Evaluation of DNA barcoding methodologies for the identification of fish species in cooked products

•DNA barcoding is a robust method for identification of species in processed fish.•Canned products showed marked decreases in sequencing success, quality, and length.•Mini-barcoding showed a slightly higher success rate than full barcoding.•Mini-barcoding and full barcoding showed similar results for species discrimination.•Mini-barcoding has high potential to be used as a complement to full barcoding.

DNA barcoding is a powerful sequencing-based tool for the detection of fish species substitution. However, various cooking methods have the potential to reduce the quality and success of DNA sequencing. The objective of this study was to determine the effects of common cooking methods on DNA sequencing results with both full-length (655 bp) and mini-barcodes (208-226 bp), and to determine the optimal methodology to use for species identification of various fish products. Six types of fish (salmon, tuna, scad, pollock, swai and tilapia) were prepared in triplicate using the following methods: uncooked, baked, fried, broiled, acid-cooked, smoked and canned. DNA was extracted from each sample and tested using full and mini-barcoding of the cytochrome c oxidase subunit I (COI) gene. The resulting sequences were compared based on quality parameters, success rates, and genetic identifications. SH-E mini-barcoding showed the highest overall success rates (92-94%), followed by full barcoding (90%), and SH-D mini-barcoding (67-90%). Across the individual cooking methods, SH-E mini-barcodes performed as well or better than full barcodes for most samples. The sequencing results were fairly consistent across cooking methods with the exception of canning, which showed marked decreases in sequencing success, quality, and length. Despite the reduced sequence length of mini-barcodes compared to full barcodes, identification of fish species was largely consistent across the methods. Overall, the results of this study show that DNA barcoding is a robust tool for fish species identification, and that mini-barcoding has high potential for use as a complement to full barcoding.