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Doorenweerd C, San Jose M, Leblanc L, Barr N, Geib SM, Chung AYC, Dupuis JR, Ekayanti A, Fiegalan E, Hemachandra KS, Aftab Hossain M, Huang CL, Hsu YF, Morris KY, Maryani A Mustapeng A, Niogret J, Pham TH, Thi Nguyen N, Sirisena UGAI, Todd T, Rubinoff D. Towards a better future for DNA barcoding: Evaluating monophyly- and distance-based species identification using COI gene fragments of Dacini fruit flies. Mol Ecol Resour 2024; 24:e13987. [PMID: 38956928 DOI: 10.1111/1755-0998.13987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/14/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024]
Abstract
The utility of a universal DNA 'barcode' fragment (658 base pairs of the Cytochrome C Oxidase I [COI] gene) has been established as a useful tool for species identification, and widely criticized as one for understanding the evolutionary history of a group. Large amounts of COI sequence data have been produced that hold promise for rapid species identification, for example, for biosecurity. The fruit fly tribe Dacini holds about a thousand species, of which 80 are pests of economic concern. We generated a COI reference library for 265 species of Dacini containing 5601 sequences that span most of the COI gene using circular consensus sequencing. We compared distance metrics versus monophyly assessments for species identification and although we found a 'soft' barcode gap around 2% pairwise distance, the exceptions to this rule dictate that a monophyly assessment is the only reliable method for species identification. We found that all fragments regularly used for Dacini fruit fly identification >450 base pairs long provide similar resolution. 11.3% of the species in our dataset were non-monophyletic in a COI tree, which is mostly due to species complexes. We conclude with recommendations for the future generation and use of COI libraries. We revise the generic assignment of Dacus transversus stat. rev. Hardy 1982, and Dacus perpusillus stat. rev. Drew 1971 and we establish Dacus maculipterus White 1998 syn. nov. as a junior synonym of Dacus satanas Liang et al. 1993.
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Affiliation(s)
- Camiel Doorenweerd
- Entomology Section, Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Michael San Jose
- Entomology Section, Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Luc Leblanc
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, Idaho, USA
| | - Norman Barr
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Plant Protection and Quarantine, Science & Technology, Insect Management and Molecular Diagnostics Laboratory, Edinburg, Texas, USA
| | - Scott M Geib
- Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Center, USDA Agricultural Research Services, Hilo, Hawaii, USA
| | - Arthur Y C Chung
- Forest Research Centre, Sabah Forestry Department, Sandakan, Sabah, Malaysia
| | - Julian R Dupuis
- Department of Entomology, University of Kentucky, Lexington, Kentucky, USA
| | - Arni Ekayanti
- Niogret Ecology Consulting LLC, Wotu, Luwu Timor, Sulawesi Seleaton, Indonesia
| | - Elaida Fiegalan
- Department of Crop Protection, College of Agriculture, Central Luzon State University, Science City of Muñoz, Nueva Ecija, Philippines
| | | | - Mohammad Aftab Hossain
- Insect Biotechnology Division, Institute of Food and Radiation Biology, Bangladesh Atomic Energy Commission, Dhaka, Bangladesh
| | - Chia-Lung Huang
- Institute of Oceanography, Minjiang University, Fuzhou, Fujian, China
| | - Yu-Feng Hsu
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan, ROC
| | - Kimberly Y Morris
- Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Center, USDA Agricultural Research Services, Hilo, Hawaii, USA
| | | | - Jerome Niogret
- Centre for Tropical Environmental & Sustainability Science, Nguma-Bada Campus, James Cook University, Smithfield, Queensland, Australia
| | - Thai Hong Pham
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology (VAST), Hue, Vietnam
- Vietnam National Museum of Nature & Graduate School of Science and Technology, VAST, Hanoi, Vietnam
| | - Nhien Thi Nguyen
- Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Uda G A I Sirisena
- Department of Plant Sciences, Faculty of Agriculture, Rajarata University of Sri Lanka, Mihintale, Sri Lanka
| | - Terrence Todd
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Plant Protection and Quarantine, Science & Technology, Insect Management and Molecular Diagnostics Laboratory, Edinburg, Texas, USA
| | - Daniel Rubinoff
- Entomology Section, Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
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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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Salgado-Roa FC, Pardo-Diaz C, Rueda-M N, Cisneros-Heredia DF, Lasso E, Salazar C. The Andes as a semi-permeable geographical barrier: Genetic connectivity between structured populations in a widespread spider. Mol Ecol 2024; 33:e17361. [PMID: 38634856 DOI: 10.1111/mec.17361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/03/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024]
Abstract
Geographical barriers like mountain ranges impede genetic exchange among populations, promoting diversification. The effectiveness of these barriers in limiting gene flow varies between lineages due to each species' dispersal modes and capacities. Our understanding of how the Andes orogeny contributes to species diversification comes from well-studied vertebrates and a few arthropods and plants, neglecting organisms unable to fly or walk long distances. Some arachnids, such as Gasteracantha cancriformis, have been hypothesized to disperse long distances via ballooning (i.e. using their silk to interact with the wind). Yet, we do not know how the environment and geography shape its genetic diversity. Therefore, we tested whether the Andes contributed to the diversification of G. cancriformis acting as an absolute or semi-permeable barrier to genetic connectivity between populations of this spider at opposite sides of the mountain range. We sampled thousands of loci across the distribution of the species and implemented population genetics, phylogenetic, and landscape genetic analyses. We identified two genetically distinct groups structured by the Central Andes, and a third less structured group in the Northern Andes that shares ancestry with the previous two. This structure is largely explained by the altitude along the Andes, which decreases in some regions, possibly facilitating cross-Andean dispersal and gene flow. Our findings support that altitude in the Andes plays a major role in structuring populations in South America, but the strength of this barrier can be overcome by organisms with long-distance dispersal modes together with altitudinal depressions.
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Affiliation(s)
- Fabian C Salgado-Roa
- Department of Biology, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Carolina Pardo-Diaz
- Department of Biology, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Nicol Rueda-M
- Department of Biology, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Diego F Cisneros-Heredia
- Colegio de Ciencias Biológicas y Ambientales, Instituto de Biodiversidad Tropical IBIOTROP, Laboratorio de Zoología Terrestre, Museo de Zoología & Extensión USFQ Galápagos GAIAS, Galapagos Science Center, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Eloisa Lasso
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
- Estación Científica Coiba AIP, Panama, Republic of Panama
| | - Camilo Salazar
- Department of Biology, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
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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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