Structural and expression divergence of WAK/WAKL receptor-like kinases in Phaseolus vulgaris reveals candidate mediators of resistance to Colletotrichum lindemuthianum

Background Wall-associated kinases (WAKs) and WAK-like proteins (WAKLs) are receptor-like kinases implicated in plant perception of extracellular cues and immune signaling. In common bean (Phaseolus vulgaris), differential resistance to Colletotrichum lindemuthianum offers an opportunity to link structural variation in these receptors to functional outcomes. Results Here, we systematically characterize the WAK/WAKL family in P. vulgaris, integrating domain architecture, gene structure, phylogeny, synteny, and transcriptomic responses in resistant (Ouro Vermelho) versus susceptible (Estilo) cultivars across infection time points. Using conserved domain annotation, PvWAKs and PvWAKLs were classified based on combinations of extracellular domains (EGF and GUB_WAK_bind) while retaining a conserved intracellular kinase core. Twenty-five distinct domains were identified, with specific sets being common or exclusive to each group, suggesting modular diversification of interaction interfaces. Phylogenetic and gene structure analyses revealed evolutionary patterns consistent with both conservation of signaling machinery and divergence in extracellular features. Integration with synteny supported retention of candidate orthologs across related species. RNA-Seq profiling at 0, 48, and 96 hours post-inoculation uncovered complex, genotype- and time-dependent expression dynamics: subsets of PvWAK/WAKL genes were differentially expressed uniquely in resistant or susceptible backgrounds, while others displayed opposing temporal patterns, highlighting nuanced regulatory contributions to resistance. Combining structural and expression evidence yielded a prioritized list of PvWAK/WAKL candidates potentially underlying anthracnose resistance. Conclusions The study delineates how conserved kinase signaling is coupled to extracellular domain variability and dynamic expression to enable functional divergence within the WAK/WAKL family in P. vulgaris. The resulting candidate genes provide a focused basis for functional validation and may inform molecular breeding strategies for enhanced disease resistance.