The Cucumis sativus kinome: identification, annotation, and expression patterns in response to powdery mildew infection

Protein kinases (PKs) are key regulators of plant development and responses to biotic and abiotic stresses. However, a comprehensive characterization of this superfamily remains lacking in cucumber ( Cucumis sativus), particularly regarding its role in powdery mildew resistance caused by Podosphaera xanthii. Here, we identified and characterized the cucumber kinome using Hidden Markov Models (HMMs), revealing 835 PKs distributed across seven chromosomes and classified into 20 groups and 123 families, with RLKs being the most abundant. Gene structure, domain composition, and subcellular localization analyses highlighted substantial structural and functional diversity. Tandem and whole-genome duplication events contributed significantly to PK expansion. Transcriptomic analyses using RNA-seq data from resistant and susceptible cultivars inoculated with P. xanthii revealed between 8 and 105 differentially expressed PK genes (DEGs), depending on the comparison. A greater number of PK DEGs were detected in susceptible genotypes, many of which are putatively associated with signaling pathways and cell cycle regulation. The expression of specific RLKs, MAPKs, CAMKs, and cyclin-dependent kinases suggests their role in defense responses. These findings enhance our understanding of the cucumber kinome and signal the potential of specific PKs in plant–pathogen interactions, providing a foundation for future functional studies and resistance-focused breeding strategies.