The complete mitochondrial DNA sequence of Gymnocypris chilianensis was determined and analyzed. The mitogenome of G. chilianensis is 16,667 bp long, containing 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 non-coding regions: control region (D-loop) and origin of light-strand replication (OL). The gene order of mitogenome is identical to that observed in most other vertebrates. The complete mitogenome sequence information of G. chilianensis can provide useful data for further studies on molecular systematic, taxonomic status, stock evaluation and conservation genetics.
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