Fig 3. Overall similarity in patterns of gene expression within and among developmental stages of B. pallida galls and normally developing oak buds.

Principle component analysis in DESeq2 of (A) gall wasp genes in gall tissues, (B) oak genes in gall tissues, and (C) oak genes in normal (ungalled) bud tissues. X-axes correspond to principle component one and y-axes to principle component two, and axis labels give the percentage of variance these axes explain in each analysis. The colour legend for each stage is given in the bottom-right quadrant. For both gall wasp and oak genes in gall samples, biologically independent replicates for the same developmental stage cluster together. Growth and Mature stage tissues are more similar for host oak tissues than they are for larval gall wasp expression. Stages S0-S4 of normally developing buds show incomplete differentiation by stage, while mature leaf tissues (S5) are clearly distinct from all earlier stages. Lack of clear separation between stages S0-S4 is maintained if S5 replicates are removed from the analysis (S2 Fig).