Figure 3: Presence and sequence similarity of symbiosis-upregulated genes from L. bicolor in 55 genomes of saprotrophic (white rots, brown rots, soil and litter decayers), mycorrhizal (ECM, ERM and ORM), pathogenic and endophytic fungi.

The heat map depicts a double-hierarchical clustering of 588 symbiosis-upregulated L. bicolor genes (rows, fold change >5, false discovery rate–corrected P < 0.05; Supplementary Data Set 1) based on their percentage sequence identity (color scale at left) with their orthologs (if any) in selected fungal species (columns). Right, color-coded gene clusters (clusters I to VI), with dots representing differentially expressed genes upregulated >100-fold; for genes with regulation less than 100-fold, the fold-change value is set to 1 (majority of the genes). The x axis is a logarithmic scale of the fold change in gene expression (natural algorithm with Euler's number). Genes of cluster VI are L. bicolor–specific (orphan) genes, whereas genes of cluster V have sequence similarity only with predicted proteins of the sister species L. amethystina. Double-hierarchical-clustering heat maps of symbiosis-upregulated genes for the ECM A. muscaria, H. cylindrosporum, P. involutus, P. croceum, S. luteus, the orchid mycorrhizal T. calospora, the ericoid mycorrhizal Oidiodendron maius, the endophytic S. vermifera and the brown-rot S. lacrymans are shown in Supplementary Figure 25, whereas double-hierarchical-clustering heat maps of symbiosis-downregulated genes are shown in Supplementary Figure 26. Species abbreviations are in Supplementary Table 1.