Complete Mitochondrial Genome of Phoxinus grumi (Cypriniformes: Leuciscidae): Characterization and Phylogenetic Position

Background: Phoxinus grumi, a small leuciscid fish endemic to the Turpan Basin in Xinjiang, China, has long been the subject of taxonomic disputes, hindering accurate species identification and the understanding of its evolutionary history. Methods: To resolve this uncertainty, we sequenced and characterized the complete mitochondrial genome of P. grumi using next-generation sequencing. Results: The circular mitogenome is 16,604 bp long and comprises the typical 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region, exhibiting gene overlap and intergenic spacing. The overall base composition shows a pronounced AT bias. Notably, all tRNA genes except tRNA-Ser1 fold into a typical cloverleaf secondary structure; tRNA-Ser1 lacks the dihydrouracil (DHU) arm, representing an unusual structural variation. All 13 PCGs have been subject to purifying selection (Ka/Ks < 1), with ATP8 evolving fastest and COX1 being the most conserved. Maximum likelihood (ML) and Bayesian inference (BI) phylogenetic analyses were conducted based on the concatenated sequences of the 13 mitochondrial PCGs, as well as the Cytb gene. Both datasets consistently placed P. grumi within the subfamily Pseudaspininae, forming a strongly supported sister relationship with the genus Rhynchocypris. This inference was further supported by Kimura two-parameter (K2P) genetic distance analyses, which revealed the smallest divergence between P. grumi and Rhynchocypris species (0.1620–0.1703), markedly smaller than that observed between P. grumi and core Phoxinus species (0.2475–0.2558). Conclusions: Together, these results support the placement of P. grumi within the East Asian Pseudaspininae lineage and help clarify its taxonomic position, which has long been debated. The complete mitochondrial genome of P. grumi provides additional mitogenomic data for phylogenetic analyses of Leuciscidae and contributes to a better understanding of the evolutionary relationships and diversification of Far Eastern leuciscids. These findings may also provide a molecular basis for future studies on the conservation genetics and environmental adaptation of this endemic cold-water fish from the arid Turpan Basin in northwestern China.