Figure captions
Figure 1: Left panel : ordination plots of the distance-based redundancy analysis (dbRDA) on the epigenetic distances between cadmium-treated and control plants (Cd vs. C; A1), and between copper-treated and control plants (Cu vs. C; A2) from four populations of the copper moss Scopelophila cataractae (n = 2-3 replicates per population and treatment). RDA1: first constrained ordination axis explaining 20.6 (A1) and 15.2 (A2) of the total variance of the data; RDA2: second constrained ordination axis explaining 14.3 (A1) and 13.3 (A2) of the total variance of the data. Asterisks mark overlapping observations from the same group. Central panel : difference in the methylation level (i.e. methylation change) of differentially methylated cytosine positions (DMPs; fdr < 0.05) between cadmium-treated and control plants (Cd vs. C; B1), and between copper-treated and control plants (Cu vs. C; B2) from four populations of the copper moss Scopelophila cataractae (Sc1 to Sc4); values at the bottom of each graph indicate the number of DMPs for each contrast (↑: up-methylated; ↓: down-methylated); red lines delimit the area in which absolute methylation differences are lower than 10.Right panel : multidimensional scaling (MDS) plot of the gene expression profiles in control and Cu-treated samples from two populations of the copper moss Scopelophila cataractae (Sc3 and Sc4; C1). Heatmap of the normalized expression levels (i.e. Row z-scores) of the differentially expressed transcripts in response to Cu shared between Sc3 and Sc4 (C2).
Figure 2: Top panel : word cloud representation of gene ontology (GO) terms related to all molecular functions significantly over-represented in the list of differentially expressed transcripts (DETs) in response to Cu in Sc3 (A; n=22 GOs) and Sc4 (B; n=4 GOs). The size of the words is proportional to the frequency of the GO term in the DETs list. GOs inside grey rectangles show under-represented terms in the DETs’ list. Bottom panel : circular plots of the functional categories created by grouping downregulated transcripts of Sc3 (C) and Sc4 (D) in response to Cu according to their annotation descriptions. The percent of transcripts within the group with respect to the total number of DETs is shown between parentheses. N: total number of DETs included in this classification for each population.