(A) Principle component analysis for 14 variables measured for each individual transposable element (TE). Each vector represents one variable, with the length signifying the importance of the variable in the dimension. The relationship between variables can be determined by the angle connecting two vectors. For angles < 90°, the two variables are correlated, while those >90° are negatively correlated. Each individual element is shown and highlighted by color and symbol as indicated by the key. Colored ellipses show the confidence interval for the four families along with a single large symbol to show the mean position for the four families. mCG, weighted CG DNA methylation; mCHG, weighted CHG DNA methylation; CRI, Composite RIP index; %GC, percent GC sequence content; Identity, Nucleotide identity as percent identity to the consensus TE sequence of a family; Length, element length; Jukes Cantor, Jukes Cantor corrected distance as proxy of TE age; RNAseq, RNA-sequencing reads from (PDB), half strength MS (HMS) or tomato xylem sap (Xylem) grown fungus expressed as variance stabilizing transformed log2 values (see Materials and methods for details); H3K9me3, log2 (TPM+1) values of mapped reads from H3K9me3 ChIP-seq; H3K27me3, log2 (TPM+1) values of mapped reads from H3K27me3 ChIP-seq; ATAC-seq, log2 (TPM+1) values for mapped reads from Assay for transposase accessible chromatin. (B) Ridge plots showing the distribution of the individual TE families per variable. The median value is shown as a solid black line in each ridge. Variables same as in A except for mCG, log2(weighted cytosine DNA methylation + 0.01). (C) Scatter plot for %GC versus CRI values for individual TE elements shown as points. The two plots are for TEs characterized as Unspecified (Unsp) or LTR, labeled in the upper left corner. Each point is colored according to log2 (TPM+1) values from H3K9me3 ChIP-seq, scale shown above each plot. A density plot is shown for both variables on the opposite side from the labeled axis. (D) Same as in C, but the y-axis is now showing the log2 (TPM+1) values from ATAC-seq.