Fig. 3

Pipeline used to describe Leptosphaeria maculans genes overexpressed in at least one condition in planta. We found that 1207 of the 13,047 annotated genes were overexpressed in at least one of the 22 sets of conditions in planta relative to the 10 sets of in vitro conditions. These genes included 272 predicted to encode small secreted proteins (SSPs). We analyzed the set of 1207 genes to identify the major expression profiles by gene expression clustering. We defined eight expression clusters (clusters 1 to 8). For each cluster, we analyzed expression patterns, functional enrichment, and the genomic localization of the genes. For the specific detection of highly coregulated waves of SSPs, we performed a linear regression analysis of the mean expression value for each SSP subset present in each cluster against the expression of all 13,047 genes. This analysis identified 95 SSP genes and 185 non-SSP genes as highly coregulated genes