ONLINE) 2020; 20:5847614. [PMID: 32458991 PMCID: PMC7251530 DOI: 10.1093/jisesa/ieaa046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Indexed: 05/26/2023]
Abstract
Helicoverpa armigera (Hübner) is a notorious agricultural pest native to the Old World. Recently, its invasion into South and Central America has become a serious problem in the New World. The rapid detection of invasive pests is essential to eradicate them and prevent establishment. However, an extremely similar species, H. zea (Boddie) distributed in the New World makes identification difficult. Helicoverpa armigera and H. zea have only minor differences in male genitalia to separate them morphologically. Both species are attracted to the same pheromone lure, and it takes considerable time and effort to identify them from bulk samples obtained during trap monitoring. Although several molecular approaches based on PCR have been reported, these methods require expensive equipment and are unsuitable for onsite diagnostics. Here, we developed a rapid and convenient diagnostic method based on the loop-mediated isothermal amplification to distinguish H. armigera from related species: H. zea, H. assulta (Guenée), H. punctigera (Wallengren), and Chloridea virescens (Fabricius). The diagnostic method makes it possible to detect H. armigera within 90 min only using simple equipment. The method also worked with mixed DNA templates containing excess DNA from H. zea at the ratio of 1:999 (H. armigera:H. zea). This method can be an effective tool for onsite diagnostics during monitoring surveys for invasive H. armigera.
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Affiliation(s)
- Takayuki Amano
- Laboratory of Applied Entomology, Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
| | - Masashi Nomura
- Laboratory of Applied Entomology, Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
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31
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Real-time loop-mediated isothermal amplification assay for rapid detection of Fusarium circinatum. Biotechniques 2020; 69:369-375. [PMID: 32336113 DOI: 10.2144/btn-2019-0168] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Fusarium circinatum is the causal agent of pitch canker, a lethal disease of pine and other conifers. Since F. circinatum is a quarantine organism, its timely detection could efficiently prevent its introduction into new areas or facilitate spread management in already infected sites. In this study, we developed a sequence-specific probe loop-mediated isothermal amplification (LAMP) assay for F. circinatum using a field-deployable portable instrument. The assay was able to recognize the pathogen in host tissues in just 30 min, and the sensitivity of the assay made it possible to detect even small amounts of F. circinatum DNA (as low as 0.5 pg/μl). The high efficiency of this method suggests its use as a standard diagnostic tool during phytosanitary controls.
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32
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Evans DM, Kitson JJ. Molecular ecology as a tool for understanding pollination and other plant-insect interactions. CURRENT OPINION IN INSECT SCIENCE 2020; 38:26-33. [PMID: 32087411 DOI: 10.1016/j.cois.2020.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/18/2019] [Accepted: 01/16/2020] [Indexed: 06/10/2023]
Abstract
Advances in molecular ecology offer unprecedented opportunities to understand the ecology and evolution of insects, the complex ways in which they interact and their role in ecosystem functioning. Rapidly developing DNA sequencing technologies are resolving previously intractable questions in taxonomic and functional biodiversity and provide significant potential to determine formerly difficult to observe plant-insect interactions. We provide an overview of the state-of-the-art and critically appraise the range of molecular approaches currently available for the study of insect pollination, host-parasitoid interactions and/or wider food-web studies. Species-interaction data are increasingly being incorporated into ecological network analyses. DNA metabarcoding offers opportunities to scale-up efforts to create large, highly resolved, phylogenetically structured networks within an exciting framework to study pressing questions in ecology and evolution.
