Table displaying the results of the module/intersection enrichment analysis.

Results are broken down into two tabs, one for leaf tissue and one for root tissue. The first column represents each stress and stress combination through single letter abbreviations (D = dry-down, P = PEG, S = salt, N = low-nutrient), the second column lists the module being tested for enrichment within the given intersection, the third column lists the under represented P-value, and the fourth column represents the over represented P-value. (XLSX)</p

Table listing the output of GO term enrichment analysis for each co-expression network module.

Each tab contains a GO term along with over represented and under represented P-values, the number of DEGs found belonging to that category, the total number of genes belonging to that category, the description of the GO term, and the GO ontology category that term belongs to. Each tab corresponds to a different module in the network. (XLSX)</p

MDS plots illustrating the transcriptomic response to each stress across samples.

(A) MDS plot based on the expression values of all genes included in this analysis for leaf tissue and (B) root tissue. (C) MDS plots generated from the expression values of DEGs shared among all four stresses for leaf tissue and (D) root tissue. Control samples were not included in panels C and D as the genes under consideration in these analyses were by definition differentially expressed relative to control.</p

Multidimensional scaling (MDS) plots created from various sample and gene sets to show how samples differentiate across gene expression space.

Samples are labeled using a common naming theme: The first letters correspond to the stress treatment (DD = dry-down, P = PEG, S = salt, N = low-nutrient), followed by a number representing the identity of that sample, followed by another letter corresponding to tissue type (L = leaf, R = root). The set of samples and genes used for each MDS plot are described in the label for each subfigure. (PDF)</p

Phenotypic means and standard deviations of all measured traits (n = 21).

Phenotypic means and standard deviations of all measured traits (n = 21).</p

Table listing the output of KEGG term enrichment analysis for each set of DEGs and each intersection of DEGs displayed in Fig 2.

Each tab contains a KEGG term along with the description of the KEGG term, over represented and under represented P-values, the number of DEGs found belonging to that category, and the total number of genes belonging to that category. Each tab is labeled by stress (D = dry-down, P = PEG, S = salt, N = low-nutrient), tissue type (L = leaf, R = root), and a descriptor of the set of genes tested for enrichment (allDEGs = the set of all DEGs from that stress, Unique = the DEGs that were unique to a given stress, Intersect = the set of DEGs that are shared among the stresses listed in the tab name). (XLSX)</p

UpSet plot depicting the number of unique DEGs shared among combinations of stresses.

DEGs shared between stresses are depicted by filled black dots in each stress category with connecting lines between them. For categories with only a single stress, the number of DEGs depicted are only those unique to that individual stress and do not contain DEGs that are shared between multiple stresses. Up and down arrows above sets represent significantly more or less DEGs than expected by chance, respectively. The total number of DEGs for a given stress is represented by the histogram in the lower left portion of each panel. (A) Shared DEGs in leaf tissue (green). (B) Shared DEGs in root tissue (orange).</p

Dendrogram of sample clustering created prior to the construction of the gene co-expression network for the purpose of identifying and removing outliers.

(TIF)</p

Table listing the output of GO term enrichment analysis for each set of DEGs and each intersection of DEGs displayed in Fig 2.

Each tab contains a GO term along with over represented and under represented P-values, the number of DEGs found belonging to that category, the total number of genes belonging to that category, the description of the GO term, and the GO ontology category that term belongs to. Each tab is labeled by stress (D = dry-down, P = PEG, S = salt, N = low-nutrient), tissue type (L = leaf, R = root), and a descriptor of the set of genes tested for enrichment (allDEGs = the set of all DEGs from that stress, Unique = the DEGs that were unique to a given stress, Intersect = the set of DEGs that are shared among the stresses listed in the tab name). (XLSX)</p

Directionality of DEG expression among stress intersections.

Directionality of DEG expression among stress intersections.</p