Pairwise comparisons between accessions for: a) TE hits; b) 22 nt siRNA hits per RPKM_TE and c) 24 nt siRNA hits per RPKM_TE.

<p>For all the cases the <i>x</i>- and <i>y</i>-axis indicate accessions under comparison (B73, PT or OAXA). Each dot represents a TE subfamily, with the regression (<i>y</i>) and correlations (<i>r²</i>) between accessions indicated. The solid line represents the regression fit, while the dashed line represents the null hypothesis. The color of the dots represents significance: red dots are significant differences between accessions at a FDR of <i>q</i><0.001, based on the χ²_Corr in panel a and the χ²_Prop for panels b and c. Blue dots are not significant.