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Affiliation(s)
- Darren M Evans
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, United Kingdom.
| | - James Jn Kitson
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, United Kingdom
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33
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Baldi P, La Porta N. Molecular Approaches for Low-Cost Point-of-Care Pathogen Detection in Agriculture and Forestry. FRONTIERS IN PLANT SCIENCE 2020; 11:570862. [PMID: 33193502 PMCID: PMC7655913 DOI: 10.3389/fpls.2020.570862] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/29/2020] [Indexed: 05/14/2023]
Abstract
Early detection of plant diseases is a crucial factor to prevent or limit the spread of a rising infection that could cause significant economic loss. Detection test on plant diseases in the laboratory can be laborious, time consuming, expensive, and normally requires specific technical expertise. Moreover, in the developing countries, it is often difficult to find laboratories equipped for this kind of analysis. Therefore, in the past years, a high effort has been made for the development of fast, specific, sensitive, and cost-effective tests that can be successfully used in plant pathology directly in the field by low-specialized personnel using minimal equipment. Nucleic acid-based methods have proven to be a good choice for the development of detection tools in several fields, such as human/animal health, food safety, and water analysis, and their application in plant pathogen detection is becoming more and more common. In the present review, the more recent nucleic acid-based protocols for point-of-care (POC) plant pathogen detection and identification are described and analyzed. All these methods have a high potential for early detection of destructive diseases in agriculture and forestry, they should help make molecular detection for plant pathogens accessible to anyone, anywhere, and at any time. We do not suggest that on-site methods should replace lab testing completely, which remains crucial for more complex researches, such as identification and classification of new pathogens or the study of plant defense mechanisms. Instead, POC analysis can provide a useful, fast, and efficient preliminary on-site screening that is crucial in the struggle against plant pathogens.
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Affiliation(s)
- Paolo Baldi
- IASMA Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
- *Correspondence: Paolo Baldi,
| | - Nicola La Porta
- IASMA Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
- The EFI Project Centre on Mountain Forests (MOUNTFOR), San Michele a/Adige, Trento, Italy
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Zheng L, Zhang Y, Yang W, Zeng Y, Jiang F, Qin Y, Zhang J, Jiang Z, Hu W, Guo D, Wan J, Zhao Z, Liu L, Li Z. New Species-Specific Primers for Molecular Diagnosis of Bactrocera minax and Bactrocera tsuneonis (Diptera: Tephritidae) in China Based on DNA Barcodes. INSECTS 2019; 10:E447. [PMID: 31842348 PMCID: PMC6956326 DOI: 10.3390/insects10120447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/06/2019] [Accepted: 12/09/2019] [Indexed: 12/17/2022]
Abstract
Tephritidae fruit flies (Diptera: Tephritidae) are regarded as important damage-causing species due to their ability to cause great economic losses in fruit and vegetable crops. Bactrocera minax and Bactrocera tsuneonis are two sibling species of the subgenus Tetradacus of Bactrocera that are distributed across a limited area of China, but have caused serious impacts. They share similar morphological characteristics. These characteristics can only be observed in the female adult individuals. The differences between them cannot be observed in preimaginal stages. Thus, it is difficult to distinguish them in preimaginal stages morphologically. In this study, we used molecular diagnostic methods based on cytochrome c oxidase subunit I and species-specific markers to identify these two species and improve upon the false-positive results of previous species-detection primers. DNA barcode sequences were obtained from 900 individuals of B. minax and 63 individuals of B. tsuneonis. Based on these 658 bp DNA barcode sequences of the cytochrome c oxidase subunit I gene, we successfully designed the species-specific primers for B. minax and B. tsuneonis. The size of the B. minax specific fragment was 422 bp and the size of the B. tsuneonis specific fragment was 456 bp. A series of PCR trials ensured the specificity of these two pairs of primers. Sensitivity assay results demonstrated that the detection limit for the DNA template concentration was 0.1~1 ng/μL for these two species. In this study, we established a more reliable, rapid, and low-cost molecular identification method for all life stages of B. minax and B. tsuneonis. Species-specific PCR can be applied in plant quarantine, monitoring and control of B. minax and B. tsuneonis.
