Establishment of a mitochondrial DNA sequence database for the identification of fish species commercially available in South Africa

Abstract

The limitations intrinsic to morphology-based identification systems have created an urgent need for reliable genetic methods that enable the unequivocal recognition of fish species, particularly those that are prone to overexploitation and/or market substitution. The aim of this study was to develop a comprehensive reference library of DNA sequence data to allow the explicit identification of 53 commercially available fish species in South Africa, most of which were locally caught marine species. Sequences of approximately 655 base pairs were generated for all species from the cytochrome c oxidase I (COI) gene, the region widely adopted for DNA barcoding. Specimens of the genus Thunnus were examined in further detail, employing additional mitochondrial DNA control region sequencing. Cumulative analysis of the sequences from the COI region revealed mean conspecific, congeneric and confamilial Kimura 2-parameter distances of 0.10%, 4.58% and 15.43%, respectively. The results showed that the vast majority (98%) of fish species examined could be readily differentiated by their COI barcodes, but that supplementary control region sequencing was more useful for the discrimination of three Thunnus species. Additionally, the analysis of COI data raised the prospect that Thyrsites atun (snoek) could constitute a species pair. The present study has established the necessary genetic information to permit the unambiguous identification of 53 commonly marketed fish species in South Africa, the applications of which hold a plethora of benefits relating to ecology research, fisheries management and control of commercial practices.

DNA barcoding reveals a high incidence of fish species misrepresentation and substitution on the South African market

“…In addition, since control region sequences have been frequently employed for intra-and interspecific genetic studies of fishes(Aboim, Menezes, Schlitt, & Rogers, 2005;Alvarado Bremer, Naseri, & Ely, 1997;Carlsson, McDowell, Dίaz-Jaimes, et al, 2004;Cawthorn, Steinman, & Witthuhn, 2011a;Lee, Conroy, Hunting Howell, & Kocher, 1995;Smith, Struthers, Paulin, McVeagh, & Daley, 2009;Viñas & Tudela, 2009), it was anticipated prior to analyses that reference sequences for this region would be readily available in DNA sequence repositories to allow identification of species not discriminated by COI sequencing.…”

Genomic Approaches in Marine Biodiversity and Aquaculture

“…The user-friendliness of DNA barcodes is also fi nding many practical applications in developing countries (Cawthorn et al, 2011;Lakra et al, 2011;Zhang & Hanner., 2012;Asgharian et al, 2011;Wang et al, 2012;de Carvalho et al, 2011;Weigt et al, 2012), which generally lack suffi cient means (financial support, research materials, scientific profi ciency and experienced personnel) to conduct their own research and surveillance activities in marine biodiversity, fi sheries management and conservation.…”

Authentication of closely related scombrid, catfish and tilapia species by PCR-based analysis and isoelectric focusing of parvalbumin

“…Nevertheless, the application of mtDNA markers is hampered by introgression of mt genomes and the occurrence of hybrid fish species [28]. For example, it is debatable whether mtDNA can be used to differentiate species of the genus Thunnus, even when a standardized DNA barcoding marker for animals (COI gene) has been applied [10,29,30]. Identification of Thunnus species using mtDNA markers (e.g.…”