Workflow of the small RNAs analysis in P. tricornutum. Top. Fragment lengths distribution of reads (histogram, center) is reported in a grey color scale distinguishing the five experimental conditions (LL, HL, NL, −Fe, D). The distribution of fragment location is also reported (pie chart, right) with a color scale indicating genes, intergenic regions, repeat regions, tRNA genes, ncRNAs and other loci. We distinguish two workflows described in boxes A and B, characterized by different local loci distributions of reads along the genome. (A) Sequence specific distribution of fragment lengths that is systematically observed for tRNA genes and intergenic regions. Reads were filtered in five steps, described in the 5 grey boxes. We obtained three main groups of results, indicated by squared boxes (number of predicted sRNAs is reported in parenthesis). The number of predicted sRNAs that were experimentally validated is also indicated, together with the experimental technique (NB, Northern Blot; PCR, Stem Loop PCR; H, sequencing data from ). (B) Distribution of fragment lengths that covers loci with overlapping reads and accumulated on both strands. This distribution pattern has been observed to either TEs or coding genes, associated to methylation. Examples of the periodic placement of sRNAs on three Codi LTR-retrotransposons on chromosome 31 and on a protein coding gene on chromosome 12 are reported. Color palette for TEs and genes is the same as above, and Highly Methylated regions are represented in purple.