Characterization of the Macropodus opercularis complete mitochondrial genome and family Channidae taxonomy using Illumina-based de novo transcriptome sequencing

•Illumina-based de novo transcriptome sequencing is an effective method to gain mitogenome data.•Complete mitochondrial genome of Macropodus opercularis is reported.•Mitogenomes strongly confirm that the family Channidae belongs to suborder Channoidei.

In this study, the complete mitochondrial genome of Macropodus opercularis was sequenced using Illumina-based de novo transcriptome technology and annotated using bioinformatic tools. The circular mitochondrial genome was 16,496 bp in length and contained two ribosomal RNAs, 13 protein-coding genes, 22 transfer RNA genes, and the control region. The gene composition and order were similar to suborder Anabantoidei. Phylogenetic analyses using concatenated amino acid and nucleotide sequences of the 13 protein-coding genes with two different methods (Neighbor-joining and Bayesian analysis) both highly supported the close relationship of M. opercularis to M. ocellatus, consistent with previous classifications based on morphological and molecular studies. Furthermore, family Channidae and Parachanna insignis were clustered in the same clade. Our results supported the inclusion of family Channidae in suborder Channoidei. The complete mitochondrial genome of M. opercularis will provide genetic markers for better understanding species identification, population genetics and phylogeographics of freshwater fishes.