Comparison of three DNA marker regions for identification of food relevant crustaceans of the order Decapoda

Abstract

As a result of the commercial importance of food relevant crustaceans belonging to the order Decapoda, reliable methods for species identification are required to protect consumers against adulteration and mislabelling of crustacean products. The aim of this present study is, therefore, to compare three marker regions for their suitability to identify food relevant crustaceans of the order Decapoda: (A) the official control method in Germany for identification of crustacean species based on 16S rDNA sequences; (B) sequencing of another 16S rDNA fragment developed by Palumbi et al.; and (C)’DNA barcoding, by sequencing of the mitochondrial cytochrome c oxidase subunit 1 gene (COI). Marker region A showed some disadvantages compared to marker region C because of inadequate amplification or resulting low-quality sequences for several decapods. Marker region B showed better species identification results than marker region A, but offered no advantage compared to marker region A combined with marker region C. Marker region A is only to be preferred for species, of which the reference sequences of COI are not yet present in public sequence databases. The results of this study show that the most suitable marker region for the identification of food relevant decapods is COI and that this marker region has the potential to supplement or even replace the current official method of Germany in the official control of foodstuff. Moreover, this study shows that for certain food relevant crustacean species, there is still a lack of reference sequences.