DOI: 10.5281/zenodo.5207514
title: Atypical molecular features of RNA silencing against the phloem-restricted polerovirus TuYV

description: The dataset contains all the original raw files sorted by figure and figure panel. NGS data has been deposited on GEO (GSE176378). The content of each file is the following: <strong>FIGURE 1:</strong> -<strong>1A</strong>: Northern blots raw TIFF image files for the detection of TuYVs81 RNA on membrane HMW7 and methylene blue staining of the same membrane. -<strong>1B</strong>: Pictures of Col-0, <em>ago1-57</em>, <em>ago1-27</em> and <em>ago1-38</em> infected with TuYVs81 WT and -P0. -<strong>1C</strong>: Axiozoom pictures of TuMV-GFP AS9 infected plants of Col-0, <em>ago2-1</em>, <em>ago1-57</em> (sup149.1) and <em>ago2-1/ago1-57</em>. Both raw czi and jpg files are provided. Additional pictures for each genotype are also provided. -<strong>1D</strong>: Western blot (W579) and Coomassie staining raw image files for the detection of GFP from TuMV-AS9-GFP infected plants. -<strong>1E&G</strong>: Northern blots raw film scan for the detection of TuYVs81 RNA and TRV-PDS RNS on membrane HMW24 and HMW25 respectively. Methylene blue staining of the same membrane. Total RNA quantification and input volumes on gel (spreadsheet). -<strong>1F&H</strong>: -<strong>1I</strong>: Signal quantification of HMW24/25 using imageJ (spreadsheet). -<strong>1J</strong>: Northern blots raw film scan and TIFF images/raw phoshphoimager .gel files for the detection of TuYVs81 RNA 3’, 5’, TuYV siRNA, mir159 and U6 probe on membrane PPM70. For the detection of PDS, mir408 and U6 on membrane PPM71 Pictures of Col-0, <em>ago2-1</em>, <em>ago1-57</em> (sup149.1) and <em>ago2-1/ago1-57</em> infected with TuYVs81 WT and TRV-PDS at 20dpi. Total RNA quantification and input volumes on gel (spreadsheet). -<strong>1K</strong>: Shortstack quantification of normalized reads per category (see legend). Original bargraph and html document retracing the analysis steps. -<strong>1L</strong>: Distribution of TuYVs81-derived sRNA reads (20-nt to 25-nt) along the TuYVs81 genome in Col-0 total RNA (library JBT5) and AGO1 IP replicate 1 (library JBT13), with MISIS. Output files from MISIS and final .png image of the distribution. <strong>FIGURE 2:</strong> -<strong>2A&C</strong>: Kinetic of systemic TuYVs81 and TuMV-GFP WT infection in Col-0, <em>ago1-57</em>, <em>ago1-27 </em>and <em>ago1-38 </em>represented as the cumulated percentage of infected plants in the inoculated population. Raw spreadsheet with day to day counting. Original graphs. -<strong>2B</strong>: Northern blots raw TIFF image files for the detection of TuYVs81 RNA on membrane HMW22 and methylene blue staining of the same membrane. -<strong>2D</strong>: Western blot (W555) and Coomassie staining raw image files for the detection of GFP from TuMV-GFP infected plants. -<strong>2E</strong>: qPCR data for the quantification of <em>TuYV</em> RNA in inoculated leaves of Col-0<em>, ago1-27</em> and <em>ago1-57</em>. <strong>2F</strong>: Western blot (W779) and Coomassie staining raw image files for the detection of RT viral proteins from TuYVs81 inoculated leaves. <strong>2G</strong>: Western blot (W626-W629) and Coomassie staining raw image files for the detection of CFP-AGO1 