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Affiliation(s)
- Linyu Zheng
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (L.Z.); (Y.Z.); (W.Y.); (Y.Z.); (Z.Z.); (L.L.)
| | - Yue Zhang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (L.Z.); (Y.Z.); (W.Y.); (Y.Z.); (Z.Z.); (L.L.)
| | - Wenzhao Yang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (L.Z.); (Y.Z.); (W.Y.); (Y.Z.); (Z.Z.); (L.L.)
| | - Yiying Zeng
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (L.Z.); (Y.Z.); (W.Y.); (Y.Z.); (Z.Z.); (L.L.)
| | - Fan Jiang
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China; (F.J.); (Y.Q.)
| | - Yujia Qin
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China; (F.J.); (Y.Q.)
| | - Jiafeng Zhang
- Hunan Plant Protection and Plant Quarantine Station, Changsha 410006, China;
| | - Zhaochun Jiang
- Guizhou Plant Protection and Plant Quarantine Station, Guiyang 550001, China;
| | - Wenzhao Hu
- Chongqing Plant Protection and Plant Quarantine Station, Yubei 401123, China;
| | - Dijin Guo
- Sichuan Plant Protection and Plant Quarantine Station, Chengdu 610041, China; (D.G.); (J.W.)
| | - Jia Wan
- Sichuan Plant Protection and Plant Quarantine Station, Chengdu 610041, China; (D.G.); (J.W.)
| | - Zihua Zhao
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (L.Z.); (Y.Z.); (W.Y.); (Y.Z.); (Z.Z.); (L.L.)
| | - Lijun Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (L.Z.); (Y.Z.); (W.Y.); (Y.Z.); (Z.Z.); (L.L.)
| | - Zhihong Li
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (L.Z.); (Y.Z.); (W.Y.); (Y.Z.); (Z.Z.); (L.L.)
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Schenkel CD, Kamber T, Schaffner F, Mathis A, Silaghi C. Loop-mediated isothermal amplification (LAMP) for the identification of invasive Aedes mosquito species. MEDICAL AND VETERINARY ENTOMOLOGY 2019; 33:345-351. [PMID: 30734975 DOI: 10.1111/mve.12366] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 10/26/2018] [Accepted: 01/07/2019] [Indexed: 06/09/2023]
Abstract
Invasive Aedes mosquito species (Diptera: Culicidae) are of public health concern in Europe because they are either recognized or potential vectors of pathogens. Loop-mediated isothermal amplification (LAMP) is a rapid and simple method for amplifying DNA with high specificity and efficiency, with the technique having potential for application in the field, including in high-throughput format. Specific LAMP assays based on rDNA internal transcribed spacers 1 or 2 sequences, considering intraspecies variability at these loci, were developed for Aedes aegypti, Aedes albopictus, Aedes japonicus, Aedes koreicus and the indigenous Aedes geniculatus. No such assays could be developed for Aedes atropalpus and Aedes triseriatus because both loci were too short to serve as target. The assays rely on the clearly visible colour change from violet to sky blue after successful amplification. Sensitivity of egg detection was confirmed with ratios of up to one mosquito egg in 99 other eggs. Simple sample preparation of adults or eggs by mechanical homogenization in water required an additional heat treatment or centrifugation step to avoid non-specific colour changes. Thus, further technical improvements are needed to render these assays truly field-applicable, which would greatly facilitate surveillance of these invasive mosquito species and allow for prompt implementation of control measures.
