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Arya V, Narayana S, Sinha T, Kandan A, Satyanarayana Raju SV. A simple PCR-based quick detection of the economically important oriental fruit fly, Bactrocera dorsalis (Hendel) from India. FRONTIERS IN PLANT SCIENCE 2024; 15:1399718. [PMID: 39045589 PMCID: PMC11263087 DOI: 10.3389/fpls.2024.1399718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 06/25/2024] [Indexed: 07/25/2024]
Abstract
The oriental fruit fly, Bactrocera dorsalis (Hendel), is a significant economic and quarantine pest due to its polyphagous nature. The accurate identification of B. dorsalis is challenging at the egg, maggot, and pupal stages, due to lack of distinct morphological characters and its similarity to other fruit flies. Adult identification requires specialized taxonomist. Existing identification methods are laborious, time consuming, and expensive. Rapid and precise identification is crucial for timely management. By analyzing the variations in the mitochondrial cytochrome oxidase-1 gene sequence (Insect barcoding gene), we developed a species-specific primer (SSP), DorFP1/DorRP1, for accurate identification of B. dorsalis. The optimal annealing temperature for the SSP was determined to be 66°C, with no cross-amplification or primer-dimer formation observed. The SSP was validated with B. dorsalis specimens from various locations in northern and eastern India and tested for cross-specificity with six other economically significant fruit fly species in India. The primer specificity was further confirmed by the analysis of critical threshold (Ct) value from a qPCR assay. Sensitivity analysis showed the primer could detect template DNA concentrations as low as 1 pg/µl, though sensitivity decreased at lower concentrations. Sequencing of the SSP-amplified product revealed over >99% similarity with existing B. dorsalis sequences in the NCBI GenBank. The developed SSP reliably identifies B. dorsalis across all developmental stages and sexes. This assay is expected to significantly impact pest identification, phytosanitary measures, and eradication programs for B. dorsalis.
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Affiliation(s)
- Varun Arya
- Insects Molecular Biology Laboratory, Institute of Agricultural Sciences, Department of Entomology and Agricultural Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Srinivasa Narayana
- Insects Molecular Biology Laboratory, Institute of Agricultural Sciences, Department of Entomology and Agricultural Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Twinke Sinha
- Insects Molecular Biology Laboratory, Institute of Agricultural Sciences, Department of Entomology and Agricultural Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Aravindaram Kandan
- Indian Council of Agricultural Research-National Bureau of Agricultural Insect Resources, Bengaluru, Karnataka, India
| | - Samantapudi Venkata Satyanarayana Raju
- Insect Physiology and Toxicology Laboratory, Institute of Agricultural Sciences, Department of Entomology and Agricultural Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
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Rizzo D, Zubieta CG, Sacchetti P, Marrucci A, Miele F, Ascolese R, Nugnes F, Bernardo U. Diagnostic Tool for the Identification of Bactrocera dorsalis (Hendel) (Diptera: Tephritidae) Using Real-Time PCR. INSECTS 2024; 15:44. [PMID: 38249050 PMCID: PMC10815988 DOI: 10.3390/insects15010044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/22/2023] [Accepted: 01/05/2024] [Indexed: 01/23/2024]
Abstract
Accurate identification of Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), commonly known as the Oriental fruit fly, is a significant challenge due to the morphological convergence and taxonomic uncertainties of species belonging to the same genus. This highly polyphagous species poses a significant threat to fruit crops. With its potential establishment in Europe becoming a growing concern, there is an urgent need for rapid and efficient diagnostic methods. The study presented here introduces a diagnostic protocol based on real-time PCR using a TaqMan probe for the early and reproducible identification of B. dorsalis. Specimens representing the genetic diversity of the Italian population were collected and analyzed. Specific primers and probe were designed based on the conserved regions and an in silico analysis confirmed their specificity. The assay conditions were optimized, and analytical sensitivity, specificity, repeatability, and reproducibility were evaluated. The protocol showed high sensitivity and specificity, accurately detecting low DNA concentrations of B. dorsalis. This standardized method provides a reliable tool for routine diagnostics, enhancing the accuracy and efficiency of identifying the Oriental fruit fly at all stages of its development, thereby facilitating effective pest management measures. The development of this diagnostic protocol is crucial for monitoring and supporting efforts to prevent the passive spread of B. dorsalis in Europe, particularly in light of the recent active infestations detected in Italy.
