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21 and 24Â nt peak distribution of the libraries. Figure S2 (a,b,c). Length distribution of total sRNAs (18 to 30Â nt) in the nine libraries. Figure S3. Distribution of siRNA Reads on Reference Genome shows coverage across the reference. Figure S4. Phylogenetic analyses of isolates of the genus Potyvirus and some selected group members based on complete genome sequences, generated using the neighbor-joining method and MEGA6 software. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) is shown next to the branches. Figure S5. Phylogenetic analyses of CMV Isolates and selected cucumoviruses based on complete genome sequences, generated using the neighbor-joining method and MEGA6 software. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) is shown next to the branches. Figure S6. Phylogenetic analyses of isolates of the genus Poleroviruss (A) and Tobamovirus (B) based on complete genome sequences, generated using the neighbor-joining method and MEGA6 software. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) is shown next to the branches. Figure S7a and b. Putative recombination event involving (a) Potato virus Y and (b) Cucumber mosaic virus isolates from Tobacco calculated by Recombination Detection Program v. 4.16. (PPTX 466Â kb)

Primer sets used in this study for RT-PCR to bridge the gaps between the assembled contigs of each isolates. Table S2. Strain, accession numbers and origin of reported Cucumber mosaic virus isolates used for phylogenetic comparison of sequence in this study. Table S3. Strain, accession numbers and origin of reported Potato virus Y isolates used for phylogenetic comparison of sequence in this study. Table S4. Strain, accession numbers and origin of reported TMV isolates retrieved from Genbank used for phylogenetic comparison and recombination analysis of sequence in this study. (DOCX 25Â kb)

Primer sets used in this study for RT-PCR to bridge the gaps between the assembled contigs of each isolates. Table S2. Strain, accession numbers and origin of reported Cucumber mosaic virus isolates used for phylogenetic comparison of sequence in this study. Table S3. Strain, accession numbers and origin of reported Potato virus Y isolates used for phylogenetic comparison of sequence in this study. Table S4. Strain, accession numbers and origin of reported TMV isolates retrieved from Genbank used for phylogenetic comparison and recombination analysis of sequence in this study. (DOCX 25Â kb)