Tandem PCR-RFLP analysis helps distinguish among three Japanese gnomefish (Teleostei: Scombropidae: Scombrops)

Scombrops boops and Scombrops gilberti are commercially important species inhabiting waters around the Japanese archipelago, and recently another undescribed species Scombrops sp. was found. Here, we developed a method using PCR-RFLP on cytochrome b gene sequences of known scombropids to distinguish among these taxa. Comparison of RFLP of the PCR products among scombropids produced a species-specific banding pattern, identifying them with close to 100% accuracy. Two misidentified specimens were identified correctly by the PCR-RFLP analysis developed previously using 16S rRNA sequences. These results showed that PCR-RFLP analysis, using 16S rRNA and cytochrome b sequences in tandem, correctly distinguishes among the three scombropids. We applied this method to 190 individuals collected around the Yonagunijima Island and got some insights into reproductive biology of the three species of Scombrops.