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Whole mitogenome analysis and phylogeny of freshwater fish red-finned catopra (Pristolepis rubripinnis) endemic to Kerala, India

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Abstract

The freshwater leaf fish Pristolepis rubripinnis belongs to the family Pristolepididae, restricted to Pamba and Chalakudy rivers of Kerala, India. In the present study, we sequenced the complete mitogenome of P. rubripinnis and analysed its phylogeny in the order Anabantiformes. The 16622-bp long genome comprised of 13 protein-coding genes, two rRNA genes, 22 transfer RNAs (tRNAs) genes and had a noncoding control region. All the protein-coding genes, tRNA and rRNA were located on the heavy strand, except nad6 and eight tRNAs (glutamine, alanine, asparagine, cysteine, tyrosine, serine, glutamic acid and proline) transcribed from L strand. The genome exhibited an overlapping between atp8 and atp6 (2 bp), nad4 and nad4l (2 bp), tRNAIle and tRNAGln (1 bp), tRNAThr and tRNAPro (1 bp). Around 157 bp, an intergenic spacer was identified. The overall GC-skews and AT-skews of the H-strand mitogenome were –0.35 and 0.079, respectively, revealing that the H-strand consisted of equal amounts of A and T and that the overall nucleotide composition was C skewed. All tRNA genes exhibited cloverleaf secondary structures, while the secondary structure of tRNASer lacked a discernible dihydrouridine stem. The phylogenetic analysis of available mitogenomes of Anabantiformes revealed a sister group relationship between Pristolepididae and Channidae. The whole mitogenome of Pristolepis rubripinnis will form a molecular resource for further taxonomic and conservation studies on this endemic freshwater fish.

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Acknowledgement

This work was supported by Centre of Excellence in Sustainable Aquaculture and Aquatic Health Management (CAAHM), Plan fund 2019-20, 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, 682 506, India

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

  2. The University Museum, University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-0033, Japan

    Yusuke Yamanoue

  3. Department of of Fisheries Resource Management, Kerala University of Fisheries and Ocean Studies, Panangad, Kochi, 682 506, India

    P. H. Anvar Ali

  4. School of Ocean Studies, Kerala University of Fisheries and Ocean Studies, Panangad, Kochi, 682 506, India

    V. M. Arjunan

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  1. S. Chandhini
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  2. Yusuke Yamanoue
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  3. Sneha Varghese
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  4. P. H. Anvar Ali
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  5. V. M. Arjunan
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  6. V. J. Rejish Kumar
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Correspondence to V. J. Rejish Kumar.

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Corresponding editor: Punyasloke Bhadury

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Chandhini, S., Yamanoue, Y., Varghese, S. et al. Whole mitogenome analysis and phylogeny of freshwater fish red-finned catopra (Pristolepis rubripinnis) endemic to Kerala, India. J Genet 100, 30 (2021). https://doi.org/10.1007/s12041-021-01292-4

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