Difficulties in DNA barcoding-based authentication of snapper products due to ambiguous nucleotide sequences in public databases

Abstract

Fishery products are traded worldwide, have long and branched supply chains and are among the most counterfeit foods. Food control authorities are responsible of controlling food labelling in order to ensure the safety and quality of products. This is particularly important for tropical and subtropical fish species, such as snappers (Lutjanidae), because certain species are known to be frequently contaminated with ciguatoxins that cause harmful Ciguatera Fish Poisoning outbreaks. The analytical method of choice for the identification of a sample at species level is ‘DNA barcoding’, the sequencing of specific genetic markers and the comparison of the sequences with international nucleotide databases, such as GenBank and BOLD. However, the results of these analyses can be severely impaired by an insufficient data basis and especially by database entries with incorrect species annotations. In this work, the available nucleotide sequences for common genetic markers (COI, cytb, 16S rDNA, 12S rDNA, rag1 and ITS) of snapper species in GenBank were subjected to careful examination with regard to their unambiguousness and clarity. Phylogenetic neighbour joining trees were prepared and checked for ambiguous and contradictory placement of species' sequences with special emphasis on the Malabar blood snapper (Lutjanus malabaricus), the two-spot red snapper (L. bohar) and the crimson snapper (L. erythropterus). The results indicate that ambiguous and contradictory database nucleotide sequences impede the DNA barcoding-based authentication of snapper products at species level. A species assignment for the Malabar snapper and the crimson snapper based solely on database queries seems questionable.