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.

Autor: Bevilaqua DR; Instituto Federal de Educação Ciência e Tecnologia do Amazonas (IFAM), Campus Avançado, Highway Manoel Urbano, km 77 - Morada do Sol, Manacapuru, AM, CEP 69400-000, Brazil. danniel.bevilaqua@ifam.edu.br., Batista JS; Coordenação de Biodiversidade (COBIO), Laboratório Temático de Biologia Molecular (LTBM), Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva (PPG-GCBEv), Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, AM, Brazil., da Mota AJ; Faculdade de Ciências Agrárias, Departamento de Ciências Fundamentais e Desenvolvimento Agrícola, Universidade Federal do Amazonas (UFAM), Manaus, AM, Brazil., da Silva ACV; Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva (PPG-GCBEv), Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, AM, Brazil., da Mota AMS; Programa de Pós-Graduação em Biotecnologia e Recursos Naturais - PPG MBT, Universidade Estadual do Amazonas - UEA, Manaus, AM, Brazil., Formiga KM; Coordenação de Biodiversidade (COBIO), Laboratório Temático de Biologia Molecular (LTBM), Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva (PPG-GCBEv), Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, AM, Brazil., de Carvalho Freitas CE; Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva (PPG-GCBEv), Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, AM, Brazil.; Faculdade de Ciências Agrárias, Departamento de Ciências Pesqueiras, Universidade Federal do Amazonas, Manaus, AM, Brazil.
Jazyk: angličtina
Zdroj: Molecular biology reports [Mol Biol Rep] 2023 Dec; Vol. 50 (12), pp. 10657-10662. Date of Electronic Publication: 2023 Nov 14.
DOI: 10.1007/s11033-023-08872-w
Abstrakt: 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 systems, 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.
(© 2023. The Author(s), under exclusive licence to Springer Nature B.V.)
Databáze: MEDLINE
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