Size distribution of small RNA sequences.

<p>(A) Reads and unique sequence distribution in all the small RNA libraries. 24 and 21nt length reads are the most abundant reads among the small RNAs. (B) Size distribution of reads originating from leaf (dark grey) and stolon (light grey) tissues expressed as a percentage of total reads. 24 and 21nt length reads are dominant in both of the tissues; in stolon tissues there are more reads for 21, 23 and 24nt length.</p

Origin of miRNA precursors.

<p>The majority of miRNA precursors are transcribed from intergenic regions. miRNA precursors originating from coding regions locates mainly in introns.</p

Heatmap representation of differentially expressed genes upon PSTVd infection.

<p>Visualization of differentially expressed genes of leaf (A) and tuber (B) tissues in mock inoculated and infected plants as indicated. Three biological replicates are shown, but for late infected tissues only two. Colour key indicates the expression change compared to mock inoculated samples.</p

Quantitative RT-PCR analysis of candidate genes.

<p>Mock infected plants were used to normalize fold change of early and late samples in leaf and tuber tissues as indicated. White bars represent the RT-qPCR analysis; grey bars show the microarray data. Error bars represent standard error (SE). L23 and PP2A genes were used as internal normalization controls. Asterisk indicates that the means of fold change of the mock and infected samples are significantly different (Student’s t-test).</p

Differentially expressed genes on three superscaffolds under the tuber shape QTLs.

<p>Differentially expressed genes on three superscaffolds under the tuber shape QTLs.</p

Representation of GO term enrichment.

<p>Selected GO term enrichments are visualized in early (A) and late (B) leaf samples. Figs (C) and (D) show GO term enrichment for early and late tuber samples, respectively. Categories are indicated on Y axis, log10[1/p] is on the X-axis where p is the p-value of the enrichment.</p