DNA chip for species identification of Korean freshwater fish: A case study

DNA barcoding is a molecular diagnostic method for species identification that uses a single standardized DNA fragment. Remarkably, mitochondrial cytochrome c oxidase subunit I (COI) gene in animal species can be used for this purpose. For molecular identification, there are several approaches available based on varying properties such as sequence similarity, length of PCR products, and hybridization. We previously developed web-based Molecular Identification System for Fish (MISF), including 53 Korean freshwater fish species, based on a profile hidden Markov model and sequence similarity. In this study, we developed a DNA chip arrayed with 16 oligonucleotide probes to identify 11 selected species of Korean freshwater fish. The COI gene was quite suitable for designing species-specific oligonucleotide probes and a DNA chip arrayed with these probes showed high resolution for species identification. Therefore, the DNA chip using the COI gene can be further developed for different purposes by optimal species selection in biodiversity studies and environmental monitoring.