Figure 2.

(A) An example of a gel representing one of 621 TE frequency assays in a panel of 48 individuals. The first three lanes are Col-0 positive controls with combinations of primers; subsequent lanes represent one individual in the panel. Large, paired bands (∼700 and ∼1500 bp) indicate presence of TE in one individual; the smaller, single band (∼400 bp) represents absence of the TE. (B) Comparison of site-frequency spectra (SFS) of sSNPs, unmethylated TEs, methylated TEs >1.5 kb from genes, and all methylated TEs. The SFS of methylated TEs contains an excess of the low-frequency TEs, consistent with a deleterious effect of TE silencing near genes. (C) Box plots showing distance to the nearest gene for polymorphic and fixed uTEs and mTEs.