Percentage of total reads from 9 tissues that mapped uniquely and to multiple locations on the tomato (Solgenomics, SL2.40) and two versions of the draft <i>N. benthamiana</i> genomes.

<p>Percentage of total reads from 9 tissues that mapped uniquely and to multiple locations on the tomato (Solgenomics, SL2.40) and two versions of the draft <i>N. benthamiana</i> genomes.</p

Species distribution of the transcriptome assembly.

<p>A BLASTx using a cutoff value of E-value <1e⁻³ was used to search the transcriptome assembly against Genbank’s non-redundant database.</p

Domains of RNAi proteins.

<p>The figure shows the domains of the RNAi proteins AGO, DCL, DRB and RDR from <i>N. benthamiana</i> (Nb), <i>A. thaliana</i> (At, from TAIR) and <i>S. lycopersicum</i> (Sl, from Solgenomics). Domains were detected with InterProScan against all its default databases, and defined according to the Pfam predictions unless otherwise annotated (*according to SMART database; **according to SUPERFAMILY database).</p

Proportion of unigenes with and without GO annotations.

<p>The figure shows the percentage of unigenes larger (green) and smaller (yellow) than 500 nt that could be annotated with (right) or without (left) GO terms. Mapping metrics show the number of uniquely and multi-mapping reads as a proportion of total number of reads used in the transcriptome assembly. For unigenes without GO terms, the total number of bases of transcripts under and over 500 nt was 14,954,024 nt and 54,714,622 nt, respectively. For unigenes assigned GO terms, the total number of bases under and over 500 nt was 890,086 nt and 18,991,774 nt, respectively.</p

Distribution of TPM and EC residuals.

<p>Boxplots of the residuals (see methods) of TPM (Transcripts Per Million) (left) and normalized EC (Expected Counts) (right) values in different tissues showing the distribution of these values about the median. For the right panel, only EC values greater than 0 were used.</p

Schematic showing the alignment of Sanger sequences to scaffolds in benthgenome.com and solgenomics.net.

<p>Schematic showing the alignment of Sanger sequences to scaffolds in benthgenome.com and solgenomics.net.</p

Relative abundances of RNAi-associated genes.

<p>The figure shows the relative abundances of RNAi genes identified in this study in terms of TPM (Transcripts Per Million) values calculated from the RSEM software. Genes with an asterisk (*) were comprised of more than oneassembled transcript, and the TPM value in this case represents the TPM sum of all its component transcripts.</p

Insertion in the RDR1 sequence of <i>N. benthamiana</i>.

<p>(A) Alignment of the RDR1 sequence from two lines of <i>N. benthamiana</i> (Nb) (16C and Lab), <i>N. tabacum</i> (Nt), <i>S. lycopersicum</i> (Sl) and <i>A. thaliana</i> (At). Only the Nb lines possess an insertion containing two stop codons. (B): PCR of region flanking the 72 base insert in Nb 16C and Lab lines, and Nt, indicating that the insertion is only present in <i>N. benthamiana</i>.</p

Number of matches from complete transcriptome (237,340 transcripts) and unigene set (119,014 transcripts) to five databases.

<p>Number of matches from complete transcriptome (237,340 transcripts) and unigene set (119,014 transcripts) to five databases.</p

List of RNAi associated genes identified and compared to tomato and <i>A. thaliana</i> counterparts.

<p>List of RNAi associated genes identified and compared to tomato and <i>A. thaliana</i> counterparts.</p