and P0-myc in N. benthamiana leaves. Northern blot raw TIFF image files for the detection of P0 CABYV, P0 BMYV and P0 PLRV on membrane HMW28 and methylene blue staining of the same membrane. Protein sequence of the P0 constructs used. <strong>2H&I</strong>: DAS-ELISA result and fresh weight of Col-0 and <em>ago1-57</em> plants infected via aphids with WT TuYV. <strong>FIGURE 3</strong>: -<strong>3A</strong>: Northern blots TIFF images/raw phoshphoimager .gel files for the detection of TuYVs81 RNA 3’, TuYV siRNA, siR255, IR71, siR1003 and U6 probe on membrane PPM102. Total RNA quantification and input volumes on gel (spreadsheet). -<strong>3B</strong>: Pictures of Col-0, <em>dcl2-1</em>, <em>dcl4-2</em>, <em>ago1-57, dcl2-1/dcl4-2, dcl2-5/dcl3-1, dcl2-1/ago1-57, dcl4-2/ago1-57, dcl2-1/dcl4-2/ago1-57 </em>infected with TuYVs81 WT at 16dpi. -<strong>3C</strong>: qPCR data for the quantification of <em>TuYV</em> RNA in TuYVs81 infected Col-0, <em>dcl2-1</em>, <em>dcl4-2</em>, <em>ago1-57, dcl2-1/dcl4-2, dcl2-5/dcl3-1, dcl2-1/ago1-57, dcl4-2/ago1-57, dcl2-1/dcl4-2/ago1-57 </em>leaves. -<strong>3D</strong>: All raw .lif files and Fiji processed TIFF microscopy images of B2-GFP expressing <em>N. benthamiana</em> plants infiltrated with tRFP, DCL2-tRFP and DCL4-tRFP are in the folder Figure S5 (related to this panel) <strong>FIGURE 4:</strong> <strong>4A</strong>: qPCR data for the quantification of <em>TuYV</em> RNA in TuYVs81 infected leaves and vasculature of Col-0 and <em>dcl2-1</em> at 17dpi. <strong>4B</strong>: Northern blots TIFF images/raw phoshphoimager .gel files for the detection of TuYVs81 RNA 3’, TuYV siRNA, siR255, IR71, miR822, miR168, miR162 and U6 probe on membrane PPM90. Total RNA quantification and input volumes on gel (spreadsheet). <strong>4C</strong>: Western blot and Coomassie staining raw image files for the detection of DCL1 (W746) and the RT viral protein (W721) from TuYVs81 infected leaves and vasculatures. <strong>4D</strong>: qPCR data for the quantification of <em>DCL2 </em><em>and </em><em>DCL4</em> RNA in whole leaves and vasculatures of TuYVs81 infected Col-0 and <em>dcl2-1</em> plants. <strong>4E</strong>: Northern blots TIFF images/raw phoshphoimager .gel files for the detection of PDS, TRV 3’UTR and U6 (PPM96) and TRV 3’UTR (HMW38) in leaf and vasculature of plants infected with TRV-PDS. Total RNA quantification and input volumes on gel (spreadsheet). <strong>4F</strong>: qPCR data for the quantification of <em>TuYV</em> RNA in TuYVs81 WT and P0- infected leaves and vasculature of Col-0 plants. Raw Ct and calculation spreadsheet are with Figure 4A. <strong>4G</strong>: Northern blots TIFF images/raw phoshphoimager .gel files for the detection of TuYV RNA 3’, TuYV siRNA and U6 (PPM102) in leaf and vasculature of Col-0 and <em>dcl2-1</em> plants infected withTuYVs81 WT or P0-. Total RNA quantification and input volumes on gel (spreadsheet). <strong>FIGURE 5:</strong> -<strong>5A</strong>: qPCR data for the quantification of <em>TuYV</em> RNA in whole leaves and vasculatures of TuYVs81 infected Col-0 and <em>ago1-57</em> plants. -<strong>5B</strong>: Western blot and Coomassie staining raw image files for the detection of AGO1 (W758) and AGO2(W759) from TuYVs81 infected leaves and vasculatures. -<strong>5C</strong>: