Figure 5. Differentially expressed genes detected by RNA-Seq.

(A) Percentage of differentially expressed genes in pair-wise comparisons of tissue types. Genes with 4 fold RPKM (reads per kilobase per million) differences were considered to be differentially expressed (negative binomial exact test p<0.001, p value adjusted with Benjamini & Hochberg correction, Table S12) (B) Gene families showing differential expression between vegetative tissue (mycelia and sporulating mycelia) and pre-infection tissues (cysts and germinating cysts). CBEL:fungal Cellulose Binding Domain Like protein, EGF:(Epidermal Growth Factor, gal_lectin: Galactose binding Lectin domain, HST: Heat shock factors, PLAC8: Placenta-specific gene 8 protein, SDF: Sodium Dicarboxylate symporter Family (Table S13). (C) Growth phase specific expression of peptidases and protease inhibitors (Table S14). (D) Relative abundance of S. parasitica and fish transcripts during interaction. (E). S. parasitica transcript distribution in pre-infection versus vegetative tissue. logFC = log₂(pre-infection/vegetative/pre-infection); logConc = the log2 of average reads counts per million of each gene in the two tissue types,). Red dots indicate significant differences (p<0.001; negative binomial test).