Figure S5 Frequency of the 59-terminal nucleotide in (+) and (2) HSVd-sRNAs. Histograms comparing the size distribution (20– 24-nt) and nucleotide at 59 termini of (+) (left panels) and (2) (right panels) HSVd-sRNAs from berry (A and B), flower (C and D) and leaf (E and F). Found at: doi:10.1371/journal.pone.0007686.s005 (9.92 MB TIF) Figure S6 Frequency of the 59-terminal nucleotide in (+) and (2) GYSVd1-sRNAs. Histograms comparing the size distribution (20– 24-nt) and nucleotide at 59 termini of (+) (left panels) and (2) (right panels) GYSVd1-sRNAs from berry (A and B), flower (C and D) and leaf (E and F). Found at: doi:10.1371/journal.pone.0007686.s006 (9.65 MB TIF) Figure S7 Mapping of the 59 termini and frequency of (+) HSVd-sRNAs from different tissues. Berry (A), tendril (B), flower (C) and leaf (D). Note that the scale is different in the four panels and that 59-39 orientation is from left to right. Mapping is referred to the HSVd (+) genomic RNA (sequence variant with the accession number X06873). Found at: doi:10.1371/journal.pone.0007686.s007 (9.65 MB TIF) Figure S8 Mapping of the 59 termini and frequency of the (2) HSVd-sRNAs from different tissues. Berry (A) tendril (B), flower (C) and leaf (D). Note that the scale is different in the four panels and that 59-39 orientation is from right to left. Mapping is referred to the HSVd (2) genomic RNA (sequence variant with the accession number X06873). Found at: doi:10.1371/journal.pone.0007686.s008 (9.71 MB TIF) Figure S9 Mapping of the 59 termini and frequency of the (+) GYSVd1-sRNAs from different tissues. Berry (A) tendril (B), flower References 1. Ding SW, Voinnet O (2007) Antiviral Immunity Directed by Small RNAs. Cell 130: 413–426. 2. Bernstein E, Caudy AA, Hammond SM, Hannon GJ (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409: 363–366. 3. 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Note that the scale is different in the panels and that 59-39 orientation is from right to left. Mapping is referred to GYSVd1 (2) genomic RNA (sequence variant GYSVd1.PN.22 with the accession number GQ995473). Found at: doi:10.1371/journal.pone.0007686.s010 (7.64 MB TIF) Materials and Methods S1 Viroid-derived small RNAs (vd- sRNAs) in the sequenced libraries were retrieved searching for the 20–24 nt sRNAs perfectly matching the viroid sequence variants deposited in databases and with the accession number indicated below, and those identified in the present study. Found at: doi:10.1371/journal.pone.0007686.s011 (0.02 MB DOC) Acknowledgments We are grateful to R. Flores for critical reading of the manuscript. Author Contributions Conceived and designed the experiments: BN VP TD FDS JB. Performed the experiments: BN VP. Analyzed the data: BN VP AG SM TD FDS JB. Contributed reagents/materials/analysis tools: AG SM GB. Wrote the paper: FDS JB. 17. 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