<b>Supplemental Data Set S1. </b>Summary of the predicted loci in <i>Arabidopsis halleri </i>and <i>A. lyrata</i>

<b>Supplemental Data Set S1. </b><b>Summary of the predicted loci in </b><b><i>Arabidopsis halleri </i></b><b>and </b><b><i>A. lyrata.</i></b> The colored cases represent the score of miRkwood prediction (from 1 to 6) (Guigon et al., 2019). The letter “S” indicates that the miRNA has been predicted by Shortstack 4.0.2 (Johnson et al., 2016).<br>Preferential loading into AGO proteins depends on abundance in AGO1 or AGO4. Reads for each sample were normalized to RPM, and the average abundance was calculated across all conditions and replicates. miRNAs were considered preferentially loaded into AGO1 or AGO4 if their abundance showed at least a five-fold difference between the two. Below this threshold, dual loading was assumed (miRNA loaded equally in both). "Not loaded" refers to small RNAs seen in the input but not in AGO1 or AGO4, while "NA" indicates the miRNA was absent in the input.<br>