Development and validation of versatile species-specific primer assays for eDNA monitoring and authentication of 10 commercially important Peruvian marine species
Molecular identification assays provide crucial support in the research and regulation of aquatic resources. Among them, species-specific primers provide significant discriminatory power for fast and simultaneous differentiation of closely related species. In this study, we developed species-specifi...
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2025
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| author | Alan Marín R. Alfaro Lorenzo E. Reyes‐Flores Claudia Ingar Luis E. Santos‐Rojas Irina B. Alvarez-Jaque Karen Rodríguez-Bernales Cleila Carbajal Angel Yon-Utrilla Eliana Zelada‐Mázmela |
| author_browse | Alan Marín Angel Yon-Utrilla Claudia Ingar Cleila Carbajal Eliana Zelada‐Mázmela Irina B. Alvarez-Jaque Karen Rodríguez-Bernales Lorenzo E. Reyes‐Flores Luis E. Santos‐Rojas R. Alfaro |
| author_facet | Alan Marín R. Alfaro Lorenzo E. Reyes‐Flores Claudia Ingar Luis E. Santos‐Rojas Irina B. Alvarez-Jaque Karen Rodríguez-Bernales Cleila Carbajal Angel Yon-Utrilla Eliana Zelada‐Mázmela |
| author_sort | Alan Marín |
| collection | Producción científica |
| description | Molecular identification assays provide crucial support in the research and regulation of aquatic resources. Among them, species-specific primers provide significant discriminatory power for fast and simultaneous differentiation of closely related species. In this study, we developed species-specific primers for environmental DNA (eDNA) monitoring and identification of 10 fish and shellfish species commonly found in the Peruvian seafood sector. To ensure versatility and high specificity, our primers were subjected to various testing methods including PCR, qPCR, and DNA sequencing, supported by robust validation assays. This validation process included a) an in-silico stage using self-generated and public DNA sequences; b) an in-vitro stage using target species sourced from vouchered specimens, as well as fresh and cooked commercial samples, early life stages, and a wide range of non-target species; and c) an in-situ stage using eDNA samples collected from different Peruvian marine ecosystems. Our novel species-specific primers successfully passed the validation process, demonstrating high efficiency and specificity by unequivocally identifying all target species with 100% accuracy and without cross-species reactions. These primers are thus valuable tools for eDNA monitoring, seafood authentication, and combating illegal, unreported, and unregulated fishing. The assays presented in this study can support effective fishery management and conservation efforts not only in the Peruvian fishery sector but also in other countries where our target species are present or imported. |
| format | Article |
| id | oai:cris.upeu.edu.pe:20.500.15037/1757 |
| institution | UPeU |
| language | English |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
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| spelling | oai:cris.upeu.edu.pe:20.500.15037/17572026-10-30T16:16:42ZDevelopment and validation of versatile species-specific primer assays for eDNA monitoring and authentication of 10 commercially important Peruvian marine speciesAlan MarínR. AlfaroLorenzo E. Reyes‐FloresClaudia IngarLuis E. Santos‐RojasIrina B. Alvarez-JaqueKaren Rodríguez-BernalesCleila CarbajalAngel Yon-UtrillaEliana Zelada‐MázmelaEnvironmental DNABiologyPrimer (cosmetics)ShellfishFisheryFishingFish <Actinopterygii>Aquatic animalEcologyBiodiversityChemistryOrganic chemistryEnvironmental DNABiologyPrimer (cosmetics)ShellfishFisheryFishingFish <Actinopterygii>Aquatic animalEcologyBiodiversityDNA, Environmental analysisDNA, Environmental analysisDNA, Environmental analysisDNA, Environmental geneticsDNA, Environmental geneticsDNA, Environmental geneticsAnimalsAnimalsAnimalsEnvironmental Monitoring methodsEnvironmental Monitoring methodsEnvironmental Monitoring methodsFishes classificationFishes classificationFishes classificationFishes geneticsFishes geneticsFishes geneticsPeruPeruPeruSpecies SpecificitySpecies SpecificitySpecies SpecificityPolymerase Chain ReactionPolymerase Chain ReactionPolymerase Chain ReactionSeafood analysisSeafood analysisSeafood analysisDNA Primers geneticsDNA Primers geneticsDNA Primers geneticsPhysical Sciences Environmental Science Ecology Environmental DNA in Biodiversity StudiesLife Sciences Biochemistry, Genetics and Molecular Biology Molecular Biology Identification and Quantification in FoodPhysical Sciences Environmental Science Global and Planetary Change Marine Ecology and Invasive SpeciesMolecular identification assays provide crucial support in the research and regulation of aquatic resources. Among them, species-specific primers provide significant discriminatory power for fast and simultaneous differentiation of closely related species. In this study, we developed species-specific primers for environmental DNA (eDNA) monitoring and identification of 10 fish and shellfish species commonly found in the Peruvian seafood sector. To ensure versatility and high specificity, our primers were subjected to various testing methods including PCR, qPCR, and DNA sequencing, supported by robust validation assays. This validation process included a) an in-silico stage using self-generated and public DNA sequences; b) an in-vitro stage using target species sourced from vouchered specimens, as well as fresh and cooked commercial samples, early life stages, and a wide range of non-target species; and c) an in-situ stage using eDNA samples collected from different Peruvian marine ecosystems. Our novel species-specific primers successfully passed the validation process, demonstrating high efficiency and specificity by unequivocally identifying all target species with 100% accuracy and without cross-species reactions. These primers are thus valuable tools for eDNA monitoring, seafood authentication, and combating illegal, unreported, and unregulated fishing. The assays presented in this study can support effective fishery management and conservation efforts not only in the Peruvian fishery sector but also in other countries where our target species are present or imported.Articlehttps://pubmed.ncbi.nlm.nih.gov/40601706https://doi.org/10.1371/journal.pone.031318110.1371/journal.pone.0313181https://hdl.handle.net/20.500.15037/1757W4411948717enPLoS ONE1932-62032025-07-022026-06-13T14:21:35Z2026-06-13T14:21:35Z |
