Complete mitogenome of vulnerable goonch catfish Bagarius bagarius: mitochondrial DNA methylation marks and phylogenetic insights

This is the authors' abstract. We don't add key points for this paper.

Background The vulnerable goonch catfish Bagarius bagarius is an ecologically important riverine species whose evolutionary history and mitochondrial regulation remain poorly understood. In this study, we generated and analyzed the complete mitogenome of B. bagarius using Oxford Nanopore long-read sequencing with adaptive sampling, followed by de novo assembly, annotation, and comprehensive comparative analyses. Results The circular mitogenome (16,524 bp) contains the typical vertebrate complement of 13 protein-coding genes, 22 tRNAs, two rRNAs, and a control region, and exhibits pronounced AT richness and strand-specific compositional asymmetry. Phylogenetic reconstruction based on complete mitogenomes robustly resolves B. bagarius as sister to Bagarius yarrelli , confirming the monophyly of the genus and supporting its placement as an early-diverging lineage within Sisorinae. Homoplasy analyses reveal limited recurrent mutation at shallow phylogenetic scales but substantial homoplasy across deeper sisorid divergences, highlighting both the strengths and limits of mitochondrial inference. Nanopore-based modified-base calling identified candidate adenine- and cytosine-associated signals across the mitogenome, with variation in their strand-wise and regional distributions. Because these signals were derived from a single individual and were not independently validated, they are interpreted as preliminary candidate modification patterns rather than definitive evidence of mitochondrial DNA methylation or functional regulation. Conclusion Overall, this study provides a complete mitogenomic resource for B. bagarius together with an exploratory dataset of nanopore-derived candidate modified-base signals, supporting future phylogenetic, conservation-genetic, and independently validated investigations of mitochondrial DNA modification in fishes.