Genome-Wide Identification and Characterization of Apple P3A-Type ATPase Genes, with Implications for Alkaline Stress Responses

The P-3A-type ATPases play crucial roles in various physiological processes via the generation of a transmembrane H+ gradient (pH). However, the P-3A-type ATPase superfamily in apple remains relatively uncharacterized. In this study, 15 apple P-3A-type ATPase genes were identified based on the new GDDH13 draft genome sequence. The exon-intron organization of these genes, the physical and chemical properties, and conserved motifs of the encoded enzymes were investigated. Analyses of the chromosome localization and omega values of the apple P-3A-type ATPase genes revealed the duplicated genes were influenced by purifying selection pressure. Six clades and frequent old duplication events were detected. Moreover, the significance of differences in the evolutionary rates of the P-3A-type ATPase genes were revealed. An expression analysis indicated that all of the P-3A-type ATPase genes were specifically expressed in more than one tissue. The expression of one P-3A-type ATPase gene (MD15G1108400) was significantly upregulated in response to alkaline stress. Furthermore, a subcellular localization assay indicated that MD15G1108400 is targeted to the plasma membrane. These results imply that MD15G1108400 may be involved in responses to alkaline stress. Our data provide insights into the molecular characteristics and evolutionary patterns of the apple P-3A-type ATPase gene family and provide a theoretical foundation for future in-depth functional characterizations of P-3A-type ATPase genes under alkaline conditions.