Systematic characterization of purple acid phosphatases provides targets for improving phosphorus use efficiency in...

Purple acid phosphatase (PAP) genes are central to plant phosphorus metabolism and stress adaptation. However, their genome-wide characterization and functional roles in cotton remain unclear. Cotton often faces phosphorus limitation, affecting growth and fiber yield. In this study, we performed a comprehensive genome-wide analysis of PAP genes in four cotton species to elucidate their evolutionary patterns and potential roles in phosphorus use efficiency, stress response, and fiber development. A total of 202 PAP encoded proteins were identified, with 63 in G. hirsutum, 69 in G. barbadense, 35 each in G. arboreum, and G. raimondii, which were classified into eight conserved subgroups. Gene structure, motif composition, and phylogenetic analysis revealed strong evolutionary conservation with evidence of subfunctionalization. Chromosomal mapping, collinearity, and Ka/Ks analysis indicated that segmental and whole-genome duplications primarily drove PAP expansion, with most genes retained under purifying selection. Promoter analysis uncovered abundant cis-elements associated with stress and hormone responses, suggesting tight transcriptional regulation under developmental and experimental cues. Expression profiling revealed tissue-specific and Pi-responsive regulation, highlighting the involvement of PAPs in root Pi acquisition, reproductive growth, and fiber development. Co-expression analysis further identified key hub genes, regulating vegetative growth (Gh_A13G1171), reproduction (Gh_D05G1806), fiber development (Gh_D05G0522), and P metabolism (Gh_A03G0451). Collectively, this study provides the first systematic characterization of the cotton PAP gene family, offering new insights into their evolutionary dynamics and functional roles, and identifies promising genetic targets for improving P use efficiency and stress resilience in cotton.