DNA barcoding of tilapia fish from Merauke, Papua and Malang, East Java-Indonesia

Abstract

Fish identification investigation is an important component of fisheries management and aquaculture. The purpose of this study is to identify tilapia fish existing in Indonesia on the basis of nucleotide composition, polymorphic sites, haplotype grouping, nucleotide BLAST, and phylogenetic tree analyses for cytochrome c oxidase I gene. This required a DNA barcoding process, which involves the production of PCR amplicons from COI gene to generate a sequence data, which is subsequently used to ascertain and distinct the organism from other species. The tilapia fish samples were collected from Merauke, Papua and Malang, East Java, and DNA amplification results showed COI gene fragment sequences, characterized by a length of 654 base pairs. A total of three haplotypes were identified from the twelve samples, with mutases occurring at 56 points (polymorphism). The nucleotide composition, polymorphic sites, haplotype grouping, BLAST analysis, and phylogenetic tree constructed by all 12 individuals were used to categorize the samples into three species, including Oreochromis mossambicus, Oreochromis niloticus and Oreochromis urolepis. In addition, the genetic distance between O. mossambicus and both O. niloticus and O. urolepis were 0.0523 and 0.0401, respectively, while between O. niloticus and O. urolepis was 0.0592. The results indicated DNA barcodes as an effective identification approach for tilapia fish, and the results have a potential for application in aquaculture and during the management of fisheries resource in Indonesia.