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

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 overlapping 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.