Discrimination of Shark species by simple PCR of 5S rDNA repeats

Abstract

Sharks are suffering from intensive exploitation by worldwide fisheries leading to a severe decline in several populations in the last decades. The lack of biological data on a species-specific basis, associated with a k-strategist life history make it difficult to correctly manage and conserve these animals. The aim of the present study was to develop a DNA-based procedure to discriminate shark species by means of a rapid, low cost and easily applicable PCR analysis based on 5S rDNA repeat units amplification, in order to contribute conservation management of these animals. The generated agarose electrophoresis band patterns allowed to unequivocally distinguish eight shark species. The data showed for the first time that a simple PCR is able to discriminate elasmobranch species. The described 5S rDNA PCR approach generated species-specific genetic markers that should find broad application in fishery management and trade of sharks and their subproducts.

Molecular organization of 5S rDNA in sharks of the genusRhizoprionodon: insights into the evolutionary dynamics of 5S rDNA in vertebrate genomes

“…It remains unclear if lampreys may also have two classes of 5S rDNA, as detected in Elasmobranchii and Teleostei, but it is probable that they contain variant copies corresponding to a single class, as is well documented in tetrapod genomes (Rosenthal & Doering, 1983;Suzuki et al, 1994 ;Frederiksen et al, 1997;Jensen & Frederiksen, 2000). Regarding the number of 5S rDNA classes in the genome of sharks, agarose electrophoresis profiles of 5S rDNA-PCR products from Sphyrna lewini, G. cuvier, Carcharhinus obscurus, Carcharhinus leucas, Carcharhinus limbatus, Carcharhinus acronotus, A. superciliosus and Isurus oxyrinchus have indicated the extensive variability present in 5S rDNA unit size (Pinhal et al, 2008). Each species showed an exclusive pattern with one to four bands of different molecular weights, possibly referring to distinct paralogous copies of 5S rDNA arrays.…”

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“…Different classes of the 5S rRNA gene, identified in many fish species, varied by length, several nucleotide mutations or chromosomal location (Messias et al, 2003;Pinhal et al, 2008;Campo, Machado-Schiaffino, Horreo, & Garcia-Vazquez, 2009;He et al, 2012He et al, , 2013. Multi-class type 5S rDNA are considered an ancestral character that originated early in the history of vertebrates (Frederiksen, Cao, Lomholt, Levan, & Hallenberg, 1997).…”

“…In some fish species, different classes of this gene have been described. Each of the different-sized 5S rDNA classes vary in length, nucleotide changes and chromosome location (Martins, 2006;Messias et al, 2003;Pinhal et al, 2008;Campo, MachadoSchiaffino, Horreo, & Garcia-Vazquez, 2009). Most fish species are characterized by the occurrence of two 5S rDNA arrays with a different NTS (Martins & Galetti Jr., 2001;He et al, 2012;Qin, Wang, Wang, Liu, & Liu, 2015).…”

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

“…Previous 5S rDNA data have reported that sequence polymorphisms in the ribosomal NTS were sufficient to distinguish subspecies of mice Mus musculus domesticus from M. m. musculus (Suzuki et al 1994), suggesting that this region was evolving at an appropriate rate for distinguishing close related species. In the same way, the NTS region has been extensively used for fish species discrimination, either through a simple PCR amplification analysis (Cespedes et al 1999;Pendás et al 1995;Pinhal et al 2008) or in combination with PCR-RFLP analysis (Aranishi et al 2005;Carrera et al 2000). NTSs seem to bear consistently low intraspecific variability and high interspecific variability independent of the vertebrate group analyzed.…”