Evolutionary trajectories of the PP2C gene family across 402 plant genomes and pan-genomic diversification in Brassica rapa
Protein phosphatase 2C (PP2C) proteins are central regulators of plant signaling and stress responses, yet their macroevolutionary origin and diversification across the plant kingdom remain incompletely resolved. In this study, we performed a large-scale genome-wide analysis of the PP2C gene family using 402 representative plant genomes and integrated phylogenetic, duplication type, motif, expression, pangenome and selection-pressure analyses. A total of 36 960 PP2C genes were identified, showing substantial lineage-specific copy-number variation and marked expansion in angiosperms. Phylogenetic reconstruction classified plant PP2Cs into 12 subfamilies within three major clades and indicated that most subfamilies originated before the establishment of land plants, whereas angiosperm diversification mainly involved quantitative expansion rather than the emergence of new subfamilies. Duplication analysis revealed that dispersed and WGD/segmental duplication were the principal forces driving PP2C expansion, while phylogenetic tree reconciliation suggested extensive lineage-specific retention and loss after ancestral duplication events. Conserved motif analysis showed strong preservation of the catalytic scaffold, especially Motif1–Motif3 and Motif5, together with flexible remodeling of peripheral motifs. Cross-species transcriptome profiling in seven angiosperms revealed phylogenetically structured expression divergence: Clade II retained broad hormone, tissue and stress responsiveness, whereas Clades I and III displayed more condition- and organ-specific specialization. In 18 Brassica rapa accessions, 2478 PP2C genes were identified, most of which belonged to core orthogroups and syntenic regions. Ka/Ks analysis further indicated predominant purifying selection, with relaxed constraints in non-core genes. Collectively, these results provide a comprehensive evolutionary framework for PP2C functional diversification and candidate resources for stress-resistance improvement in horticultural crops.