Fig. 4

Tissue-specific sRNA expression. A Principal component analysis (PCA) of sRNA expression in the six studied tissues/time points. The principal components were calculated based on the top 500 most variable sRNA genes between samples. B Number of differentially expressed genes (DEGs) resulting from pairwise differential expression analysis between tissues. Dashed square: comparisons between the same organ at different developmental stages; dotted square: comparisons between different organs at the same time point. In A and B Veg = vegetative phase; Gen = generative phase. Veg shoot indicates leaves and gen shoot indicates leaf blades. C Number of tissue-specific sRNAs. Tissue-specific expression was defined as having a FPKM higher than two in the tissue of interest and a read count of zero in all other tissues. Root or leaf (blade) samples at vegetative and generative stage were combined. The group ‘embryo + endosperm’ indicates sRNAs specifically expressed in embryo and/or endosperm. D Classification of tissue-specific sRNA genes. siRNAx = loci mainly producing siRNAs of length x; 24nt_Locus = loci from the pln24nt database. These were classified separately because no information is available on the predominant sRNA size expressed from these loci; OtherRNA = loci where less than 80% of the reads are 20-24 nt long, therefore considered as not processed by DCL enzymes