AGO1 signal quantification across five biological replicates in Mock and TuYVs81 infected leaves and vasculatures. -<strong>5D&E</strong>: All raw .lif files and Fiji processed TIFF microscopy images of B2-GFP expressing <em>N. benthamiana</em> plants infiltrated with tRFP-AGO1 and P0-tRFP are in the folder Figure S8 (related to this panel). -<strong>5F</strong>: qPCR data for the quantification of <em>AGO1 </em><em>and</em><em> AGO2</em> RNA in TuYVs81 infected leaves and vasculature of Col-0 and <em>ago1-57</em> plants. Raw Ct and calculation spreadsheet are with Figure 5A. -<strong>5G</strong>: Western blot and Coomassie staining raw image files for the detection of AGO1 and RT viral protein (W809) and AGO2 (W810) from TuYVs81 WT and TuYVs81 P0- infected leaves and vasculatures. -<strong>5H</strong>: Pictures of SUC-SUL (SS, parental), SS/pCoYMV:P0-HA WT (CWSS6-3) and SS/pCoYMV-P0-HA LP1 (CLSS6-3) adult plants. -<strong>5I</strong>: Western blot and Coomassie staining raw image files for the detection of AGO1 and P0-HA (W723) from SUC-SUL (SS), SS/pCoYMV:P0-HA WT (CWSS6-3) and SS/pCoYMV-P0-HA LP1 (CLSS6-3) leaves and vasculatures. -<strong>5J</strong>: Northern blots TIFF images/raw phoshphoimager .gel files for the detection of SUL siRNA, miR160c, miR160*, miR168, miR159 and U6 (PPM89) in leaf and vasculature from SUC-SUL (SS), SS/pCoYMV:P0-HA WT (CWSS6-3) and SS/pCoYMV-P0-HA LP1 (CLSS6-3) plants. Total RNA quantification and input volumes on gel (spreadsheet). -<strong>5K</strong>: qPCR data for the quantification of <em>CHLI1</em>, <em>CHLI2</em> and <em>AGO1 </em>RNA in leaves and vasculature of SUC-SUL (SS), SS/pCoYMV:P0-HA WT (CWSS6-3) and SS/pCoYMV-P0-HA LP1 (CLSS6-3) plants. -<strong>5L</strong>: Raw heatmap of all AGO1 IP libraries (DESeq2). Top 20 most deregulated loci. <strong>FIGURE S1:</strong> <strong>S1A</strong>: qPCR data for the quantification of <em>TuYV</em> RNA in whole leaves of TuYVs81 infected Col-0 and different ago single and combination mutants. <strong>S1B</strong>: Western blot and Coomassie staining raw image files for the detection of AGO1 and AGO2 (W603) from Col-0, <em>ago2-1</em>, <em>ago1-57</em> and <em>ago2-1/ago1-57</em> infected with TuYVs81 WT and TRV-PDS <strong>S1C</strong>: Northern blots raw TIFF image files for the detection of TuYV RNA 3’, TuYV siRNA, s81 insert siRNA, miR403, miR408, miR159 and U6 on membrane PPM60 (AGO1 IP) and PPM62 (AGO2 IP). Total RNA quantification and input volumes on gel (spreadsheet). <strong>S1D:</strong> Western blot and Coomassie staining raw image files for the detection of AGO1 (W537) and AGO2 (W538) from Col-0, <em>ago1-57</em>, <em>ago1-27</em> infected with TuYVs81 WT. <strong>S1E:</strong> Northern blots TIFF images/raw phoshphoimager .gel files for the detection of SUL siRNA, miR408, miR159 and U6 (PPM93) in AGO1 and AGO2 IPs from Col-0, SUC-SUL (SS), SS/<em>ago1-57 </em>rosette leaves. Total RNA quantification and input volumes on gel (spreadsheet). <strong>S1F</strong>: Western blot and Coomassie staining raw image files for the detection of AGO1 and AGO2 (W766) from Col-0, SUC-SUL (SS), SS/<em>ago1-57 </em>rosette leaves before and after AGO1 and AGO2 IP. <strong>FIGURE S2:</strong> <strong>S2A:</strong> Total RNA quantification