• The genes atp6, atp8, ccmB, nad4L, rpl10, and sdh4 are potential molecular markers for phylogenetic studies in Rosaceae. • Two predicted configurations mediated by repeat pairs reveal diverse recombination patterns within the Docynia delavayi mitogenome, informing its evolutionary dynamics. • The mitochondrial genome of D. delavayi exhibits highly conserved tRNA evolution, evidenced by intact tRNA genes and a minimal proportion (0.30%; 1,188 bp) of mitochondrial plastid DNA (MTPT) sequences, supporting its reliability as a reference in evolutionary research. • Phylogenetic analysis of the D. delavayi mitogenome provides new genomic evidence supporting the delineation of Docynia as a distinct genus within Rosaceae. Docynia delavayi is a highly significant and promising economic fruit tree with edible, medicinal and landscaping values. Here, the mitogenome of D. delavayi was assembled, with a total length of 397,819 bp and 32 protein-coding genes (PCGs). A total of 129 simple sequence repeats and 495 dispersed repeat pairs were identified, which fell into four categories. Four of these repeat pairs may mediate homologous recombination. Only 12 pairs of mitochondrial plastid DNA fragments (MTPTs) were detected, accounting for 0.30% of the mitochondrial genome. Predictions based on all PCGs revealed 501 RNA editing sites. A clear preference for A or T at the third codon position in the PCGs by codon usage analysis. Moreover, selection pressure analysis indicated that most PCGs have undergone purifying selection. Collinearity analysis revealed extensive genomic rearrangements and structural divergence between D. delavayi and its close relatives. Finally, mitochondrial phylogenomic analysis supported its recognition as a distinct genus within Rosaceae. This mitochondrial genome provides a foundation for further studies on the taxonomy, phylogeny, and evolution of D. delavayi .
Liu et al. (2026) studied this question.