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Figure S1. Peach phenotype and progeny of natural PLMVd variant C40(A349)-g12. The hairpin insertion of variant C40(A349)-g12 (with light blue background) and the flanking 5’ and 3’ nucleotides are depicted on the left. The sequence variability of the hairpin insertions (encircled nucleotides) and the name of the progeny variants recovered from green (g) tissues of one representative inoculated seedling are indicated. The ratio of symptomatic to infected seedlings appears between brackets on the top of the panel.

Figure S2. Relative distribution by size classes of total sRNAs from GF-305 peach leaves infected by variant C40 (blue) or mock-inoculated (red). The fraction (%) of each sRNA class of a given length has been plotted against its length.

Figure S3. Distribution by size classes, polarity and abundance of PLMVd-sRNAs in the C40-infected sample. Histograms show the total reads of (+) and (-) PLMVd-sRNAs, in green and gray, respectively, of a given length.

Figure S4. Location and frequency of the 5’ termini of PLMVd-sRNAs along the genomic RNAs. Bars above and below the x-axis represent (+) and (-) PLMVd-sRNAs reads, respectively. Note that the same numbering (referred to variant C40) is used in (+) polarity (5’ to 3’ orientation is from left to right) and in (-) polarity (5’ to 3’ orientation is from right to left). Blue and red horizontal lines denote, respectively, (+) and (-) PLMVd-sRNAs with at least one nucleotide mapping within the hairpin insertion. Bars with blue and red asterisks indicate that the corresponding reads (223401 and 86844) for (+) and (-) PLMVd-sRNAs with 5’ termini at positions 216 and 251, respectively, are out of the scale.

Figure S5. Number and location of the 5’ termini of 21-nt non-redundant (nr) PLMVd-sRNAs along the genomic RNAs (panel a) and nucleotide variability detected in variant C40 and its progeny (panel b). (a) Bars above and below the x-axis represent numbers of (+) and (-) nr-PLMVd-sRNAs, respectively. Note that the same numbering (referred to variant C40) is used in (+) polarity (5’ to 3’ orientation is from left to right) and in (-) polarity (5’ to 3’ orientation is from right to left) and that numbering starts at position 23 to avoid splitting the hairpin insertion. Red and green squares denote, respectively, (+) and (-) PLMVd-sRNAs with at least one nucleotide within the hairpin insertion. Horizontal arrows map (+) (in red) and (-) (in green) 21-nt PLMVd-sRNAs with potential targets in the peach genome. Arrowheads indicate the 5’-3’ orientation of the PLMVd-sRNAs. (b) y-axis, number of polymorphisms detected at each position of variant C40 and its progeny. Nucleotide insertions and deletions are denoted by upwards and downwards arrows, respectively. Note that most PLMVd-sRNAs with potential targets in the peach span regions with high number of nr-PLMVd-sRNAs and high sequence variability.

Figure S6. Distribution by size classes, polarity and abundance of PLMVd-sRNAs in the green tissue of C40- and P1.148-infected samples. Histograms show the total reads of (+) and (-) PLMVd-sRNAs, in green and gray, respectively, of a given length.

Figure S7. Duplexes potentially formed by the cHSP90 mRNA and PLMVd-sRNAs with hairpin insertions obtained by deep sequencing of sRNA libraries from green leaves of C40- and P1.148-infected peach seedlings (panels a and b, respectively). Nucleotides in bold correspond to the hairpin insertion. The scores of RNA duplexes are calculated as in Fahlgren and Carrington (2010), and the number of reads is indicated between brackets on the right.

Table S1. Predicted peach mRNAs targeted by PLMVd-sRNAs matching perfectly the genomic sequence of variant C40 and its progeny.

Table S2. Chloroplast transit peptides and their length in cHSP90 of five species predicted by the ChloroP program.

Appendix S1. PLMVd-sRNAs (18-26 nt) from albino leaf sectors infected with PLMVd variant C40.

Appendix S2. Experimental procedure. Construction of plasmids containing head-to-tail PLMVd-cDNA dimeric inserts.

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