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.
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
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Aranishi F, Okimoto T, Izumi S (2005) Identification of gadoid species (Pisces, Gadidae) by PCR-RFLP analysis. J Appl Genet 46:69–73
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
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
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
Heist EJ, Gold JR (1999) Genetic identification of sharks in the US Atlantic large coastal shark fishery. Fish Bull 97:53–61
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
Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinfo 5:150–163
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
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
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
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
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
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
Suzuki H, Moriwaki K, Sakurai S (1994) Sequences and evolutionary analysis of mouse 5S rDNAs. Mol Biol Evol 11:704–710
Vincze T, Posfai J, Roberts RJ (2003) NEBcutter: a program to cleave DNA with restriction enzymes. Nucleic Acids Res 31:3688–3691
Acknowledgment
The authors are grateful to Fundação de Amparo à Pesquisa do Estado de São Paulo for financial support.
Author information
Authors and Affiliations
Corresponding author
Rights 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
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s12686-009-9008-9