Comprehensive mitogenomic insights into Hemibagrus velox endemic to Sumatra, Indonesia and its phylogenetic relationships within the Bagridae lineage

Background The bagrid catfish genus Hemibagrus, comprising large-bodied species widely distributed across tropical and subtropical Asia, has long posed taxonomic challenges, which have been increasingly addressed through mitogenomic data, demonstrating its reliability as an integrated tool for resolving phylogenetic ambiguities. Hence, the present study aims to characterize the novel complete mitochondrial genome of Hemibagrus velox, a species endemic to Sumatra, Indonesia, and to conduct a comprehensive comparative analysis of gene structure and variation among its congeners, as well as to evaluate its phylogenetic position within the Bagridae family. Results The current investigation reveals the mitogenome of H. velox (16,512 bp), comprising 37 genes, a non-coding control region (CR), an overall A + T bias of 58.09%, eleven intergenic spacers, and six overlapping regions. Most protein-coding genes (PCGs) in Hemibagrus species initiate translation with the standard ATG start codon, except for the COI gene, which utilizes the GTG codon. The amino acid composition analysis exhibited a high frequency of leucine, serine, and arginine residues, whereas methionine and tryptophan were the least abundant. The ratio of nonsynonymous to synonymous substitutions indicated strong purifying selection acting on the PCGs across Hemibagrus species. The secondary structure of 21 transfer RNAs showed the typical cloverleaf structure, except for tRNA-Ser (S1), which lacked the dihydrouridine arm. The comparative analysis of conserved sequence blocks within the CR among eight Hemibagrus species established variation in length and nucleotide composition, with tandem repeats exclusively present in Hemibagrus guttatus within the extended termination-associated sequence region. The phylogenetic analyses employing Bayesian inference, Maximum-likelihood, and Neighbor-joining methods demonstrated that Hemibagrus is a non-monophyletic group within the family Bagridae. The present matrilineal evolutionary pattern further corroborates earlier hypotheses concerning the genus Tachysurus and strengthens recent taxonomic revisions of Leiocassis, Pseudobagrus, and Pelteobagrus. Conclusions Collectively, this study presents novel mitogenomic data for H. velox, offering detailed genetic characterization in comparison with its congeners and confirming its phylogenetic placement within the Bagridae lineages. Furthermore, the findings underscore the urgent need to expand mitogenomic datasets for other bagrid species to enhance the resolution of their systematics and evolutionary relationships, thereby facilitating evidence-based conservation efforts and effective fisheries management.