Differential gene expression in wild and cultivated cacti reveals diverse metabolic pathways for stressful environments

Background and aims Comparing field and horticultural (common garden) conditions is particularly relevant to understanding many aspects of plant physiology, phenotypic plasticity, and environmental adaptation. Species that reproduce through vegetative propagation offer a unique opportunity to study gene expression changes in the same genetic material across wild and controlled environments. Here, we investigate patterns of differential gene expression in five target species of the genus Cereus Mill. (Cactaceae), which occur across distinct biomes. The studied species include Cereus jamacaru DC, C. calcirupicola Ritter, C. pierre-braunianus Esteves, C. hildmannianus K.Schum, and C. fernambucensis Lem. Methods Epidermal tissue was collected from three adult individuals per species in the wild, alongside stems for greenhouse cultivation under standardized soil, lighting, nutritional, and watering conditions. After one year, epidermal tissue was recollected from the same individuals for RNA extractions. Whole transcriptomes from wild and common garden samples (30 transcriptomes) were analyzed for differential gene expression and co-expression patterns. Key Results Genes upregulated under wild conditions (WT) predominantly related to stress response and defense pathways, contrasting with those expressed in common garden (CG) conditions. Gene expression plasticity across diverse metabolic pathways highlights significant environmental responses, with distinct patterns linked to the phytogeographic domain and biome-specific factors. Conclusions Cereus species demonstrate significant gene expression plasticity, with stress-response and metabolic regulation genes enabling adaptation to diverse environmental pressures. This flexibility underscores their ecological and evolutionary resilience in arid and nutrient-poor habitats.