A phylogenomic atlas of PP2C and PYL families across 377 plant genomes illuminates the evolution of core ABA signalling

Abscisic acid (ABA) receptors of the PYR/PYL/RCAR (PYL) family and ABA-related clade A type 2C protein phosphatases (PP2Cs) form an obligate co-receptor pair in which the receptor’s principal biochemical output is inhibition of its partner phosphatase. Whether such physically coupled families are also coupled evolutionarily has not been tested at genomic scale. We analysed 3315 PYL and 29 808 PP2C genes across 377 plant genomes spanning nine major lineages as a single interacting module. Phylogenetic generalized least squares regression revealed significant copy-number coupling after correcting for phylogenetic non-independence and total protein-coding gene number, and branch-wise evolutionary rates of orthologous PYR1-like PYLs and ABA-related clade A PP2Cs covaried across matched terminal branches. The families differed sharply in origin: PP2Cs resolved into four clades comprising 15 sub-lineages, all four clades already represented in algae, whereas two sub-lineages arose only in land plants and the sublineage containing the canonical ABA-related clade A phosphatases occurred in only two of 26 algal genomes; PYLs were confined to land plants. This asymmetry supports a model in which ligand-gated receptor control was superimposed on a pre-existing phosphatase scaffold during terrestrialization. Dispersed duplication dominated in algae and early-diverging lineages, whole-genome and segmental duplication drove angiosperm expansion, and PP2Cs were embedded in far denser transcription-factor networks than PYLs, suggesting that ABA output is tuned preferentially through PP2C rewiring. Yeast one-hybrid and electrophoretic mobility shift assays demonstrated direct binding of CdHOX and CdNAC to the CdPYL04 and CdPP2C105 promoters in bermudagrass, where antisense silencing produced opposing oxidative phenotypes under cold stress.