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Summary  The cyclic adenosine monophosphate–protein kinase A (c AMP – PKA ) pathway is a central signalling cascade that transmits extracellular stimuli and governs cell responses through the second messenger cAMP. The importance of cAMP signalling in fungal biology has been well documented and the key conserved components, adenylate cyclase ( AC ) and the catalytic subunit of  PKA  ( CPKA ), have been functionally characterized. However, other genes involved in this signalling pathway and their regulation are not well understood in filamentous fungi. Here, we performed a comparative transcriptomics analysis of  AC  and  CPKA  mutants in two closely related fungi:   F usarium graminearum  ( Fg ) and   F . verticillioides  ( Fv ). Combining available  Fg  transcriptomics and phenomics data, we reconstructed the  Fg  cAMP signalling pathway. We developed a computational program that combines sequence conservation and patterns of orthologous gene expression to facilitate global transcriptomics comparisons between different organisms. We observed highly correlated expression patterns for most orthologues (80%) between  Fg  and  Fv.  We also identified a subset of 482 (6%) diverged orthologues, whose expression under all conditions was at least 50% higher in one genome than in the other. This enabled us to dissect the conserved and unique portions of the cAMP– PKA  pathway. Although the conserved portions controlled essential functions, such as metabolism, the cell cycle, chromatin remodelling and the oxidative stress response, the diverged portions had species‐specific roles, such as the production and detoxification of secondary metabolites unique to each species. The evolution of the cAMP– PKA  signalling pathway seems to have contributed directly to fungal divergence and niche adaptation.

molecular plant pathology

Conservation and divergence of the cyclic adenosine monophosphate–protein kinase A (cAMP– PKA ) pathway in two plant‐pathogenic fungi:  Fusarium graminearum  and   F . verticillioides