Pan-genome analysis of the P-type ATPase gene family in Prunus mume and functional characterization of PmAHA3 in organic acid accumulation

Organic acid accumulation is a key determinant of fruit flavor and processing quality in Prunus mume, yet its underlying molecular mechanisms remain poorly understood. P-type ATPases are membrane proteins that drive the active transport of ions and molecules via ATP hydrolysis and play important roles in organic acid accumulation However, their genome-wide features and functions in P. mume remain poorly understood. Here, 49 P-type ATPase genes were identified from the P. mume pan-genome, including 29 core, 6 near-core, 11 dispensable, and 3 private genes, and classified into six subfamilies. Dispersed and whole-genome duplication were the major force driving gene family expansion, and most genes experienced strong negative selection. Expression profiling identified the P3A-type gene PmAHA3 as highly expressed in fruit, with vacuolar membrane localization. Both transient RNAi silencing in fruit and CRISPR/Cas9 knockout in callus significantly reduced the contents of malic and citric acid, demonstrating their roles in organic acid accumulation. These results provide insight into the evolution and function of P-type ATPases, offering potential targets for improving fruit quality.