The complete mitochondrial genome of the medicinal fish, Cyprinion semiplotum: Insight into its structural features and phylogenetic implications.

Abstract Assamese kingfish (Cyprinion semiplotum) belonging to the subfamily Barbinae is an important food as well as aquarium fish having identified pharmacological benefits. The species has a complex taxonomic history and its phylogenetic position remains uncertain. Molecular data employed in earlier phylogenetic studies was inadequate for its phylogenetic placement. Therefore, we characterized 16,671 bp long complete mitogenome of C. semiplotum using next-generation sequencing. The mitogenome encodes the typical set of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and two non-coding regions. Its gene organization, distribution pattern, nucleotide composition, tRNA secondary structure and codon usage was similar to other Cyprinid mitogenomes. However, a distinctive 90 bp insertion was found in 3′ periphery of the AT-rich control region. This can be a tool for identification of the species at the population level. Further, we reconstructed the most comprehensive phylogenetic trees of Cyprinidae based on complete mitogenome. In the resulting phylogenetic trees, C. semiplotum clustered tightly with other Barbinae species and exhibited a sister relationship with the species of the genera Aulopye, Barbus, Luciobarbus and Capoeta. The results presented herein will support future investigations on molecular taxonomy, population genetics, evolution and molecular phylogeny of C. semiplotum and its relatives.