Additional file 1 of The role of strigolactones in P deficiency induced transcriptional changes in tomato roots

Additional file 1:