Fig. 4

Heatmap obtained by clustering the 1207 Leptosphaeria maculans genes upregulated in planta. For each set of conditions, we calculated the mean FPKM value of the replicates, which we then subjected to Log₂ transformation and scaling. The self-organizing map method was used on the Log₂(FPKM+ 1) values, to define eight expression clusters (clusters 1 to 8) for the 1207 genes. The level of expression ranged from 4 (yellow) to − 4 (green). Genes located in AT-rich regions (AT) or encoding small secreted proteins (SSPs) are indicated by red and black lines, respectively, on the left. The conditions are described in the legend to the x-axis of the heatmap. Three sample features are described: (i) the experimental conditions: IPF, in planta field conditions; IPC, in planta controlled conditions; RF, residues in field conditions; (ii) the type of plant tissue sampled; and (iii) the sampling time points (DPI, days post inoculation; MPS, months post sowing; MPH, months post harvest. The ten sets of in vitro conditions are ordered as follows: conidia (a. non-germinating, b. germinating); incompatible mating conditions (c. JN2 x JN2 7 days (d), d. JN2 x JN2 20d, e. JN2 x JN2 35d); compatible mating conditions (f. JN2 x Nz-T4 7d, g. JN2 x Nzt4 20d, h. JN2 x Nz-T4 35d); mycelial growth (i. in liquid medium, j. on solid medium)