Properties of sRNAs covering transposons. (A) Repartition of the sRNA sequences in the different diatom transposon families (only for TE annotation above 300 bp). We report the number of transposons with a sRNA coverage above 5 RPKM (grey) or with a low or no sRNA coverage (black). (B) 5′ end nucleotide composition of the reads (from position 1 to 5) aligning to transposons. (C) Relationship between sRNA coverage and autonomous TEs expression or autonomous TEs methylation. From left to right: transcript expression according to RNA-seq evidence, or cDNA libraries, and methylation status in transposons. (D) Experimental validation of the transcriptional activity level of autonomous transposons by qPCR. The transposons are grouped on the x-axis with an increasing coverage in sRNAs: low (sRNA RPKM < 5), middle (5 < RPKM < 10) and high (RPKM > 10) coverage. A grey shaded box is reported when the product could not be amplified. Autonomous transposons whose expression is supported by both EST and RNA-seq evidence are annotated with the symbols “++”. Labels above bins correspond to the Genbank identifier and localization of the transposons. (E) Comparison of methylation level and sRNA coverage on all Copia-type LTR transposons longer than 50 nt. Boxes are colored according to the length of the transposons region: 50 to 1000 nt (light grey), 1000 to 4000 nt (grey) and more than 4000 nt (dark grey). Methylation level is computed as the proportion of methylated probes that overlap the transposon region.