Fig. 2

Small RNAs from euchromatic and heterochromatic transposons exhibit distinct developmental dynamics. a Line graphs illustrating 24-nt siRNA levels from class A and B TEs in embryonic and post-embryonic tissues. Dashed lines represent the detection criteria used to select TEs yielding siRNAs (2 RPM, reads per million genome-matching reads). The number of TEs belonging to each class are indicated. Polygons represent the standard deviation of mean 24-nt siRNA levels. fb, floral buds; pg, preglobular; gl, globular; eh, early heart; lh, late heart; et, early torpedo; lt, late torpedo; bc, bent cotyledon; mg, mature green; lf, leaf. b Heat map depicting 24-nt siRNA levels (RPM) from class A and B TEs across development. siRNA levels from ± 2 kb of TEs are color-coded according to the key, and samples are labeled as in a. Rows were ordered based on total 24-nt siRNA levels. c Line metaplot showing 24-nt siRNA levels from class A and B TEs. TEs were aligned on their 5′ ends, which are indicated by the gray vertical line. Samples are labeled according to the key and as in a. d Circos plot representing densities of siRNA-deficient (-siRNAs; gray), class A (red) and class B (purple) TEs across the five Arabidopsis chromosomes (chr). Centromeres are indicated by dots. e Boxplot of TE lengths for either all annotated, siRNA-deficient, class A, or class B TEs. Dashed red line represents the median size of all annotated TEs. Thick horizontal bars indicate medians, and the top and bottom edges of the box indicate the 75th and 25th percentiles, respectively. kb, kilobases; P values < 0.0001 based on Mann-Whitney U test of differences between all annotated and TE classes are represented by *. f Stacked bar charts illustrating proportion of TEs that are CHH hypomethylated in drm1/drm2 (RdDM; red), cmt2 (CMT2; purple), both drm1/drm2 and cmt2 (both; yellow) or which were not methylated (unmethyl; black) in leaves [26]. See also Additional file 2: Figure S2