Abstract
Most species live in a variable environment in nature. Yet understanding the evolutionary processes underlying molecular adaptation to fluctuations remains a challenge. In this study we investigate the transcriptome of the fungal wheat pathogenZymoseptoria triticiafter experimental evolution under stable or fluctuating temperature, by comparing ancestral and evolved populations simultaneously. We found that temperature regimes could have a large and pervasive effect on the transcriptome evolution, with as much as 38% of the genes being differentially expressed between selection regimes. Although evolved lineages showed different changes of gene expression based on ancestral genotypes, we identified a set of genes responding specifically to fluctuation. We found that transcriptome evolution in fluctuating conditions was repeatable between parallel lineages initiated from the same genotype for about 60% of the differentially expressed genes. Further, we detected several hotspots of significantly differentially expressed genes in the genome, in regions known to be enriched in repetitive elements, including accessory chromosomes. Our findings also evidenced gene expression evolution toward a gain of robustness (loss of phenotypic plasticity) associated with the fluctuating regime, suggesting robustness is adaptive in changing environment. This work provides valuable insight into the role of transcriptional rewiring for rapid adaptation to abiotic changes in filamentous plant pathogens.