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.