Fig. 2

The miRNA abundance, rather than target mRNA abundance, is the major determinant of target cleavage. a miRNAs causing target cleavage tend to have higher abundance. Kolmogorov-Smirnov (KS) plot showing the abundance of expressed miRNAs in dark and light (W3 h). + Degradome (red) indicates miRNAs with valid target cleavages identified; − degradome (black) indicates expressed miRNAs without target cleavage identified. Dashed lines indicate 50th percentile of sRNAs. b Target mRNA abundance was relatively unchanged regardless of being cleaved. KS plot showing the abundance of target mRNA with (green) or without (black) degradome signatures under dark or light (W4 h). Only expressed target genes with RPKM > 0.01 were plotted. c Degradome signatures were preferentially detected in mRNAs with high miRNA-to-target ratios. KS plot showing distribution of pairwise miRNA-to-target ratios in dark and light (W3 h/W4 h). + Degradome (orange) indicates miRNA–target pairs with target cleavage identified; − degradome (black) indicates miRNA–target pairs without target cleavage identified. d The abundance is relatively lower for siRNAs than expressed miRNAs. e Target mRNAs, but not miRNAs, are downregulated by light. Light/dark ratios indicate the relative levels of miRNAs (W3 h/W0 h) and mRNAs (W4 h/W0 h). + and – degradome indicate miRNAs/targets with or without identified degradome signatures, respectively. Data are the mean of all biological replicates (three replicates for sRNAs and two for mRNAs). * p < 0.01 by Student’s t-test. The bottom, middle, and top of the box represent the 25th, 50th, and 75th percentiles, and whiskers are the 10th and 90th percentiles, respectively