Fig. 3.

Shown are hierarchical clustering of logtwofold changes of TE centroids differentially expressed in at least one high-CO₂ phenotype treatment (A), the distribution of TE copies within different genomic elements (B), and the distribution of TE centroids and their corresponding genome copies (C). (A) Hierarchical clustering of log-twofold changes of differentially expressed TE centroids in at least one high-CO₂ phenotype treatment (SI Materials and Methods) resulting in two well-defined clusters with one representing TE centroids with increased average log-twofold changes in the high-CO₂ phenotype (blue) treatments relative to the 380-selected and vice versa for the “decreased” cluster (red). Bolded/asterisked labels indicate differentially expressed TE clusters in all high-CO₂ phenotype treatments vs. the 380-selected treatment. (B) Pie chart of the distribution of all detected TE copies in the genome. (C) A genome plot of TE centroids and their corresponding copies as well as all detected TE copies in the genome. Going from outside to inside: Track 1 shows TE copies in the genome on the forward strand and is colored according to genomic element. Track 2 is the same, but on the minus strand. Track 3 contains the names and symbols for differentially expressed TE centroids in A relative to the 380-selected treatment. Track 4 shows the distribution of the corresponding copies of differentially expressed TE centroids in track 3 via blue and red colored links. Underlying gray links represent paralogous copies from TE clusters showing no change in expression.