Comparative mitochondrial genome analyses of Diptychus maculatus (Actinopterygii, Cypriniformes, Cyprinidae) uncover conserved genome features and phylogenetic relationships of Schizopygopsinae

The subfamily Schizopygopsinae (Cyprinidae), endemic to high-altitude Asian ecosystems, is widely used as a model for studying adaptive evolution, owing to specialized hypoxia tolerance and reduced squamation in high-altitude environments. Despite advances in mitochondrial genomics, comprehensive analyses of conserved genomic features and phylogenetic relationships within this subfamily remain limited. Herein, we sequenced and annotated the mitochondrial genome of Diptychus maculatus Steindachner, 1866 (16 764 bp; GenBank: ON872378) and comparatively analyzed the mitogenomes across 56 Cyprinidae species, including 33 Schizopygopsinae members, 21 Schizothoracinae members and two Leuciscinae outgroups ( Leuciscus baicalensis , Rutilus rutilus ). The mitochondrial genome of D. maculatus exhibited conserved teleost features, including 13 protein-coding genes (PCGs), 22 tRNAs, and 2 rRNAs. Its gene order and strand distribution align with those of related taxa. Notable AT bias (54.3%) and negative GC skew (−0.163) were observed, consistent with mutation-driven thymine accumulation in PCGs. Codon usage analysis revealed a preference for A/T-ending codons, with lineage-specific reductions in relative synonymous codon usage in Diptychus . Phylogenetic reconstructions using Bayesian and maximum likelihood methods resolved Schizopygopsinae and Schizothoracinae into two primary clades, supporting their monophyly but revealing paraphyly in genera Schizothorax and Gymnocypris , which are likely due to rapid radiation and ecological diversification. The placement of D. maculatus as sister to Gymnodiptychus underscores shared adaptations to plateau environments. Our findings highlight conserved mitogenomic architecture shaped by mutation pressure and selection, while phylogenetic discordance with morphology-based classifications emphasizes the need for integrative taxonomic approaches. This study provides critical genomic insights into the evolutionary mechanisms driving high-altitude adaptation and diversification in Schizopygopsinae and offers a foundation for future research on Cyprinidae biogeography and speciation.