PCR-based identification of Adriatic specimen of three scorpionfish species (Scorpaenidae, Teleostei)

The identification of three scorpionfish species, the black scorpionfish (Scorpaena porcus; Linnaeus, 1758), the large-scaled scorpionfish (S. scrofa; Linnaeus, 1758) and the small red scorpionfish (S. notata; Rafinesque, 1810) is possible in adults by morphometry, but often problematic in juveniles due to their similar phenotypes. To develop a molecular species identification tool, first, we have analyzed the genetic similarity of the three species by a PCR-based ‘blind method’ that amplified bands from various locations of the genome. We found high levels of nucleotide similarity between S. porcus and S. scrofa, whereas S. notata showed a higher level of divergence from the other two species. Then, we have searched these patterns for differences between the genomes of Adriatic specimen of these three species and identified several species-specific products in two of them. For the third one a species-specific primer pair amplifying from the 16S ribosomal DNA was designed. One marker for each species was cloned, sequenced and converted into Sequence Characterized Amplified Region (SCAR) markers amplified by specific primer pairs. The SCAR markers amplified robust bands of limited variability from the target species, while no or only occasional weak products were obtained from the other two, proving that they can be used for molecular identification of these three species. These markers can help the conservation and future analysis of these three species as well as their possible selection programs for aquaculture purposes.