The Analysis of Genetic Variation in the Mitochondrial ND6 Gene and its Application for the Identification of Indonesian Catfish Species

Abstract

Background: Catfish is a freshwater and saltwater fish type with a wide distribution throughout the Indonesian archipelago. This study was conducted to analyze Indonesian catfish’s genetic diversity and evolutionary relationships based on the mitochondrial ND6 gene. Methods: Twenty-eight catfish samples were collected from nine rivers and one ocean in seven provinces of Indonesia. The MT-ND6 gene was amplified by using a set of primers (BaungND6F and BaungND6R). The MEGA X software was used to examine the MT-ND6 sequences for genetic variation and phylogenetic relation between Indonesian catfish populations. Result: There were 167 nucleotide site variations and thirty-two amino acid variations in the MT-ND6 gene. The genetic difference among populations ranges from 0.9 to 25% and the average evolutionary divergence in the overall populations was 14%, with catfish BB and PM having the closest genetic distance, while the farthest is BF to MP and BF to MS. In conclusion, the phylogenetic tree indicated that there were four distinct catfish clades in this study: MP, MS, KR, PM, BB and KS had been grouped with Hemibagrus nemurus (Bagridae family), EM had been grouped with Mystus vittatus (Bagridae family), BSBJ had been grouped with Pangasius pangasius (Pangasiidae family) and PD and BF had been grouped with Netuma thalassina (Ariidae family).