of TuYVs81 infected Col-0 and <em>ago1-57</em> plant pools (#1 and #2) used for sRNA deepseq. Powerpoint presentation of all plant pool used, WB results and bioanalyzer profile of the total RNA. Spreadsheet with sequencing and mapping statistic for all 16 JBT libraries. <strong>S2B</strong>: Western blot and Coomassie staining raw image files for the detection of AGO1 (W398-W402) before and after AGO1 IP for sRNA deepseq samples. <strong>S2C:</strong> See figure 1K. Original bargraphs for 21-nt, 22-nt and 24-nt mapped reads in all JBT libraries. <strong>S2D</strong>: Distribution of TuYVs81-derived sRNA reads (20-nt to 25-nt) along the TuYVs81 genome in Col-0 total RNA (libraries JBT5 and JBT6), <em>ago1-57</em> total RNA (libraries JBT7 and JBT8), Col-0 AGO1 IP (libraries JBT13 and JBT14) and <em>ago1-57</em> AGO1 IP (libraries JBT15 and JBT16), with MISIS. Output files from MISIS and final .png image of the distribution. <strong>S2E:</strong> TuYVs81 nucleotide composition % (spreadsheet) and 5’ nucleotide frequency of the vsiRNA reads mapped to the TuYVs81 genome in JBT5, JBT7, JBT13 and JBT15 (.png). 5’ graphs were generated using MISIS. <strong>FIGURE S3:</strong> <strong>S3A</strong>: Kinetic of systemic TuYVs81, TuMV-GFP and TRV-PDS infection in Col-0 and <em>ago1-57</em>, represented as the cumulated percentage of infected plants in the inoculated population. Raw spreadsheet with day to day counting. Original graphs. <strong>S3B</strong>: qPCR data for the quantification of <em>TuYV</em> RNA in inoculated leaves of Col-0<em>, ago1-27</em> and <em>ago1-57</em>. Biological replicate to the experiment in Figure 2E. <strong>FIGURE S4:</strong> <strong>S4A:</strong> Leaf pictures of Col-0, <em>dcl2-1</em>, <em>dcl4-2</em>, <em>dcl2-1/dcl4-2, rdr6-12, sgs3-14 </em>infected with TuYVs81 WT at 17dpi. Leaves are from two different individuals. <strong>S4B:</strong> Northern blots raw TIFF images and scans files for the detection of TuYVs81 RNA 3’ siRNA and U6 in Col-0, <em>ago1-57, dcl2-1, dcl4-2, dcl2-1/dcl4-2, rdr6-12, sgs3-14</em> infected with TuYVs81 WT on membrane PPM39. Total RNA quantification and input volumes on gel (spreadsheet). <strong>S4C:</strong> Northern blots raw TIFF images files for the detection of TuYVs81 RNA 3’ in Col-0, <em>ago1-57, dcl2-1, rdr6-12, sgs3-14</em> infected with TuYVs81 WT on membrane HMW8. Methylene blue stain of the membrane. Total RNA quantification and input volumes on gel (spreadsheet) with figure S4B. <strong>S4D</strong>: Kinetic of systemic TuYVs81 infection in Col-0, <em>ago1-57</em>, <em>dcl2-1, dcl4-2, dcl2-1/dcl4-2, rdr6-12, sgs3-14</em> represented as the cumulated percentage of infected plants in the inoculated population. Raw spreadsheet with day to day counting. Original graphs. <strong>FIGURE S5:</strong> All raw .lif files and Fiji processed TIFF microscopy images of B2-GFP expressing <em>N. benthamiana</em> plants infiltrated with tRFP, DCL2-tRFP and DCL4-tRFP. Note that more images are available that those in the manuscript. <strong>FIGURE S6:</strong> <strong>S6A:</strong> qPCR data for the quantification of <em>TuYV</em> RNA in whole leaves and vasculatures of TuYVs81 infected Col-0. <strong>S6B:</strong> See Figure 4B <strong>S6C:</strong> qPCR data for the quantification