Time series transcriptome of Venturia inaequalis (apple scab) infecting Malus domestica (apple)

V. inaequalis causes apple scab disease, the most economically important disease of apples. In this study, we generated a comprehensive RNA-seq transcriptome of V. inaequalis during host colonization of apple, with six in planta time points (12hpi, 24hpi, 2dpi, 3dpi, 5dpi, 7dpi) and one in culture reference (fungus grown on cellophane membranes overlaying potato dextrose agar). Analysis of this transcriptome identified five in planta gene expression clusters or waves corresponding to three specific infection stages: early, mid and mid-late infection of subcuticular biotrophic host-colonization. In our analysis we focus on general fungal nutrition (plant cell wall degrading enzymes and transporters) as well as effectors (proteinaceous effectors and secondary metabolites). Early infection was characterized by the expression of genes that encode plant cell wall-degrading enzymes (PCWDEs) and proteins associated with oxidative stress responses. Mid-late infection was characterized by genes that encode PCWDEs and effector candidates (ECs). Overall design: Deatached apple leaves were infected with V. inaequalis MNH120 (also known as ICMP 13258 and Vi1) spores. Infected leaves were collected at 12hpi, 24hpi, 2dpi, 3dpi, 5dpi, 7dpi. As in culture reference, V. inaequalis spores were added to a cellophane membrane overlaying potato dextrose agar and mycelia grown on the cellophane membrane surface was collected at 7 dpi. Four biological replicates per time point were collected for each sample.