Differentially expressed transcripts between inoculation and wounding treatments.

<p>^# BaseMean values indicate the normalized read frequency data.</p><p>^§ The indicated expression values are the average Log 2 fold change values over all genotypes relative the controls (0 dpi) as determined with the condition based negative binominal distribution test (<i>nbinomTest</i>).</p><p>^¥<i>Padj</i> indicates the <i>P</i>-value after adjustment for false discovery rate with the Benjamini-Hochberg procedure.</p><p>Differentially expressed transcripts between inoculation and wounding treatments.</p

Expression pattern of selected transcripts in an independent Norway spruce material compared to the RNAseq frequency data.

<p>Isotig01779, <i>beta-glucosidase</i> (a); isotig04668 <i>GLP2</i> (b); isotig00380, <i>OPR-like</i> (c); contig00509, <i>isoflavone reductase-like</i> (d); isotig06030, <i>ns-LTP</i> (e) and isotig06890, <i>hin1-like</i> (f). The columns indicate relative expression levels over the control, determined with qPCR, for each time point and treatments. The bars indicate the standard error (SE) and superscript letters indicate significant differences between treatments (<i>P</i><0.05, Kruskal-Wallis test with Dunn´s post test), N = 3. The circles indicate the basemean data reported by DEseq, where shaded symbols were significantly different from un-treated bark.</p

Differentially expressed transcripts in inoculation and wounding treatment relative to the control at different time points.

<p>A Venn diagram showing the differentially expressed genes (<i>P</i>-value <0.05 after FDR [Benjamini-Hochberg procedure]) at 5 dpi inoculation with <i>H</i>. <i>annosum</i> (green) or wounding (yellow) and 15 dpi inoculation with <i>H</i>. <i>annosum</i> (red) or wounding (blue).</p

Annotation statistics of the assembled transcripts.

<p>^# Total number of isotigs (putative splice variants of genes) assembled with Newbler 2.6.</p><p>^§ Isotigs annotated with Blast2GO [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0131182#pone.0131182.ref018" target="_blank">18</a>]</p><p>^† Taxonomic assignation with MEGAN4 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0131182#pone.0131182.ref019" target="_blank">19</a>]</p><p>^¥ Isotigs with best hit to <i>Picea sitchensis</i> proteins in Genbank</p><p>*Reciprocal best blastn hit with the <i>P</i>. <i>abies</i> 1.0 transcript database [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0131182#pone.0131182.ref027" target="_blank">27</a>]</p><p>^¤ Isotigs without a significant hit in the <i>P</i>. <i>abies</i> 1.0 transcript database, and of these likely <i>Pinaceae</i> and fungal genes are reported.</p><p>Annotation statistics of the assembled transcripts.</p

Two-way clustering of the 150 most highly expressed transcripts.

<p>A two–way clustering of normalized 454 sequence count data using Ward’s hierarchical cluster algorithm. The increasing intensity of red in the heat map visualise counts from white (no counts in the particular condition) to red. Clusters are indicated by numbers and the enriched GO categories are noted for each cluster. Clusters containing significantly regulated genes are highlighted in colour, with orange for cluster 3, containing genes significantly induced in inoculated samples and blue for clusters with genes more highly expressed in control than in wounding. Please refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0131182#pone.0131182.s005" target="_blank">S4 Table</a> for information about specific isotigs found in the clusters.</p