Length-dependent TE DNA methylation in Spirodela polyrhiza. (A) CHG and CHH methylation levels (%) across all TEs (≥100 bp) in Arabidopsis and Spirodela split by size into short (≥100 bp, <500 bp), intermediate (>500 bp, ≤4 kbp), and long (>4 kbp). Number values for each size category in each genome is indicated within the plot for mCHH. (B) Waffle chart of the relative contribution of different TE superfamilies over the total genomic space occupied by TEs in Spirodela. (C,D) CG and CHG methylation levels (%) between different length range groups for RLC: Ty1/Copia (C) and RLG: Ty3/Gypsy (D) in Arabidopsis and Spirodela. Number values are indicated in panels G and H. (E,F) Presence and number of RCL (E) and RLG (F) TE protein domains, determined by TEsorter, across TE annotations of varying sizes in Arabidopsis and Spirodela. Bubble plots depict domain count distributions for TEs with at least one domain. Numbers above the TE size category denotes TE annotations with at least one domain, with percentages shown in brackets relative to total TE annotations per size category. (G,H). Bubble size is relative to the number of TEs (indicated within or next to the bubble). Schematic representation of RLC and RLG protein and domain structure is included on top of each plot. (GAG) Nucleocapsid, (PR) protease, (IN) integrase, (RT) reverse transcriptase, (RH) RNase H, and (CHR) chromodomain, present only in the Chromoviridae genus of RLG. (G,H) Number of TE annotations and relative contribution to total genomic TE load (TE occupancy %) at each size category for RLC (G) and RLG (H). (*) P-value < 0.01, (**) P-value < 0.0001 (Wilcoxon rank-sum test). In all box plots, the median is indicated by solid bar; the boxes extend from the first to the third quartile; and whiskers stretch to the furthest value within 1.5 times the interquartile range. (At) Arabidopsis, (Sp) Spirodela.
