Fig. 2

Genes of Venturia inaequalis upregulated during infection of susceptible apple cultivar ‘Royal Gala’ display five distinct temporal waves of expression. A Expression profile of the five distinct temporal expression waves at 12 and 24 h post-inoculation (hpi), as well as 2, 3, 5 and 7 days post-inoculation (dpi), relative to growth in culture on the surface of cellophane membranes overlaying potato dextrose agar at 7 dpi. B Heatmap of all V. inaequalis genes upregulated in planta when compared with growth in culture. Gene expression data are scaled rlog-normalized counts across all samples (Z-score), averaged from four biological replicates. Genes upregulated in planta were clustered using hclust according to the Ward.D2 and Euclidean distance methods. Early (12 and 24 hpi), mid (2 and 3 dpi) and mid-late infection (5 and 7 dpi) refer to the stage of infection where peak gene expression was observed. Coloured block labels on the left indicate gene expression waves. Numbers in brackets indicate number of genes per wave. The black asterisk indicates the wave significantly enriched for genes encoding effector candidates (ECs) (p value: 3.644e−14). Grey boxes indicate enriched gene ontology (GO) terms. p: p value