A Novel Mitochondrial Genome Resource for the Endemic Fish Gymnodiptychus integrigymnatus and Insights into the Phylogenetic Relationships of Schizothoracinae

<i>Gymnodiptychus integrigymnatus</i> is a small endemic fish species found in southwest China. This study aimed to investigate the phylogenetic relationships and mitogenomic characteristics of <i>G. integrigymnatus</i>. The complete mitochondrial genome of one individual of <i>G. integrigymnatus</i> was sequenced using the Illumina HiSeq X Ten sequencing platform and comprehensively characterized. The mitochondrial genome was 16,714 bp in length, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a typical control region. The genome composition showed a positive A + T skew (0.029) and a negative G + C skew (-0.198). All tRNAs were predicted to form typical cloverleaf secondary structures, except for tRNA-Ser (GCT), which lacked the DHU stem. Phylogenetic reconstruction based on 13 PCGs revealed that the subfamily Schizothoracinae was not a monophyletic group. Two major clades were identified within this subfamily: one comprising primitive taxa (<i>Percocypris</i>, <i>Aspiorhynchus</i>, and <i>Schizothorax</i>) and the other consisting of specialized and highly specialized groups. <i>Gymnodiptychus integrigymnatus</i> was distinct from both its congeners and the specialized clade and was instead recovered within a highly specialized group of the Schizothoracinae subfamily. This study offers novel perspectives on the taxonomy and phylogenetic relationships within the Schizothoracinae subfamily, with a specific focus on <i>G. integrigymnatus</i>, thereby enhancing the understanding of the systematics and phylogeny of the Schizothoracinae subfamily.