dataset belonging to Bezemer et al. Journal of Ecology

data from a greenhouse study. data include plant biomass, soil chemistry, fungal composition (TRFLP) and calculated plant growth parameters. explanations are in the fil

Amino acid concentrations in the shoots.

<p>Amino acid concentrations were measured by HPLC in the shoots after RJA, SJA and CON at day 1, 3, 7 and 14. The concentration of almost all amino acids was affected by JA treatment, whereby some (Arg, Asp, Gln, His, Phe) responded differently to RJA than SJA. Concentrations are expressed in nmol/mg dry plant material after RJA (dotted line, open circles), SJA (dashed line, squares) or control treatment (solid line, triangles). Error bars represent standard errors. Samples with a significantly different concentration compared to control are marked with an asterisk (p-value <0.05, t-test independent samples assuming unequal variances).</p

The correlation coefficients of the transcriptome profiles of all treatment groups.

<p>For calculation of the correlation coefficients, we used the fold changes in expression compared to control treatment for all measured genes after RJA and SJA. The number of genes that were statistically significantly up or down regulated compared CON (ANOVA with FDR corrected <i>P</i>-value <0.1) are shown at the bottom of the table.</p

Gene expression in the glucosinolate synthesis pathway.

<p>The JA response of the genes involved in glucosinolate synthesis was weaker in the roots than in the shoots. In the shoots, RJA resulted in a stronger induction of several transcription factors and enzymes involved in the biosynthesis of aliphatic glucosinolates than SJA. In contrast, for the indole glucosinolate pathway, SJA lead to a stronger induction of the involved genes than RJA. Histograms represent the log₂ of the fold changes in expression after RJA or SJA compared CON for all genes that were significantly affected in at least one of the treatment groups (ANOVA, FDR corrected <i>P</i>-value <0.1). Samples showing a significantly different expression compared to CON are marked with an asterisk. RRJA, Root tissue RJA treatment; RSJA Root tissue SJA treatment, SRJA, Shoot tissue RJA treatment, SSJA, Shoot tissue SJA treatment.</p

Volatile terpene biosynthesis genes respond differently to RJA versus SJA Treatment.

<p>In the roots, RJA strongly induced the monoterpene synthesis genes, while SJA did not. In the shoots, the homoterpene synthesis gene <i>TPS04</i> was only induced by SJA, while RJA even significantly repressed the homoterpene synthesis gene <i>CYP82G1</i>. Expression is shown as log₂ of fold changes RJA or SJA compared to CON. Samples in which the gene showed a significantly altered expression compared to CON are marked with an asterisk (ANOVA, FDR corrected <i>P</i>-value <0.1). RRJA, Root tissue RJA treatment; RSJA Root tissue SJA treatment; SRJA, Shoot tissue RJA treatment; SSJA, Shoot tissue SJA treatment.</p

The number of different genes in each functional classification bin showing at least a 3-fold difference in expression after RJA versus SJA in the roots, shoots or in total in both tissues.

<p>The number of different genes in each functional classification bin showing at least a 3-fold difference in expression after RJA versus SJA in the roots, shoots or in total in both tissues.</p

Differential expression of JAZ genes depending on tissue as well as site of induction.

<p>In the shoots, <i>JAZ1, 2, 5, 6</i> and <i>12</i> were induced after JA treatment, while in the roots mainly <i>JAZ1, 2, 3 5, 6</i> and <i>10</i> responded. In the roots, a 10-fold induction was found of <i>JAZ10</i> after RJA, while only a two-fold after SJA. Gene expression is shown as log₂ of fold changes after RJA or SJA compared to CON. Samples in which the gene showed a significantly altered expression compared to CON are marked with an asterisk (ANOVA, FDR corrected <i>P</i>-value <0.1).</p

Average fold change analysis per gene functional classification bin.

<p>The average fold change per bin was analyzed with PageMan on all measured genes in roots and shoots at 6, 18 and 30 h after JA treatment. The shoots showed a more extensive JA response than the roots. In roots and shoots, the Amino Acid and Protein Synthesis bins were strongly induced, indicating large metabolic changes. In both tissues, several bins were only affected by one of the treatments. Fold changes were either RJA/CON, SJA/CON or SJA/RJA. Bins showing a significantly higher or lower average fold change compared to all other bins are highlighted with a red or green gradient, respectively, while bins that were not significantly affected in any of the treatment groups were omitted from the table (Wilcoxon test with Benjamini-Hochberg multiple testing correction).</p

Gene expression in the JA synthesis pathway.

<p>In the shoots, a strong induction was observed of <i>LOX2</i> after JA treatment, whereas in the roots <i>LOX2</i> did not respond and only a two-fold up regulation of <i>LOX1</i> was observed. In both roots and shoots, RJA and SJA differentially affected the expression of the <i>AOC</i> and <i>OPR3</i> genes. Heat maps represent the log₂ of the fold changes in expression after RJA or SJA compared to CON for all genes that were significantly affected in at least one of the treatment groups (ANOVA, FDR corrected <i>P</i>-value <0.1). RRJA, Root tissue RJA treatment; RSJA Root tissue SJA treatment; SRJA, Shoot tissue RJA treatment; SSJA, Shoot tissue SJA treatment.</p

Sugar concentrations in the shoots.

<p>Sugar concentrations were measured by HPLC in the shoots after RJA, SJA and CON at day 1, 3, 7 and 14 after JA application. RJA and SJA resulted in a decreased concentration of sucrose, glucose as well as fructose at day 1, 3 and 7. Concentrations are expressed in nmol/mg dry plant material. RJA, dotted line and open circles; SJA, dashed line and squares; CON; solid line and triangles. Error bars represent standard errors. Samples with a significantly different concentration compared to control are marked with an asterisk (p-value <0.05, t-test independent samples assuming unequal variances).</p