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In this study, the complete mitogenome sequence of balitorid fish, giant stone loach Triplophysa siluroides, which collected from the Yellow River, China has been sequenced by the long polymerase chain reaction method. The mitogenome, consisting of 16,574 base pairs (bp), had typical vertebrate mitochondrial gene arrangement, including 13 protein coding genes, 22 transfer RNAs, 2 ribosomal RNA genes and a noncoding control region (CR). CR of 918 bp length is located between tRNA(Pro) and tRNA(Phe). The overall base composition of Triplophysa siluroides is 28.8% for A, 28.7% for T, 25.0% for C, and 17.5% for G, with a slight AT bias of 57.5%. The complete mitochondrial genome may provide rather informative data for reconstructing and addressing new molecular perspectives for balitorid phylogenies.

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