Figure 1.

Overview of the infection transcriptomic sequence analyses. (A) Photographs of representative infected wheat leaves for the entire time course of the experiment (3–56 days post‐infection, dpi). (B) Total RNAseq reads originating from both fungal and wheat transcripts were aligned against the IPO323 reference genome of Zymoseptoria tritici. The percentage of aligned reads is indicative of the fungal biomass accumulation in infected leaves (Rudd et al., 2015). Two RNAseq datasets were generated: a six‐time‐point experiment spanning 3–56 dpi, termed ‘Time course’, and a replicated three‐time‐point experiment comprising 7, 13 and 56 dpi, termed ‘Replicated dataset’. Variation among replicates is expressed as the standard error. (C) Normalized transcription profiles of all Z. tritici genes based on the six‐time‐point experiment were clustered using self‐organizing maps. A robust clustering algorithm was used to identify seven main transcription profile clusters. The transcription profile clusters were characterized according to peak transcription and assigned to the different stages of the infection. Standard errors show variation among the genes included in each cluster. (D) For each of the seven main transcription profile clusters, the number of genes and the percentage of genes for which a secretory function was predicted (Morais do Amaral et al., 2012) are shown.