Fig. 2

Small RNA expression in various rice tissues. A Number of expressed sRNAs detected in the 6 studied tissues. sRNA genes were considered expressed when they had an FPKM value higher than 2 for each of the biological replicates. B Types of expressed sRNA genes. MiRNA = loci producing miRNAs; nearMiRNA = loci predicted to be miRNA loci, but lacking the miRNA* passenger strand [21]; 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 and therefore considered not processed by DCL enzymes. C Frequency of occurrence of each nucleotide at the 5′ end of expressed sRNA loci in each tissue. D Association of expressed sRNAs in the 6 tissues/time points with 5 TE families. Permutation tests were conducted as described in Figure 2. Bars were not shown if the permutation null distribution did not resemble a normal distribution. DTM = DNA transposon mutator, RSU = retroelement short interspersed nuclear element; RLC = retroelement long tandem repeat Copia; RLG = retroelement long tandem repeat Gypsi; RLX = retroelement long tandem repeat ‘Unknown’. In all panels: Veg = vegetative phase; Gen = generative phase. Veg shoot indicates leaves and gen shoot indicates leaf blades