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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.); (C.G.Z.); (A.M.)
| | - Claudia Gabriela Zubieta
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Via Ciliegiole 99, 51100 Pistoia, Italy; (D.R.); (C.G.Z.); (A.M.)
| | - Patrizia Sacchetti
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Piazzale delle Cascine, 18, 50144 Florence, Italy;
| | - Andrea Marrucci
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Via Ciliegiole 99, 51100 Pistoia, Italy; (D.R.); (C.G.Z.); (A.M.)
- Department of Agricultural Food and Agro-Environmental Sciences, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Fortuna Miele
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), P.le Enrico Fermi 1, 80055 Portici, Italy; (F.M.); (R.A.); (F.N.)
| | - Roberta Ascolese
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), P.le Enrico Fermi 1, 80055 Portici, Italy; (F.M.); (R.A.); (F.N.)
- Department of Biology, University of Naples Federico II, Via Vicinale Cupa Cintia 21, 80126 Napoli, Italy
| | - Francesco Nugnes
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), P.le Enrico Fermi 1, 80055 Portici, Italy; (F.M.); (R.A.); (F.N.)
| | - Umberto Bernardo
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), P.le Enrico Fermi 1, 80055 Portici, Italy; (F.M.); (R.A.); (F.N.)
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Andrews KJ, Bester R, Manrakhan A, Maree HJ. Utilisation of a mitochondrial intergenic region for species differentiation of fruit flies (Diptera: Tephritidae) in South Africa. BMC Genomics 2022; 23:793. [DOI: 10.1186/s12864-022-09038-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/22/2022] [Indexed: 12/02/2022] Open
Abstract
Abstract
Background
Fruit flies (Diptera: Tephritidae) comprise species of agricultural and economic importance. Five such fruit fly species are known to affect commercial fruit production and export in South Africa: Ceratitis capitata, Ceratitis cosyra, Ceratitis rosa, Ceratitis quilicii, and Bactrocera dorsalis. Management practices for these pests include monitoring, application of pest control products, post-harvest disinfestation measures and inspection of consignments both prior to shipment and at ports of entry. In activities relating to monitoring and inspection, accurate identification of these pests to species level is required. While morphological keys for adult stages of these fruit fly species have been well developed, morphological keys for earlier life stages remain problematic. In instances where closely related species cannot be reliably distinguished morphologically, there is a need for molecular tools to assist in identifying these five fruit fly species during surveillance practices, where sequencing-based approaches would be beneficial.
Results
Two complete mitochondrial genomes were assembled for each fruit fly species investigated using high throughput sequencing data generated in this study. A single primer set was designed to amplify a region between tRNAile and tRNAmet. The amplicon consists of a partial segment of tRNAile, intergenic region I (tRNAile - tRNAgln), the complete sequence of tRNAgln, intergenic region II (tRNAgln - tRNAmet), and a partial segment of tRNAmet. PCR amplicons were generated for 20 specimens of each species, five of which were colony adult males, five colony larvae, and 10 wild, trap-collected specimens. Upon analysis of the amplicon, intergenic region I was identified as the most informative region, allowing for unambiguous identification of the five fruit fly species. The similarity in intergenic region II was too high between C. rosa and C. quilicii for accurate differentiation of these species.
Conclusion
The identity of all five fruit flies investigated in this study can be determined through sequence analysis of the mitochondrial intergenic regions. Within the target amplicon, intergenic region I (tRNAile - tRNAgln) shows interspecific variation sufficient for species differentiation based on multiple sequence alignment. The variation in the length of intergenic region I is proposed as a potential tool for accurately identifying these five fruit flies in South Africa.
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