Complete mitogenome of vulnerable goonch catfish Bagarius bagarius: mitochondrial DNA methylation marks and phylogenetic insights
Abstract
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.
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BibTeX
@article{rout2026complete,
title = {{Complete mitogenome of vulnerable goonch catfish Bagarius bagarius: mitochondrial DNA methylation marks and phylogenetic insights}},
author = {Ajaya Kumar Rout and Anuj Tyagi and Pooja Badoni and Satya Narayan Parida and Sushree Swati Rout and Neelesh Kumar and Lekiningroy Dann and Nandkishor A. Ingole and Abhishek Srivastava and Partha Sarathi Tripathy and Bijay Kumar Behera and Pramod Kumar Pandey},
journal = {BMC Genomics},
year = {2026},
month = oct,
doi = {10.1186/s12864-026-13489-x},
url = {https://link.springer.com/article/10.1186/s12864-026-13489-x},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Complete mitogenome of vulnerable goonch catfish Bagarius bagarius: mitochondrial DNA methylation marks and phylogenetic insights
AU - Ajaya Kumar Rout
AU - Anuj Tyagi
AU - Pooja Badoni
AU - Satya Narayan Parida
AU - Sushree Swati Rout
AU - Neelesh Kumar
AU - Lekiningroy Dann
AU - Nandkishor A. Ingole
AU - Abhishek Srivastava
AU - Partha Sarathi Tripathy
AU - Bijay Kumar Behera
AU - Pramod Kumar Pandey
PY - 2026
DA - 2026/10/21
JO - BMC Genomics
DO - 10.1186/s12864-026-13489-x
UR - https://link.springer.com/article/10.1186/s12864-026-13489-x
AB - 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.
SN - 1471-2164
ER -