Skip to main content
Log in

Genetic identification of the sharks Rhizoprionodon porosus and R. lalandii by PCR-RFLP and nucleotide sequence analyses of 5S rDNA

  • Technical Note
  • Published:
Conservation Genetics Resources Aims and scope Submit manuscript

Abstract

A molecular approach based on nuclear 5S rDNA sequence variability was applied successfully to correctly identify samples from the two Rhizoprionodon species collected in the wild or sold in markets. The sequence of the non-transcribed spacer (NTS) of the 5S rDNA showed high interspecific variability and no intraspecific polymorphism, making it a useful marker for sharpnose shark identification. Polymorphisms in the NTS sequences of Rhizoprionodon sharks also created unique restriction patterns for each species after PCR-RFLP analysis. The 5S rDNA polymorphism represents a fast and non expensive tool to access species identification when rapid and unequivocal identification of shark products is needed, particularly for future management and other investigations.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3

References

  • Aljanabi SM, Martinez I (1997) Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Res 25:4692–4693

    Article  CAS  PubMed  Google Scholar 

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    CAS  PubMed  Google Scholar 

  • Aranishi F, Okimoto T, Izumi S (2005) Identification of gadoid species (Pisces, Gadidae) by PCR-RFLP analysis. J Appl Genet 46:69–73

    PubMed  Google Scholar 

  • Carrera E, Garcia T, Céspedes A, Fernández A, Hernández PE, Martín R (2000) Differentiation of smoked Salmo solar, Onconhynchus mykiss and Brama raii using the nuclear marker 5S rDNA. Int J Food Sci Tech 35:401–406

    Article  CAS  Google Scholar 

  • Cespedes A, Garcia T, Carrera E, Gonzalez I, Fernandez A, Hernández PE, Martin R (1999) Identification of sole (Solea solea) and greenland halibut (Reinhardtius hippoglossoides) by PCR amplification of the 5S rDNA gene. J Agric Food Chem 47:1046–1050

    Article  CAS  PubMed  Google Scholar 

  • Compagno LJV (1984) FAO species catalogue, vol 4. Sharks of the world. Part 2. Carcharhiniformes. FAO fish. Synopsis 125:251–655

  • Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  • Heist EJ, Gold JR (1999) Genetic identification of sharks in the US Atlantic large coastal shark fishery. Fish Bull 97:53–61

    Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  CAS  PubMed  Google Scholar 

  • Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinfo 5:150–163

    Article  CAS  Google Scholar 

  • Lessa RPT, Vooren CM, Araújo MLG, Kotas JE, Almeida PC, Rincón G, Santana FM, Gadig OBF, Sampaio C (2005) Brazilian national plan for conservation and management of elasmobranch fishes stocks. SBEEL, Recife, pp 100

    Google Scholar 

  • Motta FS, Gadig OBF, Namora RC, Braga FMS (2005) Size and sex compositions, length–weight relationship, and occurrence of the Brazilian sharpnose shark, Rhizoprionodon lalandii, caught by artisanal fishery from southeastern Brazil. Fish Res 74:116–126

    Article  Google Scholar 

  • Pendás AM, Móran P, Martínez JL, Garcia-Vasquez E (1995) Applications of 5S rDNA in Atlantic salmon, brown trout, and in Atlantic salmon x brown trout hybrid identification. Mol Ecol 4:275–276

    Article  PubMed  Google Scholar 

  • Pinhal D, Gadig OBF, Wasko AP, Oliveira C, Foresti F, Martins C (2008) Discrimination of shark species by simple PCR of 5S rDNA repeats. Genet Mol Biol 31:361–365

    Article  CAS  Google Scholar 

  • Pinhal D, Araki CS, Gadig OBF, Martins C (2009) Molecular organization of 5S rDNA in sharks of the genus Rhizoprionodon: insights into the evolutionary dynamics of 5S rDNA in vertebrate genomes. Genet Res 91:1–12

    Article  Google Scholar 

  • Shivji MS, Clarke S, Pank M, Natanson L, Kohler N, Stanhope M (2002) Genetic identification of pelagic shark body parts for conservation and trade monitoring. Conserv Biol 16:1036–1047

    Article  Google Scholar 

  • Suzuki H, Moriwaki K, Sakurai S (1994) Sequences and evolutionary analysis of mouse 5S rDNAs. Mol Biol Evol 11:704–710

    CAS  PubMed  Google Scholar 

  • Vincze T, Posfai J, Roberts RJ (2003) NEBcutter: a program to cleave DNA with restriction enzymes. Nucleic Acids Res 31:3688–3691

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgment

The authors are grateful to Fundação de Amparo à Pesquisa do Estado de São Paulo for financial support.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Cesar Martins.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Pinhal, D., Gadig, O.B.F. & Martins, C. Genetic identification of the sharks Rhizoprionodon porosus and R. lalandii by PCR-RFLP and nucleotide sequence analyses of 5S rDNA. Conservation Genet Resour 1, 35 (2009). https://doi.org/10.1007/s12686-009-9008-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s12686-009-9008-9

Keywords

Navigation