Genome-wide analysis, expression profiling and molecular docking of tomato (Solanum lycopersicum) calmodulin (SlCaM) proteins in cadmium stress adaptation

Calcium ions (Ca²⁺) are essential for plant development and stress responses, including heavy metal (HM) stress. However, the roles and mechanisms of calmodulin proteins (SlCalMs) in mediating cadmium (Cd) stress in Solanum lycopersicum, a model crop, remain poorly understood. This study aimed to investigate the calcium-mediated stress response in S. lycopersicum by identifying and characterizing the SlCalMs gene family, a key subfamily of calcium-binding proteins (CBPs), to elucidate their potential roles in stress tolerance. A genome-wide identification of SlCalMs was conducted using Oryza sativa sequences as a reference. Bioinformatics analyses included BLASTP searches, sequence alignment, phylogenetics, assessment of physicochemical properties, gene structure and motif analysis, chromosomal mapping and duplication events. Gene expression was assessed under Cd stress using RNA-seq and validated by quantitative real-time polymerase chain reaction (qRT-PCR). Molecular docking simulations evaluated Cd-binding affinities, and protein–protein interaction networks, and Gene Ontology (GO) enrichment were used to explore biological functions. Eight distinct SlCalM groups were identified, varying in gene size, exon number and isoelectric point. Conserved motifs, exon–intron patterns and stress-responsive cis-elements were identified. Chromosomal analysis revealed segmental duplications. Under Cd stress, several SlCalMs showed differential expression; notably, Solyc04g077830 was significantly downregulated and showed strong Cd-binding affinity in silico, suggesting a role in Cd sequestration. GO and interaction network analyses confirmed their involvement in Ca²⁺ signalling, metal ion binding and stress-related pathways. This study provides comprehensive insight into the structure, evolution and functional roles of SlCalMs in tomato. Their involvement in Ca²⁺ signalling and Cd stress response highlights their potential for improving HM tolerance, offering valuable targets for future genetic or biotechnological interventions in crop improvement.