Genome-wide identification, evolutionary analysis, and expression profiling of protein phosphatase 2C genes in sweet potato (Ipomoea batatas L.)

Protein phosphatase 2C ( PP2C ) genes, key regulators of cellular signaling and stress responses, were comprehensively identified and characterized at the genomic level in sweet potato ( Ipomoea batatas L.). A total of 50 PP2C genes were identified, exhibiting conserved domains and motif structures with variable exon–intron architectures, indicating functional diversification. IbPP2C genes were unevenly distributed across chromosomes, with notable clustering on linkage groups LG1, LG7, LG8, and LG13. Twelve duplicated gene pairs (six segmental and six tandem) were identified, most of which had Ka/Ks < 1, suggesting strng purifying selection during evolution. Phylogenetic analysis grouped PP2C proteins from five plant species into seven subfamilies (A–G). IbPP2Cs were unevenly distributed among these groups, revealing conserved evolutionary relationships and a common ancestral origin. Collinearity analysis revealed that IbPP2C genes exhibited stronger syntenic relationships with Arabidopsis thaliana PP2C s than with tomato PP2C s. Promoter analysis identified diverse hormone- and stress-responsive cis -elements, highlighting potential regulatory complexity. Gene expression profiling of selected IbPP2C genes using qRT-PCR under salt and drought stress revealed that IbPP2C8 showed the strongest induction under salt stress but minimal response to drought, whereas IbPP2C4 was suppressed under both salt and drought stress. These results present valuable insights into the evolutionary and functional dynamics of PP2C genes, contributing to improved stress resilience and crop sustainability in sweet potato.