Abstract
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.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Borsa, P., Collet, A., Durand, J. D. (2004) Nuclear-DNA markers confirm the presence of two anchovy species in the Mediterranean. C. R. Biol. 327, 1113–1123.
Caputo, V., Sorice, M. (1999) Electrophoretic studies on some species of Scorpaeniformes (Teleostei, Percomorpha). Italian J. Zool. 66, 79–85.
Caputo, V., Sorice, M., Vitturi, R., Magistrelli, R., Olmo, E. (1998) Cytogenetic studies in some species of Scorpaeniformes (Teleostei: Percomorpha). Chromosome Res. 6, 255–262.
Chang, A., Liew, W. C., Chuah, A., Lim, Z., Lin, Q. et al. (2007) FluoMEP: a new genotyping method combining the advantages of randomly amplified polymorphic DNA and amplified fragment length polymorphism. Electrophoresis 28, 525–534.
Hureau, J. C., Litvinenko, N. I. (1986) Scorpaenidae. In: Whitehead, P. J. P., Bauchot, M. L., Hureau, J. C., Nielsen, J., Tortonese, E. (eds) Fishes of the North-Eastern Atlantic and the Mediterranean. UNESCO, Paris, France, pp. 1211–1229.
Knowlton, N. (2000) Molecular genetic analyses of species boundaries in the sea. Hybdrobiologia 420, 73–90.
Kochzius, M., Nölte, M., Weber, H., Silkenbeumer, N., Hjörleifsdottir, S. et al. (2008) DNA microarrays for identifying fishes. Mar. Biotechnol. 10, 207–217.
Liew, W. C., Bartfai, R., Lim, Z., Sreenivasan, R., Siegfried, K. R. et al. (2012) Polygenic sex determination system in zebrafish. PLoS ONE 7, e34397.
Matic-Skoko, S., Dulcic, J., Krajevic, M., Tutman, P., Pallaoro, A. (2008) Recent status of coastal ichthyocommunities along the Croatian coast. In: 43rd Croatian and 3rd International Symposium on Agriculture, 18/02/2008–21/02/2008, Opatija, Croatia, pp. 737–741.
Mesa, G. (2005) A revised description of Scorpaena maderensis (Scorpaenidae) by means of meristic and morphometric analysis. Mar. Biol. Assoc. UK 85, 1263–1270.
Milligan, B. G., Leebens-Mack, J., Strand, A. E. (1994) Conservation genetics: beyond the maintenance of marker diversity. Mol. Ecol. Notes 3, 423–435.
MSIP (2013) Marine Species Identification Portal: Scorpaena porcushttps://doi.org/species-identification.org/species.php?species_group=fnam&id=2129&menuentry=soorten (accessed on 25th of March, 2013).
MSIP (2013) Marine Species Identification Portal: Scorpaena scrofahttps://doi.org/species-identification.org/species.php?species_group=fnam&id=2130&menuentry=soorten (accessed on 25th of March, 2013).
MSIP (2013) Marine Species Identification Portal: Scorpaena notatahttps://doi.org/species-identification.org/species.php?species_group=fnam&id=2128&menuentry=soorten (accessed on 25th of March, 2013).
Nei, M., Li, W.-H. (1979) Mathematical modelling for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 76, 5269–5273.
Nelson, J. (2006) Fishes of the World. Wiley and Sons, New York, NY, USA, 624 p.
Németh, S., Budaházi, A., Szűcs, R., Bercsényi, M. (2008) Out of the season artificial propagation of the black scorpionfish (Scorpaena porcus) in captivity. Mediterr. Aqua J. 1, 1–8.
Sukumaran, R. (2008) Computational analysis of genotypes produced by fluoMEP. Honours Year Project Report. National University of Singapore, Singapore, 88 p.
Turan, C., Gunduz, I., Gurlek, M., Yaglioglu, D., Erguden, D. (2009) Systematics of Scorpaeniformes species in the Mediterranean Sea inferred from mitochondrial 16S rDNA sequence and morphological data. Folia Biol. (Krakow) 57, 219–226.
van der Land, J., Costello, M. J., Zavodnik, D., Santos, R. S., Porteiro, F. M. et al. (2001) Pisces. In: Costello, M. J., Emblow, C., White, R. (eds) European Register of Marine Species: A Check-List of the Marine Species in Europe and a Bibliography of Guides to their Identification. Collection Patrimoines Naturels, 50. Muséum national d’Histoire naturelle, Paris, France, pp. 357–374.
Vos, P., Hogers, R., Bleeker, M., Reijans, M., van de Lee, T. (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 23, 4407–4414.
Welsh, J., McClelland, M. (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 18, 7213–7218.
Williams, J. G., Kubelik, A. R., Livak, K. J., Rafalski, J. A., Tingey, S. V. (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18, 6531–6535.
Williams, J. G., Reiter, R. S., Young, R. M., Scolnik, P. A. (1993) Genetic mapping of mutations using phenotypic pools and mapped RAPD markers. Nucleic Acids Res. 21, 2697–2702.
Author information
Authors and Affiliations
Corresponding authors
Rights and permissions
This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
About this article
Cite this article
Saju, J.M., Németh, S., Szűcs, R. et al. PCR-based identification of Adriatic specimen of three scorpionfish species (Scorpaenidae, Teleostei). BIOLOGIA FUTURA 65, 132–143 (2014). https://doi.org/10.1556/ABiol.65.2014.2.2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1556/ABiol.65.2014.2.2