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Development and validation of versatile species-specific primer assays for eDNA monitoring and authentication of 10 commercially important Peruvian marine species

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Publicat a:PLoS One vol. 20, no. 7 (Jul 2025), p. e0313181
Autor principal: Marín, Alan
Altres autors: Alfaro, Ruben, Reyes-Flores, Lorenzo E, Ingar, Claudia, Santos-Rojas, Luis E, Alvarez-Jaque, Irina B, Rodríguez-Bernales, Karen, Carbajal, Cleila, Yon-Utrilla, Angel, Zelada-Mázmela, Eliana
Publicat:
Public Library of Science
Matèries:
Peru
United States > US
DNA sequencing
Fisheries
Shellfish
Identification
Supermarkets
Biodiversity
Marine ecosystems
Samples
Reptiles & amphibians
Fishery management
Nucleotide sequence
Monitoring
Restaurants
Seafood
Environmental DNA
Species
Fisheries management
Gene sequencing
Assaying
Primers
Taxonomy
Supply chains
Authentication
Morphology
Nontarget organisms
Fish
Environmental
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Resum: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.
ISSN:1932-6203
DOI:10.1371/journal.pone.0313181
Font:Health & Medical Collection