The ya-fish, Schizothorax prenanti, is a well-known commercial cold-water fish species with the hexaploid karyotype distributed in the upper reaches of the Yangtze River and its tributaries on the western Sichuan Plateau in China. The complete mitogenome of S. prenanti is 16,587 bp in length, containing 37 genes of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region (D-loop). The gene nucleotide composition of S. prenanti is 29.6% A, 25.4% T, 27.1% C and 17.9% G, with a slight AT bias of 55.0%. The complete mitogenome sequence of S. prenanti could provide useful data for further studies on genetic structure and diversity, as well as the artificial cultivation and breeding of S. prenanti.
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