Downregulation is the dominant effect of new regulatory mutations in a fungal pathogen

Well-tuned gene regulation is essential for an organism’s survival. However, the ancestral state and predominant effects of regulatory mutations remain poorly understood outside of model fungi, such as Baker’s yeast with a highly compact genome organization. Here, we analysed a large panel of genome sequencing data of the major fungal wheat pathogen Zymoseptoria tritici to recapitulate the evolutionary history of cis -regulatory mutations. We found that new mutations are predominantly linked with the downregulation of the associated genes. The dominance of downregulation is reinforced for mutations occurring closest to the coding sequence and downstream. Mutations associated with the strongest downregulation segregate at high frequencies in populations despite their recent origin. This suggests that selection may have played a role in their rapid increase since speciation. Overall, our study highlights the power of mapping populations combined with genomic surveys to unravel fundamental patterns of regulatory evolution.