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.</p

The number of significantly differences in pairwise comparisons between genotypes for TE, 22

a<p>The standard χ² test based on a 2×2 table of the relative proportions of hits.</p>b<p>The χ² corrected by the coverage to the FGS.</p>c<p>The χ² test of proportionality; see text and Supplement <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004298#pgen.1004298.s007" target="_blank">Text S1</a>.</p

Age of the TE subfamilies included in groups R1 and R2 [22].

<p>The boxes indicate the first quartile (bottom line), the median (central line) and the third quartile (upper line). The boxes, whiskers and dots for the boxplots are defined in the caption of <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004298#pgen-1004298-g001" target="_blank">Figure 1</a>, as are the lower case letters above the boxes.</p

Average Fold Change (FC) estimates for the three TE groups, based on pairwise comparisons between accessions.

1<p>FC is the average fold-change TE abundance and 22 nt and 24 nt siRNA across all of the TE subfamilies in each group. For each TE subfamily, the FC is the log 2 ratio of coverages between the two accessions, where coverage is #hits/#total hits.</p

Boxplots of Fold Change in 22(FC₂₂ and FC₂₄) between accessions (B73, PT and OAXA), based on normalization by the upper quartile (Methods).

<p>The meaning of the boxes, whiskers and dots is defined in the legend of the <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004298#pgen-1004298-g004" target="_blank">Figure 4</a>.</p

Boxplots of Fold Change in genomic reads for TEs (FC_TE) within the D, R1 and R2 groups.

<p>The pairwise comparisons between accessions (B73, PT and OAXA) are indicated on the figure. The boxes indicate the first quartile (bottom line), the median (central line) and the third quartile (upper line). The whiskers represent the highest and lowest values of the data that are within 1.5 times the interquartile range of the box edges. The outliers are represented by dots.</p

Characteristics of TE families within the R1 and R2 groups.

1<p>Designations and descriptions from <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004298#pgen.1004298-Wicker1" target="_blank">[25]</a>. TE families are listed when they consist of >10 subfamilies.</p

Characteristics of the three groups of TEs in B73, as defined by class and copy number.

<p>a) Histograms of the RPKM of TEs (left) and RNA elements, based on genomic reads. b) The empirical distribution function for DNA TEs (left) and RNA elements (right). The dots represent individual TE subfamilies and the dashed line is a fitted log-normal distribution. The vertical dashed red line is used to define groups R1 and R2. c) Lengths of the exemplar elements in the three groups. d) Characteristics of the three groups for TE, 22 nt siRNA and 24 nt siRNA abundances (RPKM values). e) Characteristics of the three TE groups for the 24 : 22 nt siRNA ratio (left) and a proxy for the number of 22 nt and 24 nt siRNA hits per TE copy (siRNA RPKM : RPKM_TE). f) Graphs about the location of TEs based on paired reads: left, the percentage of paired reads in which both reads map to different TE exemplars of the UTE; middle, the proportion of paired reads in which one read maps to the UTE and the other to the FGS; right, the proportion of paired reads in which one of the reads maps to the UTE and the other to the KnobC database. For all boxplots in panels c, d, e and f, the boxes indicate the first quartile (bottom line), the median (central line) and the third quartile (upper line). The whiskers represent the highest and lowest values of the data that are within 1.5 times the interquartile range of the box edges. The outliers are represented by crosses. The lower case letters above the boxes represent significance groupings after a pairwise comparison. Boxplots sharing the same lower case letter are not significantly different at <i>p</i><0.05.</p

Expression characteristics of the three TE groups.

<p>a) Overall expression (RPKM_RNAseq) and b) expression per TE copy (RPKM_RNAseq : RPKM_TE) for the three TE groups based on RNAseq data from transition leaves <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004298#pgen.1004298-Sekhon1" target="_blank">[57]</a> c) Fold-change in TE expression (FC_mop) between wild type (<i>wt</i>) and the <i>mop1</i> mutant for a subset of 340 TEs <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004298#pgen.1004298-Jia1" target="_blank">[13]</a>. d) A plot of FC_mop and the 24∶22 nt siRNAs ratio for the same 340 TE subfamilies (dots). The diameter of the dots is proportional to the length of the TE exemplar. The boxes, whiskers and dots for the boxplots are defined in the caption of <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004298#pgen-1004298-g001" target="_blank">Figure 1</a>, as are the lower case letters above the boxes.</p