Supplemental Fig. S 2Cluster Tree Involving All the Biological Samples of the Leaves And

Supplemental Fig. S2Cluster tree involving all the biological samples of the leaves and roots of Brassica napus seedlings, which were cultivated under B deficiency (0.25 μM H3BO3), sufficiency (25 μM H3BO3) and toxicity (1,500 μM H3BO3) conditions for 10 d. The distances of expressed genes are calculated by euclidean method. The algorithm of sum of squares of deviations isused to calculate the distance between samples so that cluster tree can be built. Y axis means height in the cluster tree. When the biological samples have similar height values, they are easily tobe gathered. Rep. = replicate.

Supplemental Fig. S3Intersection heat-maps of gene expression for each cluster plan for the leaves and roots of Brassica napus seedlings,which were cultivated under B deficiency (0.25 μM H3BO3), sufficiency (25 μM H3BO3) and toxicity (1,500 μM H3BO3) conditions for 10 d. Genes that are expressed in all samples of each cluster plan are used to build this heat-map. Gradient colorbarcode at the right top indicates the log2(FPKM) values. Each row represents a gene and each column represents a sample. Genes with similar expression value are clustered both at row and column level. Rep. = replicate.

Supplemental Fig. S4 Gene ontology (GO) functional classification on the differentially expressed genes (DEGs) that were detected in the leaves (L) and roots (R) of Brassica napus seedlings, which were cultivated under B deficiency (0.25 μM H3BO3, Bd), sufficiency (25 μM H3BO3, Bs) and toxicity (1500 μM H3BO3, Bt) conditions for 10 d. GO enrichment analysis of the DEGs in the leaf under B deficiency (a) and B toxicity (b); GO enrichment analysis of the DEGs in the root under B deficiency (c) and B toxicity (d). The B sufficiency condition was used as the control. X axis means the number of DEGs, and Y axis represents GO terms. All the GO terms are grouped in to three ontologies: blue is for biological process, green is for cellular component and red is for molecular function.

Supplemental Fig. S4 S5 Kyoto Encyclopedia of Genes and Genomes (KEGG) ( (Kanehisa et al. 2008) enrichment analysis of the differentially expressed genes (DEGs) that were detected in the leaves and roots of Brassica napus seedlings, which were cultiavted under B deficiency (0.25 μM H3BO3), sufficiency (25 μM H3BO3) and toxicity (1,500 μM H3BO3) conditions for 10 d.(a) KEGG enrichment analysis of the DEGs in the leaf. (b) KEGGGO enrichment analysis of the DEGs in the root. The B sufficiency condition was used as the control, and the criterion for the identification of DEGs was as follows: false discovery rate (FDR) ≤ 0.05 and the absolute value of log2 (fold-change) ≥ 1.