Fig. 3: Differential gene expression between roots and peat matrix for robust bacterial root colonizers.
a Circle plot (computed with circos83) depicting differentially expressed genes (DEGs) for the top 20 abundant bacterial root colonizers. DEGs (roots vs matrix samples) were computed independently for each strain using DESeq239. The outer ring indicates strain phylogeny (order), transcripts log2FC is represented on the y axis (8, 0, −8 log2FC scale) and transcripts are colored in green if upregulated in roots (log2FC > 1.5), orange if downregulated in roots (log2FC < −1.5) and dark gray if not differentially enriched between roots and matrix. The inner gray barplot depicts the relative abundance (%) of each strain in root samples (see also Fig. 1a). Principal coordinate analysis based on Bray–Curtis distances between bacterial strains in all samples computed on orthogroup relative abundances (relative number of transcripts) colored by orders (b) and sample types (c). All samples are represented for each strain (i.e., 6 samples per strain). Principal coordinate analysis based on Bray–Curtis distances between fungal strains in all samples computed on orthogroup relative abundances (relative number of transcripts) colored by orders (d) and sample types (e). All samples are represented for each strain (i.e., 6 samples per strain). Source data are provided as a Source Data file.
