Acta Biologica Hungarica

, Volume 65, Issue 2, pp 132–143 | Cite as

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

  • J. M. Saju
  • Sz. Németh
  • Réka Szűcs
  • Rashmi Sukumaran
  • Z. Lim
  • L. Wong
  • L. OrbánEmail author
  • M. BercsényiEmail author


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.


Scorpaena molecular species ID 16S rDNA fluoMEP SCAR molecular aquaculture 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    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.CrossRefGoogle Scholar
  2. 2.
    Caputo, V., Sorice, M. (1999) Electrophoretic studies on some species of Scorpaeniformes (Teleostei, Percomorpha). Italian J. Zool. 66, 79–85.CrossRefGoogle Scholar
  3. 3.
    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.CrossRefGoogle Scholar
  4. 4.
    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.CrossRefGoogle Scholar
  5. 5.
    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.Google Scholar
  6. 6.
    Knowlton, N. (2000) Molecular genetic analyses of species boundaries in the sea. Hybdrobiologia 420, 73–90.CrossRefGoogle Scholar
  7. 7.
    Kochzius, M., Nölte, M., Weber, H., Silkenbeumer, N., Hjörleifsdottir, S. et al. (2008) DNA microarrays for identifying fishes. Mar. Biotechnol. 10, 207–217.CrossRefGoogle Scholar
  8. 8.
    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.CrossRefGoogle Scholar
  9. 9.
    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.Google Scholar
  10. 10.
    Mesa, G. (2005) A revised description of Scorpaena maderensis (Scorpaenidae) by means of meristic and morphometric analysis. Mar. Biol. Assoc. UK 85, 1263–1270.CrossRefGoogle Scholar
  11. 11.
    Milligan, B. G., Leebens-Mack, J., Strand, A. E. (1994) Conservation genetics: beyond the maintenance of marker diversity. Mol. Ecol. Notes 3, 423–435.CrossRefGoogle Scholar
  12. 12.
    MSIP (2013) Marine Species Identification Portal: Scorpaena porcus (accessed on 25th of March, 2013).Google Scholar
  13. 13.
    MSIP (2013) Marine Species Identification Portal: Scorpaena scrofa (accessed on 25th of March, 2013).Google Scholar
  14. 14.
    MSIP (2013) Marine Species Identification Portal: Scorpaena notata (accessed on 25th of March, 2013).Google Scholar
  15. 15.
    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.CrossRefGoogle Scholar
  16. 16.
    Nelson, J. (2006) Fishes of the World. Wiley and Sons, New York, NY, USA, 624 p.Google Scholar
  17. 17.
    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.CrossRefGoogle Scholar
  18. 18.
    Sukumaran, R. (2008) Computational analysis of genotypes produced by fluoMEP. Honours Year Project Report. National University of Singapore, Singapore, 88 p.Google Scholar
  19. 19.
    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.CrossRefGoogle Scholar
  20. 20.
    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.Google Scholar
  21. 21.
    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.CrossRefGoogle Scholar
  22. 22.
    Welsh, J., McClelland, M. (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 18, 7213–7218.CrossRefGoogle Scholar
  23. 23.
    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.CrossRefGoogle Scholar
  24. 24.
    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.CrossRefGoogle Scholar

Copyright information

© Akadémiai Kiadó Zrt. 2014

This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, 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.

Authors and Affiliations

  • J. M. Saju
    • 1
  • Sz. Németh
    • 2
  • Réka Szűcs
    • 2
  • Rashmi Sukumaran
    • 1
    • 3
  • Z. Lim
    • 1
    • 4
  • L. Wong
    • 3
  • L. Orbán
    • 1
    • 2
    • 4
    Email author
  • M. Bercsényi
    • 2
    Email author
  1. 1.Reproductive Genomics Group, Strategic Research Program, Temasek Life Sciences Laboratory, 1 Research LinkNational University of SingaporeSingapore
  2. 2.Department of Animal Sciences and Breeding, Georgikon FacultyUniversity of PannoniaKeszthelyHungary
  3. 3.School of Computing, National University of SingaporeSingapore
  4. 4.Department of Biological SciencesNational University of SingaporeSingapore

Personalised recommendations