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Deciphering the mitochondrial genome of Malabar snakehead, Channa diplogramma (Teleostei; Channidae)

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Abstract

The whole mitogenome of the freshwater fish Channa diplogramma (Malabar snakehead), a vulnerable species of snakehead from the Western Ghats, India was sequenced for the first time. The genome is 16,571 bp in length, comprised of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a non-coding control region. All the protein-coding genes, tRNA and rRNA were located in the heavy strand except nad6 and 8 tRNAs (Glutamine, Alanine, Asparagine, Cysteine, Tyrosine, Serine, Glutamic acid and Proline) transcribed from L strand. The genome exhibited an overlap** of 7 bp in 2 different locations from 8100 to 10,342 bp. These overlaps were detected between protein-coding genes (atp8 – atp6, nad4l – nad4). In addition, intergenic spacers of 167 bp were also present. The overall GC- and AT-skews of the H-strand mitogenome were 0.1077 and − 0.2439, respectively revealing that the H-strand had equal amounts of A and T and that the overall nucleotide composition was C skewed. All tRNA genes had cloverleaf secondary structures, while the secondary structure of tRNASer lacked a discernible dihydrouridine stem. The phylogenetic analysis of C. diplogramma shows its close similarity to C. micropeltes, native to Southeast Asia, Malay Peninsula and Indonesia.

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Abbreviations

tRNA:

Transfer RNA

rRNA:

Ribosomal RNA

nad :

NADH ubiquinone oxidoreductase complex

cox :

Cytochrome c oxidase

atp :

ATP synthases

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Acknowledgments

This work was supported by Centre of Excellence in Sustainable Aquaculture and Aquatic Health Management (CAAHM), Plan fund, Kerala University of Fisheries and Ocean Studies.

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Authors and Affiliations

  1. Department of Aquaculture, Kerala University of Fisheries and Ocean Studies, Panangad, Kochi, 682506, India

    S. Chandhini, Sneha Vargheese & V. J. Rejish Kumar

  2. Department of Zoology, Nirmalagiri College, Kannur, Kerala, 670 701, India

    Siby Philip

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  1. S. Chandhini
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Chandhini, S., Vargheese, S., Philip, S. et al. Deciphering the mitochondrial genome of Malabar snakehead, Channa diplogramma (Teleostei; Channidae). Biologia 75, 741–748 (2020). https://doi.org/10.2478/s11756-019-00385-x

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