of <em>DCL2 </em><em>and </em><em>DCL4</em> RNA in whole leaves and vasculatures of TuYVs81 infected Col-0 plants. <strong>FIGURE S7:</strong> <strong>S7A:</strong> qPCR data for the quantification of <em>TuYV</em> RNA in vasculatures and protoplast cells of TuYVs81 infected Col-0. <strong>S7B:</strong> Western blot and Coomassie staining raw image files for the detection of AGO1 and RT viral protein (W283), AGO2 and AGO4 (W328) in vasculatures and protoplast cells of TuYVs81 infected Col-0 and <em>ago1-57</em>. <strong>S7C:</strong> Northern blots raw TIFF images for the detection of miR168 and U6 on membrane PPM47 in vasculatures and protoplast cells of TuYVs81 infected Col-0. Total RNA quantification and input volumes on gel (spreadsheet). <strong>S7D:</strong> qPCR data for the quantification of <em>TuYV</em> and <em>AGO1</em> RNA in mock and TuYVs81 infected leaves of Col-0, <em>ago1-57</em>, pSUC:Flag-AGO1 #1 (ASWW1b3) and #2 (ASWW2b1). <strong>S7E:</strong> qPCR data for the quantification of <em>AGO1</em> RNA in TuYVs81 WT and P0- infected leaves and vasculature of Col-0 and <em>dcl2-1</em> plants. <strong>S7F:</strong> Western blot and Coomassie staining raw image files for the detection of AGO1 and RT viral protein (W708) in whole leaves of TuYVs81 infected Col-0, <em>ago1-57</em>, pSUC:Flag-AGO1 #1 (ASWW1b3) and #2 (ASWW2b1). <strong>S7G</strong>: qPCR data for the quantification of <em>Flag-AGO1</em> RNA in mock and TuYVs81 infected leaves of Col-0, pSUC:Flag-AGO1 #1 (ASWW1b3) and #2 (ASWW2b1). <strong>FIGURE S8:</strong> <strong>S8A:</strong> All raw .lif files and Fiji processed TIFF microscopy images of B2-GFP expressing <em>N. benthamiana</em> plants infiltrated with tRFP-AGO1. Note that more images are available that those in the manuscript. <strong>S8B:</strong> All raw .lif files and Fiji processed TIFF microscopy images of B2-GFP expressing <em>N. benthamiana</em> plants infiltrated with P0-tRFP. Note that more images are available that those in the manuscript. <strong>FIGURE S9:</strong> <strong>S9A: </strong>Pictures of 11-day old seedlings grown on MS media: Col-0, SUC-SUL (SS), SS/pSuc:P15-FHA, SS/pCoYMV:P0-HA WT (CWSS6-3) and SS/pCoYMV:P0-HA LP1 (CLSS6-3). <strong>S9B:</strong> qPCR data for the quantification of <em>P0-HA </em><em>and</em><em> AGO1</em> RNA in seedlings of Col-0, SUC-SUL (SS), SS/pSuc:P15-FHA, SS/pCoYMV:P0-HA WT (CWSS6-3) and SS/pCoYMV:P0-HA LP1 (CLSS6-3). <strong>FIGURE S10:</strong> <strong>S10A:</strong> Raw heatmap of all AGO1 Total RNA libraries (DESeq2). Top 18 most deregulated loci. <strong>S10B:</strong> MA plot of AGO1 IP in Col-0 TuYV <em>vs.</em> AGO1 IP in Col-0 mock (DESeq2). MA plot of AGO1 IP in <em>ago1-57</em> TuYV <em>vs.</em> AGO1 IP in <em>ago1-57</em> mock (DESeq2). <strong>S10C:</strong> Northern blots raw TIFF images/raw phoshphoimager .gel files for the detection of SUL3’ siRNA, TuYV 3’ siRNA and U6 on membrane PPM64 (Col-0<em>, ago1-57, dcl2-1, dcl4-2, dcl2/4</em> infected with TuYVs81 and Col-0 plus ago1-57 infected with aphid transmitted TuYV WT) and PPM68 (Col-0<em>, ago1-57, rdr6-12, sgs3-14, dcl2/4 </em>infected with TuYVs81 as well as Col-0 and<em> ago1-57</em> infected with TuMV-GFP). Total RNA quantification and input volumes on gel (spreadsheet).