| spellingShingle | Environmental DNA Biology Primer (cosmetics) Shellfish Fishery Fishing Fish <Actinopterygii> Aquatic animal Ecology Biodiversity Chemistry Organic chemistry Environmental DNA Biology Primer (cosmetics) Shellfish Fishery Fishing Fish <Actinopterygii> Aquatic animal Ecology Biodiversity DNA, Environmental analysis DNA, Environmental analysis DNA, Environmental analysis DNA, Environmental genetics DNA, Environmental genetics DNA, Environmental genetics Animals Animals Animals Environmental Monitoring methods Environmental Monitoring methods Environmental Monitoring methods Fishes classification Fishes classification Fishes classification Fishes genetics Fishes genetics Fishes genetics Peru Peru Peru Species Specificity Species Specificity Species Specificity Polymerase Chain Reaction Polymerase Chain Reaction Polymerase Chain Reaction Seafood analysis Seafood analysis Seafood analysis DNA Primers genetics DNA Primers genetics DNA Primers genetics Physical Sciences Environmental Science Ecology Environmental DNA in Biodiversity Studies Life Sciences Biochemistry, Genetics and Molecular Biology Molecular Biology Identification and Quantification in Food Physical Sciences Environmental Science Global and Planetary Change Marine Ecology and Invasive Species Alan Marín R. Alfaro Lorenzo E. Reyes‐Flores Claudia Ingar Luis E. Santos‐Rojas Irina B. Alvarez-Jaque Karen Rodríguez-Bernales Cleila Carbajal Angel Yon-Utrilla Eliana Zelada‐Mázmela Development and validation of versatile species-specific primer assays for eDNA monitoring and authentication of 10 commercially important Peruvian marine species |
| title | Development and validation of versatile species-specific primer assays for eDNA monitoring and authentication of 10 commercially important Peruvian marine species |
| title_full | Development and validation of versatile species-specific primer assays for eDNA monitoring and authentication of 10 commercially important Peruvian marine species |
| title_fullStr | Development and validation of versatile species-specific primer assays for eDNA monitoring and authentication of 10 commercially important Peruvian marine species |
| title_full_unstemmed | Development and validation of versatile species-specific primer assays for eDNA monitoring and authentication of 10 commercially important Peruvian marine species |
| title_short | Development and validation of versatile species-specific primer assays for eDNA monitoring and authentication of 10 commercially important Peruvian marine species |
| title_sort | development and validation of versatile species specific primer assays for edna monitoring and authentication of 10 commercially important peruvian marine species |
| topic | Environmental DNA Biology Primer (cosmetics) Shellfish Fishery Fishing Fish <Actinopterygii> Aquatic animal Ecology Biodiversity Chemistry Organic chemistry Environmental DNA Biology Primer (cosmetics) Shellfish Fishery Fishing Fish <Actinopterygii> Aquatic animal Ecology Biodiversity DNA, Environmental analysis DNA, Environmental analysis DNA, Environmental analysis DNA, Environmental genetics DNA, Environmental genetics DNA, Environmental genetics Animals Animals Animals Environmental Monitoring methods Environmental Monitoring methods Environmental Monitoring methods Fishes classification Fishes classification Fishes classification Fishes genetics Fishes genetics Fishes genetics Peru Peru Peru Species Specificity Species Specificity Species Specificity Polymerase Chain Reaction Polymerase Chain Reaction Polymerase Chain Reaction Seafood analysis Seafood analysis Seafood analysis DNA Primers genetics DNA Primers genetics DNA Primers genetics Physical Sciences Environmental Science Ecology Environmental DNA in Biodiversity Studies Life Sciences Biochemistry, Genetics and Molecular Biology Molecular Biology Identification and Quantification in Food Physical Sciences Environmental Science Global and Planetary Change Marine Ecology and Invasive Species |
| topic_facet | Environmental DNA Biology Primer (cosmetics) Shellfish Fishery Fishing Fish <Actinopterygii> Aquatic animal Ecology Biodiversity Chemistry Organic chemistry Environmental DNA Biology Primer (cosmetics) Shellfish Fishery Fishing Fish <Actinopterygii> Aquatic animal Ecology Biodiversity DNA, Environmental analysis DNA, Environmental analysis DNA, Environmental analysis DNA, Environmental genetics DNA, Environmental genetics DNA, Environmental genetics Animals Animals Animals Environmental Monitoring methods Environmental Monitoring methods Environmental Monitoring methods Fishes classification Fishes classification Fishes classification Fishes genetics Fishes genetics Fishes genetics Peru Peru Peru Species Specificity Species Specificity Species Specificity Polymerase Chain Reaction Polymerase Chain Reaction Polymerase Chain Reaction Seafood analysis Seafood analysis Seafood analysis DNA Primers genetics DNA Primers genetics DNA Primers genetics Physical Sciences Environmental Science Ecology Environmental DNA in Biodiversity Studies Life Sciences Biochemistry, Genetics and Molecular Biology Molecular Biology Identification and Quantification in Food Physical Sciences Environmental Science Global and Planetary Change Marine Ecology and Invasive Species |
| url | https://pubmed.ncbi.nlm.nih.gov/40601706 https://doi.org/10.1371/journal.pone.0313181 https://hdl.handle.net/20.500.15037/1757 |
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