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Genomic analysis and phylogenetic characterization of Himalayan snow trout, Schizothorax esocinus based on mitochondrial protein-coding genes

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Abstract

Background

Mitochondrial DNA (mtDNA) has become a significant tool for exploring genetic diversity and delineating evolutionary links across diverse taxa. Within the group of cold-water fish species that are native to the Indian Himalayan region, Schizothorax esocinus holds particular importance due to its ecological significance and is potentially vulnerable to environmental changes. This research aims to clarify the phylogenetic relationships within the Schizothorax genus by utilizing mitochondrial protein-coding genes.

Methods

Standard protocols were followed for the isolation of DNA from S. esocinus. For the amplification of mtDNA, overlapping primers were used, and then subsequent sequencing was performed. The genetic features were investigated by the application of bioinformatic approaches. These approaches covered the evaluation of nucleotide composition, codon usage, selective pressure using nonsynonymous substitution /synonymous substitution (Ka/Ks) ratios, and phylogenetic analysis.

Results

The study specifically examined the 13 protein-coding genes of Schizothorax species which belongs to the Schizothoracinae subfamily. Nucleotide composition analysis showed a bias towards A + T content, consistent with other cyprinid fish species, suggesting evolutionary conservation. Relative Synonymous Codon Usage highlighted leucine as the most frequent (5.18%) and cysteine as the least frequent (0.78%) codon. The positive AT-skew and the predominantly negative GC-skew indicated the abundance of A and C. Comparative analysis revealed significant conservation of amino acids in multiple genes. The majority of amino acids were hydrophobic rather than polar. The purifying selection was revealed by the genetic distance and Ka/Ks ratios. Phylogenetic study revealed a significant genetic divergence between S. esocinus and other Schizothorax species with interspecific K2P distances ranging from 0.00 to 8.87%, with an average of 5.76%.

Conclusion

The present study provides significant contributions to the understanding of mitochondrial genome diversity and genetic evolution mechanisms in Schizothoracinae, hence offering vital insights for the development of conservation initiatives aimed at protecting freshwater fish species.

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Data availability

The data that support the findings of this study are openly available in GenBank via Bankit: http://www.ncbi.nlm.nih.gov/BankIt/.

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Acknowledgements

The authors extend gratitude to the Department of Zoology, University of Kashmir and the Division of Animal Biotechnology, SKUAST-K for laboratory facilities. Appreciation is also expressed to the Council of Scientific & Industrial Research (CSIR), Government of India, for providing financial support through a CSIR fellowship to author Ms. Gulshan Akhter.

Funding

This research received no specific grant from any funding agency.

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Authors and Affiliations

  1. Fish Nutrition Research Laboratory, Department of Zoology, University of Kashmir, Hazratbal, Srinagar, Jammu and Kashmir, 190 006, India

    G. Akhter & I. Ahmed

  2. Division of Biotechnology, Faculty of Veterinary Sciences & Animal Husbandry, Sher-E-Kashmir University of Agricultural Sciences and Technology, Srinagar, India

    S. M. Ahmad

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Contributions

Gulshan Akhter: Conceptualization; formal analysis; validation; Data curation; visualization; writing—original draft, writing- review and editing. Imtiaz Ahmed: Conceptualization; validation; visualization; supervision; writing- review and editing. S.M. Ahmad: Conceptualization; formal analysis; writing- review and editing.

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Correspondence to I. Ahmed or S. M. Ahmad.

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Sampling of the target organism aligns with ethical standards and approved protocols established by an Animal Ethical Committee known as, Committee for the Purpose of Control and Supervision on Experiments on Animals (Reference Number 801/Go/RE/S/2003/CPCSEA).

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Akhter, G., Ahmed, I. & Ahmad, S.M. Genomic analysis and phylogenetic characterization of Himalayan snow trout, Schizothorax esocinus based on mitochondrial protein-coding genes. Mol Biol Rep 51, 659 (2024). https://doi.org/10.1007/s11033-024-09622-2

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