FishDNAIDs: DNA barcoding as a tool in the development and validation in silico and in vitro of detection systems to four species of Characiformes of commercial importance in the Brazilian Amazon

FishDNAIDs: DNA barcoding as a tool in the development and validation in silico and in vitro of detection systems to four species of Characiformes of commercial importance in the Brazilian Amazon

Background The COI mitochondrial gene has been chosen as the “DNA barcode in animals” and the large quantity of genetic information in public databanks gives solid support for the use of DNA barcoding as a promising tool for the development of a specific molecular detection system. Methods and resul...

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Bibliographic Details
Published in:Molecular biology reports Vol. 50; no. 12; pp. 10657 - 10662
Main Authors: Bevilaqua, Danniel Rocha, Batista, Jacqueline Silva, da Mota, Adolfo José, da Silva, Ana Caroline Viana, da Mota, Andreza Mikeyne Silva, Formiga, Kyara Martins, de Carvalho Freitas, Carlos Edwar
Format: Journal Article
Language:English
Published: Dordrecht Springer Netherlands 01-12-2023
Springer Nature B.V
Subjects:
Animal Anatomy
Animal Biochemistry
Animals
Aquatic ecosystems
Biomedical and Life Sciences
Brazil
Characiformes
Characiformes - genetics
Commercial fishing
Cytochrome
Cytochrome-c oxidase
DNA
DNA barcoding
DNA Barcoding, Taxonomic - methods
DNA Primers
Ecosystem biology
Fish
Fisheries
Fishing
Histology
Humans
Life Sciences
Molecular biology
Morphology
Nucleotide sequence
Phylogeny
Primers
Short Communication
Species
Sustainable development
Brazil
Sustainable development goals
DNA barcode
Detection
Monitoring
Conservation
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Summary:Background The COI mitochondrial gene has been chosen as the “DNA barcode in animals” and the large quantity of genetic information in public databanks gives solid support for the use of DNA barcoding as a promising tool for the development of a specific molecular detection system. Methods and results The present study aimed to develop a Specific Molecular Detection System (SMDS: FishDNAIDs) (primers and probe sets) for the following four target species: Prochilodus nigricans , Potamorhina altamazonica , Psectrogaster rutiloides and Triportheus angulatus , in qPCR assays. In silico and in vitro tests (using gDNA) were performed to test these sets. The database generated contained the cytochrome c oxidase subunit I (COI) nucleotide sequence for 183 specimens of Characiformes, distributed in 34 species representing eight families. In silico, primers designed for the target species amplified different species from the same genus, except for P. rutiloides , which amplified only the target species. In the in vitro test, using the SYBRGreen tm and TaqMan® fluorescence system s , both sets detected the respective target species ( P. nigricans , P. altamazonica , P. rutiloides and T. angulatus ). In the qPCR assays using SYBRGreen tm , species considered to be related were also detected, in addition to the target species, with the exception of P. amazonica and P. essequibensis (correlated to P. rutiloides ). All target species were detected in the qPCR assays using the TaqMan® system; however, with the SMDS PALT, the target species P. altamazonica was detected with low C T values (22.21 ± 0.17) as well as the correlates of P. latior and P. pristigaster , though with high C T values (23.51 ± 0.19 and 30.21 ± 0.95). This assay uniquely identifies known adult tissue samples from all four species. Conclusions The primers and probe sets developed can act as powerful tools for detecting the target Characiformes species.
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ISSN:0301-4851
1573-4978
DOI:10.1007/s11033-023-08872-w