Thirty one well-characterized RNAi associated genes (RNAi genes from here on) from A. thaliana (Table S4) were used to search for homologues in N. benthamiana. Protein sequences were retrieved from TAIR, and first screened against the tomato predicted protein database (SL2.40) at Solgenomics using BLASTp [34]. Both A. thaliana and tomato RNAi protein sequences were then used to screen the transcriptome assembly of N. benthamiana using tBLASTn. The most significant matches to A. thaliana and tomato queries were manually assessed and in cases of multiple matches, the query coverage (%) and identity (%) of high-scoring segment pairs were analysed further. Where possible, a full length sequence was manually reconstituted from the shorter transcript sequences, and where this was not possible, sequence **data** from our draft genome assembly [7] and/or from the N. benthamiana sequences deposited in the Solgenomics database [12] was used. All putative transcripts were subsequently translated and reciprocally checked against the TAIR and tomato databases to compare and confirm their identities. Domain searches of the translated sequences of the RNAi genes was performed with InterProScan (http://www.ebi. ac.uk/Tools/pfa/iprscan/), using all the default databases. An Evalue of 1e 23 was used as the cut-off threshold, and Pfam results were given precedence. Abundances of the transcripts constituting an RNAi gene are reported as TPM values as described above.