Transposon methylation and expression. CG methylation levels of individual TEs plotted against their size (kb) and expression levels (Log2 RPKM (reads per kilobase per million mapped reads)) in FB. A three-dimensional scatter plot is shown from two views. TEs belonging to different classes are displayed as different color dots as indicated. Only TEs with detectable expression levels (RPKM >0) are shown; a total of 1,414 TEs for FB. The plane cut at log2 RPKM = 0 (corresponding to RPKM = 1) was set as a threshold for expressed TEs. The results of a similar analysis conducted on FLM and on TEs with undetectable expression levels are shown in Figure S9 in Additional file 1.