Molecular Mechanisms Underlying the Claviceps purpurea–Secale cereale Interaction: From Floral Biotrophy to Ergot Alkaloid Biosynthesis

Claviceps purpurea is a highly specialized biotrophic ascomycete that colonizes floral tissues of grasses, including economically important cereal crops, causing ergot disease and producing ergot alkaloids with significant agricultural, pharmaceutical, and biotechnological relevance. Despite extensive research on its biology and secondary metabolism, the molecular mechanisms underlying host recognition, floral specificity, establishment of biotrophy, and developmental differentiation remain incompletely understood. This review integrates current knowledge derived from genomic, transcriptomic, proteomic, metabolomic, and functional genetic studies to provide an overview of the molecular basis of the C. purpurea–host interaction. Particular emphasis is placed on recent advances in fungal development, host immune modulation, hormonal signalling, sclerotial differentiation, and ergot alkaloid biosynthesis. Current evidence indicates that successful colonization depends on coordinated regulation of host recognition, secretion of effector proteins, carbohydrate-active enzymes, and manipulation of host signalling pathways to establish and maintain a biotrophic lifestyle. The transition from the sphacelial stage to sclerotial development represents a major developmental and metabolic reprogramming event associated with fungal differentiation and activation of the ergot alkaloid biosynthetic pathway. Recent multi-omics approaches have further revealed complex regulatory networks connecting fungal development and secondary metabolism. Claviceps purpurea has emerged as a valuable model for studying floral biotrophy and fungal secondary metabolism; however, key questions remain regarding the molecular basis of host specificity, effector function, hormonal crosstalk, and developmental regulation. Future integration of multi-omics approaches with functional genomics will be essential to resolve these processes and to support sustainable disease management strategies and the biotechnological exploitation of ergot alkaloids.