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Affiliation(s)
- C D Schenkel
- National Centre for Vector Entomology, Institute of Parasitology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
| | - T Kamber
- National Centre for Vector Entomology, Institute of Parasitology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
| | - F Schaffner
- National Centre for Vector Entomology, Institute of Parasitology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
| | - A Mathis
- National Centre for Vector Entomology, Institute of Parasitology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
| | - C Silaghi
- National Centre for Vector Entomology, Institute of Parasitology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
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Piper AM, Batovska J, Cogan NOI, Weiss J, Cunningham JP, Rodoni BC, Blacket MJ. Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance. Gigascience 2019; 8:giz092. [PMID: 31363753 PMCID: PMC6667344 DOI: 10.1093/gigascience/giz092] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 06/25/2019] [Accepted: 07/09/2019] [Indexed: 12/21/2022] Open
Abstract
Trap-based surveillance strategies are widely used for monitoring of invasive insect species, aiming to detect newly arrived exotic taxa as well as track the population levels of established or endemic pests. Where these surveillance traps have low specificity and capture non-target endemic species in excess of the target pests, the need for extensive specimen sorting and identification creates a major diagnostic bottleneck. While the recent development of standardized molecular diagnostics has partly alleviated this requirement, the single specimen per reaction nature of these methods does not readily scale to the sheer number of insects trapped in surveillance programmes. Consequently, target lists are often restricted to a few high-priority pests, allowing unanticipated species to avoid detection and potentially establish populations. DNA metabarcoding has recently emerged as a method for conducting simultaneous, multi-species identification of complex mixed communities and may lend itself ideally to rapid diagnostics of bulk insect trap samples. Moreover, the high-throughput nature of recent sequencing platforms could enable the multiplexing of hundreds of diverse trap samples on a single flow cell, thereby providing the means to dramatically scale up insect surveillance in terms of both the quantity of traps that can be processed concurrently and number of pest species that can be targeted. In this review of the metabarcoding literature, we explore how DNA metabarcoding could be tailored to the detection of invasive insects in a surveillance context and highlight the unique technical and regulatory challenges that must be considered when implementing high-throughput sequencing technologies into sensitive diagnostic applications.
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Affiliation(s)
- Alexander M Piper
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Jana Batovska
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Noel O I Cogan
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - John Weiss
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
| | - John Paul Cunningham
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
| | - Brendan C Rodoni
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Mark J Blacket
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
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Bragard C, Dehnen-Schmutz K, Di Serio F, Gonthier P, Jacques MA, Jaques Miret JA, Fejer Justesen A, Magnusson CS, Milonas P, Navas-Cortes JA, Parnell S, Potting R, Reignault PL, Thulke HH, Van der Werf W, Vicent Civera A, Yuen J, Zappalà L, Malumphy C, Czwienczek E, MacLeod A. Pest categorisation of Thrips palmi. EFSA J 2019; 17:e05620. [PMID: 32626236 PMCID: PMC7009038 DOI: 10.2903/j.efsa.2019.5620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The EFSA Panel on Plant Health (PLH) performed a pest categorisation of Thrips palmi (Thysanoptera: Thripidae), for the EU. T. palmi is listed in Annex IAI of 2000/29 EC. Using molecular methods, cryptic speciation has been shown although no new species from the group have been formally described. Here, we consider T. palmi sensu lato as a defined species native to southern Asia, which has spread to tropical and subtropical countries in Asia, the Pacific, North, Central and South America, Africa and Australia. T. palmi has been reported from many different hosts in 20 botanical families; Cucurbitaceae, Solanaceae and Orchidaceae are of primary importance. T. palmi has been intercepted many times on plants from these families. Wild and cultivated hosts are widespread in the EU. However, as a subtropical and tropical species, only a small area of the EU provides climatic conditions where establishment may be possible outdoors. Several host plants are cultivated in glasshouses where conditions may be more favourable for establishment in year-round crops. There have been past outbreaks of T. palmi in EU glasshouses and outdoors in Portugal. T. palmi causes feeding and oviposition damage and populations in Asia are competent vectors of tospoviruses. Impacts could occur on many hosts, especially Cucurbitaceae, Solanaceae and ornamental plants particularly in glasshouses. Phytosanitary measures aim to prevent the entry of T. palmi specifically on cut flowers of Orchidaceae and fruits of Momordica and Solanum melongena. The species meets all the criteria assessed by the PLH Panel to satisfy the definition of a Union quarantine pest, while it does not satisfy all the criteria for it to be regarded as a Union regulated non-quarantine pest (RNQP).
