DNA methylation and expression levels in different TE subclasses. (A) Pie-chart diagram of TE distribution and relative occupancy (expressed as cumulative size) in the T. melanosporum genome. (B) The total number of TEs in each subclass (black bars) and the number of expressed TEs (RPKM >1) in FB (red bars) and FLM (striped red bars) are indicated. Percentage values shown above solid red and striped bars indicate the fraction of expressed TEs in each subclass. (C,D) Box plots of CG methylation (C) and expression levels (D) for the indicated TE subclasses in FB (white bars) and FLM (striped bars). Median methylation levels in (C) are close to zero for non-LTR retrotransposons. TE classes with different expression levels in FB and FLM are indicated (t-test significance: **P-value <0.001; *P-value <0.05). Log2 RPKM values in (D) are only reported for TEs with at least one mapped read (RPKM >0). (E) Box plot of all TEs (white bars) and TEs expressed in at least one developmental stage (FB/FLM) (red bars).