Fig. 1: Overview of the experimental design and genetic and transcriptome relationships among the yeast strains.

a Schematic representation of the experimental workflow. MA strains, derived from the ancestral strain BY4741 through a laboratory mutation accumulation experiment, and natural strains, collected from natural environments, were cultured in four distinct conditions. Transcriptome were sequenced using a high-throughput platform. The four colors represent four different environments, and the black and gray dots in the scatter plot correspond to natural strains and MA lines. Created in BioRender https://biorender.com/x07m898. b Phylogenetic relationship among the MA lines. c Phylogenetic relationship among the natural strains. Phylogenetic trees were reconstructed using the maximum likelihood method implemented in IQ-TREE (v3.0.1) based on all identified variant sites. The TVM substitution model was applied, as determined by model selection within IQ-TREE. d Growth rate of the ancestor BY4741, 15 MA lines, and 22 natural strains in the four environments, with the ancestral strain BY4741 represented by a black triangle. The center black lines represent the median; the box represents the 25th–75th percentiles; whiskers extend to 1.5× IQR; and points beyond the whiskers indicate outliers. P values were calculated using two-sided t-tests. “***” represents P < 0.001 and “****” represents P < 0.0001. e UMAP visualization of gene expression profiles for the ancestor BY4741, 15 MA lines, and 22 natural strains. Colors represent different environments, and shapes represent distinct strain groups.