Integrative Transcriptomic and Evolutionary Analysis of Drought and Heat Stress Responses in Solanum tuberosum and Solanum lycopersicum

Abiotic stresses such as drought and heat severely constrain the growth and productivity of Solanaceae crops, including potato (Solanum tuberosum L.) and tomato (Solanum lycopersicum L.), yet the conserved regulatory mechanisms underlying their stress adaptation remain incompletely understood. Here, we performed an integrative meta-analysis of publicly available transcriptomic datasets, complemented by comparative and evolutionary analyses across the Solanum genus. Functional annotation revealed coordinated transcriptional reprogramming characterized by induction of protective processes, including molecular chaperone activity, oxidative stress responses, and immune signaling, accompanied by repression of photosynthetic and primary metabolic pathways, reflecting energy reallocation under stress conditions. Promoter motif and transcription factor enrichment analyses implicated the bZIP, bHLH, DOF, and BBR/BPC families as central regulators of drought- and heat-induced transcriptional programs. Orthogroup inference and $K_a/K_s$ analysis across representative Solanum species demonstrated a predominance of purifying selection, indicating evolutionary conservation of regulatory network architecture. Integration of motif occurrence, co-expression profiles, and protein–protein interaction data enabled reconstruction of regulatory networks and identification of conserved hub transcription factors coordinating stress responses. Comparative analysis revealed distinct but conserved transcriptional signatures for heat and drought shared between potato and tomato, indicative of conserved abiotic stress strategies across Solanaceae.