Complete mitochondrial DNA sequence of Atlantic horse mackerel Trachurus trachurus and molecular identification of two commercially important species T-trachurus and T-japonicus using PCR-RFLP

To characterize and identify mitochondrial DNA (mtDNA) nucleotide sequence variation in two commercially important Trachurus species, Trachurus trachurus and T. japonicus, the complete mtDNA sequence of T. trachurus was determined. The T. trachurus mtDNA consists of 16 559 bp, containing 22 transfer RNA (tRNA) genes, two rRNA genes, and 13 protein-coding genes. Comparing the mtDNA nucleotide sequences of the Trachurus species, a polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP) method was developed to differentiate these two commercially important species. The primer pair Lt1-ND5 and Ht1-ND5, corresponding to ND5, was designed to amplify a 360-bp fragment. Following digestion with Eco RI, the PCR product for T. japonicus resulted in 93- and 267-bp fragments, while T. trachurus lacked a restriction site for Eco RI. In contrast, after digestion with Hin fI, the T. trachurus PCR product yielded 44-, 84-, and 232-bp fragments, while the T. japonicus product was not digested. The PCR-RFLP analysis established in the present study was useful for identifying T. trachurus and T. japonicus.