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Simultaneous Detection of Different Zika Virus Lineages via Molecular Computation in a Point-of-Care Assay. Viruses 2018; 10:v10120714. [PMID: 30558136 PMCID: PMC6316447 DOI: 10.3390/v10120714] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 12/08/2018] [Accepted: 12/11/2018] [Indexed: 02/06/2023] Open
Abstract
We have developed a generalizable “smart molecular diagnostic” capable of accurate point-of-care (POC) detection of variable nucleic acid targets. Our isothermal assay relies on multiplex execution of four loop-mediated isothermal amplification reactions, with primers that are degenerate and redundant, thereby increasing the breadth of targets while reducing the probability of amplification failure. An easy-to-read visual answer is computed directly by a multi-input Boolean OR logic gate (gate output is true if either one or more gate inputs is true) signal transducer that uses degenerate strand exchange probes to assess any combination of amplicons. We demonstrate our methodology by using the same assay to detect divergent Asian and African lineages of the evolving Zika virus (ZIKV), while maintaining selectivity against non-target viruses. Direct analysis of biological specimens proved possible, with crudely macerated ZIKV-infected Aedes aegypti mosquitoes being identified with 100% specificity and sensitivity. The ease-of-use with minimal instrumentation, broad programmability, and built-in fail-safe reliability make our smart molecular diagnostic attractive for POC use.
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Blaser S, Diem H, von Felten A, Gueuning M, Andreou M, Boonham N, Tomlinson J, Müller P, Utzinger J, Frey B, Frey JE, Bühlmann A. A Loop-mediated Isothermal Amplification (LAMP) Assay for Rapid Identification of Bemisia tabaci. J Vis Exp 2018. [PMID: 30417877 PMCID: PMC6235616 DOI: 10.3791/58502] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The whitefly Bemisia tabaci (Gennadius) is an invasive pest of considerable importance, affecting the production of vegetable and ornamental crops in many countries around the world. Severe yield losses are caused by direct feeding, and even more importantly, also by the transmission of more than 100 harmful plant pathogenic viruses. As for other invasive pests, increased international trade facilitates the dispersal of B. tabaci to areas beyond its native range. Inspections of plant import products at points of entry such as seaports and airports are, therefore, seen as an important prevention measure. However, this last line of defense against pest invasions is only effective if rapid identification methods for suspicious insect specimens are readily available. Because the morphological differentiation between the regulated B. tabaci and close relatives without quarantine status is difficult for non-taxonomists, a rapid molecular identification assay based on the loop-mediated isothermal amplification (LAMP) technology has been developed. This publication reports the detailed protocol of the novel assay describing rapid DNA extraction, set-up of the LAMP reaction, as well as interpretation of its read-out, which allows identifying B. tabaci specimens within one hour. Compared to existing protocols for the detection of specific B. tabaci biotypes, the developed method targets the whole B. tabaci species complex in one assay. Moreover the assay is designed to be applied on-site by plant health inspectors with minimal laboratory training directly at points of entry. Thorough validation performed under laboratory and on-site conditions demonstrates that the reported LAMP assay is a rapid and reliable identification tool, improving the management of B. tabaci.
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Affiliation(s)
- Simon Blaser
- Department of Method Development and Analytics, Agroscope; Swiss Tropical and Public Health Institute; University of Basel;
| | - Hanspeter Diem
- Swiss Federal Plant Protection Service, Federal Office for Agriculture
| | | | | | | | - Neil Boonham
- Fera Science Limited; School of Natural and Environmental Sciences, Newcastle University
| | | | - Pie Müller
- Swiss Tropical and Public Health Institute; University of Basel
| | - Jürg Utzinger
- Swiss Tropical and Public Health Institute; University of Basel
| | - Beatrice Frey
- Department of Method Development and Analytics, Agroscope
| | - Jürg E Frey
- Department of Method Development and Analytics, Agroscope
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