The Sparidae mitochondrial genomes comparison may provide alternative barcode markers

The molecular markers used for differentiating fish species to detect fraudulent substitutions in prepared and transformed fishery products are mitochondrial (mt) DNA sequence fragments. The most used belong to the genes encoding for ribosomal 16S and 12S subunits, cytochrome b (cytb), and cytochrome c oxidase I (COI). The genetic variability of the complete mt genome of the perciform fishes of the family Sparidae has never been investigated before and remains elusive. Prompted by the aim to identify new specie-specific genetic markers to use against frauds, we analyzed and compared the complete mitogenome of thirteen Sparidae species, including four newly sequenced ones. We searched for mtDNA regions with high interspecific variability (barcodes) flanked by sequences with high sequence conservation (primer). Results showed that the nucleotide sequence variability in NAD group genes (NAD1 39%, NAD2 50%, NAD3 39%, NAD4L 39%, NAD4 43%, NAD5 41%, NAD6 44%) was much higher than in the molecular markers used for species identification, i.e. cyt b (36%), COI (32%) and ribosomal 16S (24%) and 12S (21%). Further, NAD group genes showed a very high discrimination capacity, suggesting their utilization as alternative DNA barcodes for the Sparidae fishes. In particular, the NAD5 gene allows to seek for regions with high nucleotide variability flanked by conserved areas appropriate to design Sparidae-specific primers. This study highlights the importance of complete mtDNA genome comparisons of commercially valuable fish species to identify regions with high (barcode) and low (primer) interspecific nucleotide variation, to be used for species identification of fishery products.