Background: Mitochondrial cytochrome c oxidase subunit I (COI) gene-based DNA barcoding provides a reliable approach for identification and phylogenetic analysis of Bagridae catfishes, which are often difficult to distinguish morphologically. This study assessed molecular identification and phylogenetic relationships among selected Bagridae species of the Beki River Basin, Assam, along with three-dimensional (3D) structural characterization of the COI protein. 
 
Methods: Four species, namely Mystus tengara, Mystus vittatus, Mystus cavasius and Rita rita, were analyzed using PCR-amplified COI gene sequences. Phylogenetic relationships were inferred using the Maximum- Likelihood (ML) method with Kimura 2-parameter (K2P) distance model. COI protein structure was predicted through homology modelling and validated using Ramachandran plot and SASA analysis. 
 
Result: COI sequence lengths ranged from 667-685 bp with highest AT content in Rita rita (57.12%) and highest GC content in Mystus tengara (46.71%). Highest pairwise similarity was observed between Mystus tengara and Mystus vittatus (88), while Rita rita showed maximum divergence (74-79). Mean genetic distance among species was 0.01, with greatest divergence between Rita rita and Mystus spp. (0.109-0.228). Phylogenetic analysis placed Rita rita as an outgroup, while Mystus tengara and Mystus vittatus formed a sister clade with strong bootstrap support (92-93%). Predicted COI models showed &gt;91% residues in favored regions with conserved SASA (~11,200-11,400 &Aring;2); active site volume was highest in Mystus vittatus (1485.12 &Aring;3) and lowest in Rita rita (531.33 &Aring;3).

Molecular Identification, Phylogenetic Inference and COI Protein Modelling of Four Bagridae Catfishes from the Beki River Basin, Assam, Northeast India

<div>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&rsquo;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.&nbsp; 
 
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).</div>

Molecular Identification, Phylogenetic Inference and COI Protein Modelling of Four Bagridae Catfishes from the Beki River Basin, Assam, Northeast India

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