Additional file 1 of Transcriptomic analysis at organ and time scale reveals gene regulatory networks controlling the sulfate starvation response of Solanum lycopersicum

Additional file 1: Figure S1. Total leaf area is reduced by sulfate deficiency from 3 weeks after sowing. Figure S2. A) Number of differentially expressed genes by sulfate starvation in roots, leaves or shared by both organs at 2, 3 and 4 weeks after sowing. B) Venn diagrams showing the overlap between early sulfate-regulated genes in roots and late regulated genes in leaves. Figure S3. qPCR validation of RNA-seq data. A) Correlation between relative mRNA levels of qPCR and RNA-seq data on selected transcripts. The list of selected differentially expressed genes by sulfate starvation is shown in Table S3. B) Heatmap comparing the expression patterns of selected genes analyzed by qPCR and RNA-seq. Figure S4. Hierarchical clustering of 52 genes included in the GO term “cellular response to phosphate starvation”, the most enriched GO term of sulfate-responsive orthologous gene families that are found exclusively in tomato plants. Figure S5. Co-expression clusters down-regulatedby sulfate starvation of genes significantly affected by sulfate and time in roots (left) and leaves (right) (q-value 1). On each box, the central mark indicates the median, and the bottom and top edges of the box indicate the 25th and 75th percentiles, respectively. Whisker indicates standard deviation of the expression data of all genes belongs to the cluster. Figure S6. Co-expression clusters up-regulated by sulfate starvation of genes significantly affected by sulfate and time in leaves (q-value 1). On each box, the central mark indicates the median, and the bottom and top edges of the box indicate the 25th and 75th percentiles, respectively. Whisker indicates standard deviation of the expression data of all genes belongs to the cluster. Figure S7. A) Distribution of Cluster 1 genes regulated by sulfate and time in leaves across different categories of the primary metabolism using Mapman4 annotation framework. B) Mapman analysis of sulfate starvation responsive genes in at least one time in leaves. C) Mapman analysis of sulfate starvation responsive genes in at least one time in roots. Figure S8. The root regulatory network. Blue nodes represent TFs and red nodes represent target genes. Figure S9. The leaf regulatory network. Blue nodes represent TFs and red nodes represent target genes. Figure S10. Expression profiles of the phosphate transporter genes Solyc02g088220, Solyc09g066410 and Solyc09g090080 in response to sulfate starvation at 2, 3 and 4 weeks after sowing.