Supplemental Material for Sunitha et al., 2019

<div><b>Supplementary Figure S1. </b>Size distributions of adapter-trimmed and pre-filtered reads in the 28 UV experimental sRNA libraries.<b><br><br>Supplementary Figure S2. </b>Functional validation of differentially expressed miRNA/tasiRNA activities under high-fluence solar UV-B in the field by qRT-PCR of target genes. <b>A)</b> Schematic alignment of vvi-TAS4a, -TAS4b and -TAS4c primary transcript sequences flanking the miR828 binding and TAS4 3’ D4(-) phasi-RNA positions, and location of locus-specific primers used for qRT-PCR. <b>B)</b> Expression profile of miR828* (left panel; only sRNA reads mapping to vvi-MIR828) and pre-MIR828 transcript abundance. Panels <b>C-E</b>: Expression profiles of TAS4a, TAS4b and TAS4c siRNAs (left panels) and their cognate primary undiced transcript abundances. <b>C)</b> TAS4a 3’ D1(+) trans acting siRNA expression profile and the expression profile of TAS4a primary transcript. <b>D)</b> TAS4b 3’ D4(-) trans acting siRNA expression profile and the expression profile of TAS4b primary transcript. <b>E)</b> TAS4c 3’ D4(-) trans acting siRNA expression profile and the expression profile of TAS4c primary transcript. <b>F)</b> TAS4-3'D4(-) target MYBA6 phasi-RNA-3'D6(+) expression profile and the expression profile of MYBA6 mRNA. <b>G)</b> TAS4-3'D4(-) target MYBA7 phasi-RNA-3'D6(+) expression profile and the expression profile of MYBA7 mRNA. Error bars are s.d., except panel B: s.e.m. Asterisks (*) denote significant differences based on analysis of variance (n=4 biological replicates) and comparisons using the Tukey-Kramer honestly significance test (HSD; p < 0.05). Insets, <b>B-G:</b> Target:miRNA/tasi-RNA binding positions (mRNA nucleotide coordinates) and primer binding sites (arrows) are depicted to scale. Target:miRNA binding depicted in Red; Target:tasiRNA binding depicted in Green; Target:phasiRNA binding depicted in Pink; miR828* species is depicted in Peach.<b><br><br>Supplementary Figure S3.</b> miR403f mature expression profile and the expression profile of MIR403f primary transcript, showing concordant inductions during berry development. Error bars are s.d. Asterisks (*) denote significant differences based on analysis of variance (n=4 biological replicates) and comparisons using the Tukey-Kramer honestly significance test (HSD; p < 0.05). Inset: pre-MIR403f:miRNA binding position (mRNA nucleotide coordinates) and primer binding sites (arrows) are depicted to scale. Target:miRNA binding depicted in Red.<b><br><br>Supplementary File S4.</b> CleaveLand-validated miRNA target T plots.<b><br><br>Supplementary File S5. </b>PhaseTank Align and Cascades Output, UV-regulated PHASI loci<b>.<br><br>Supplementary File S6. </b>Novel MIRNA loci characterized de novo by ShortStack, drawn from reads of libraries constructed from UV-B treated samples.<b><br><br>Supplementary File S7. </b>List of primers and parameters used in this study.<br><b><br>Supplementary Table 1a and 1b. </b>small RNA library (a) and degradome (b) quality control parameters.<b><br><br>Supplementary Table 2a and 2b. a) </b>List of validated miRNA targets by CleaveLand4.4 analysis of Pantaleo et al. (2010) degradome dataset. b) Meta-analysis of validated miRNA targets for three published datasets for transcriptome changes of berry skins in response to: UV-C (Suzuki et al., 2015), UV-B (Carbonell-Bejerano et al., 2017) and development (Massonnet et al., 2017).<b><br><br>Supplementary Table 3a-d. </b>DESeq2 output and associated ShortStack raw Counts dataset parameters for differentially expressed miRNA comparisons outlined in Table 1 summarized for target functions, and normalized reads per 20M for visualization of compared effects.<b><br><br>Supplementary Table 4. </b>PhaseTank output of degradome TAS loci targets and miRNA/phasi-RNA trigger predictions.<b><br></b></div>