Fig. 3

C. intermedia growth, sugar consumption and transcriptional profiles in media with different sugar compositions. a–d Growth (OD₆₀₀) and extracellular sugar and metabolite concentrations over time. µmax represents the maximum growth rate (h⁻¹) of the cultures. Vertical dashed lines represent the sampling time points for RNA-seq. e MDS plot of gene expression of 12 RNA-seq libraries. Samples cluster by carbon source and concentration. f Heatmap plot of differently expressed genes using the hierarchical clustering method, displaying seven main clusters. Each row of the heatmap represents the z-score transformed log 2 values of one differentially expressed gene across all samples (blue, low expression; red, high expression). Colours above the heatmap indicate carbon source and concentration (G20—glucose 20 g L⁻¹; G200—glucose 200 g L⁻¹; X20—xylose 20 g L⁻¹; X20—xylose 200 g L⁻¹). The dendrogram displays how the samples cluster based on their differential expression patterns