Genome-wide identification and transcriptional characterization of the receptor-like kinase (RLK) gene family in Coffea arabica var. Geisha during Hemileia vastatrix colonization

Carrillo-Ordoñez G.A.; Carrasco-Lozano E.C.; Correa F.; Bustamante D.E.; Calderon M.S. · Physiological and Molecular Plant Pathology (2026) · DOI: 10.1016/j.pmpp.2026.103217

Resumen

Receptor-like kinases (RLKs) serve as primary sensors for pathogen-associated molecular patterns (PAMPs) and trigger pattern-activated immunity (PTI) in plants. Through deep genomic analysis of Coffea arabica var. Geisha, we identified 634 RLK genes (CaRLK) distributed on 22 chromosomes and classified them into 29 groups and 58 subfamilies. The most abundant subfamilies were leucine-rich repeats (LRRs) and receptor-like cytoplasmic kinases (RLCKs), with 249 and 145 proteins, respectively. Physicochemical analysis revealed that most RLKs were medium-sized, acidic, stable, thermostable and predominantly hydrophilic. Gene Ontology (GO) analysis revealed that CaRLK proteins were involved primarily in protein phosphorylation events at the plasma membrane and were integral to plant‒pathogen interactions. Three-dimensional structural predictions revealed that LRR-RLKs shared homology with FERONIA, LysM-like receptors, RIPK, and the well-established receptor FLS2, whereas RLCKs were similar to proteins such as CARK1 and BIR2, supporting their roles in plant‒pathogen interactions. Analysis of the cis -regulatory region of CaRLK genes predicted for plant‒pathogen interactions revealed the presence of transcription factor binding motifs for phytohormone and fungal elicitor responses, suggesting tightly controlled transcriptional regulation during pathogen invasion. Quantitative RT‒PCR profiling of C. arabica var. Geisha during the initial symptomatic stages of Hemileia vastatrix infection under field condition revealed distinct patterns of CaRLK gene regulation. Specifically, CaLRRII , CaLRRXIIb and CaLysMI were upregulated, whereas CaLRRXI , CaLRRVII , CaLRRXII , CaCrRLKLI and CaRLCKVIII were downregulated. Our results suggest that CaRLK genes, given their structural diversity and regulatory involvement, could be essential candidate targets for the development of resistance strategies against the fungus H. vastatrix .

Instituciones: Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas