PCR-RFLP analysis of the internal transcribed spacer (ITS) region for identification of 3 clam species

Restriction site analysis of the internal transcribed spacer (ITS) region amplified by the polymerase chain reaction (PCR) was used for the specific identification of 3 clam species: Ruditapes decussatus (grooved carpet shell), Venerupis pullastra (pullet carpet shell), and Ruditapes philippinarum (Japanese carpet shell). PCR amplification using pruners based on nucleotide sequences of Mytilus ITS regions produced a fragment of 1195 bp in R. decussatus, 1074 bp in V pullastra, and 1188 bp in R. philippinarum. Digestion of the PCR products with endonucleases Hinf I and Rsa I, followed by agarose gel electrophoresis of the digested products, yielded specific restriction profiles that enabled direct visual identification of the species analyzed.