Adaptive evolution of transcriptome and transcriptomic plasticity in stable and fluctuating environments

Adaptation to new environments often involves multiple genes and can induce substantial changes in biological systems, but the overall consequences of the genetic response to specific environmental pressures remain poorly understood. Here, we investigate the large-scale effects of adaptation to new temperature regimes on the whole transcriptome from experimental evolution carried on the fungus Zymoseptoria tritici. Two distinct strains from the wild were grown in constant cool (17{degrees}C), constant warm (23{degrees}C), and fluctuating temperature environments, for about 250 clonal generations. The expression of > 10,000 genes was estimated by RNA-seq before and after evolution at several temperatures. We observed massive convergent change in both gene expression and gene expression plasticity. Fluctuating environments did not favor plastic gene expression in general, although fluctuating populations did evolve towards the optimal reaction norms. Some of our observations were at odds with common expectations; adaptive mutations were highly pleiotropic, and adaptation to stable temperature conditions did not match gene expression plasticity. We thus showed that the evolution of complex biological systems follow some general patterns which challenge gene-centered or quantitative genetics predictions.