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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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He R, Wang S, Li Q, Wang Z, Mei Y, Li F. Phylogenomic analysis and molecular identification of true fruit flies. Front Genet 2024; 15:1414074. [PMID: 38974385 PMCID: PMC11224437 DOI: 10.3389/fgene.2024.1414074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 05/30/2024] [Indexed: 07/09/2024] Open
Abstract
The family Tephritidae in the order Diptera, known as true fruit flies, are agriculturally important insect pests. However, the phylogenetic relationships of true fruit flies, remain controversial. Moreover, rapid identification of important invasive true fruit flies is essential for plant quarantine but is still challenging. To this end, we sequenced the genome of 16 true fruit fly species at coverage of 47-228×. Together with the previously reported genomes of nine species, we reconstructed phylogenetic trees of the Tephritidae using benchmarking universal single-copy ortholog (BUSCO), ultraconserved element (UCE) and anchored hybrid enrichment (AHE) gene sets, respectively. The resulting trees of 50% taxon-occupancy dataset for each marker type were generally congruent at 88% nodes for both concatenation and coalescent analyses. At the subfamily level, both Dacinae and Trypetinae are monophyletic. At the species level, Bactrocera dorsalis is more closely related to Bactrocera latifrons than Bactrocera tryoni. This is inconsistent with previous conclusions based on mitochondrial genes but consistent with recent studies based on nuclear data. By analyzing these genome data, we screened ten pairs of species-specific primers for molecular identification of ten invasive fruit flies, which PCR validated. In summary, our work provides draft genome data of 16 true fruit fly species, addressing the long-standing taxonomic controversies and providing species-specific primers for molecular identification of invasive fruit flies.
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Affiliation(s)
- Rong He
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Shuping Wang
- Technical Centre for Animal, Plant and Food Inspection and Quarantine, Shanghai Customs, Shanghai, China
| | - Qiang Li
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Zuoqi Wang
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yang Mei
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fei Li
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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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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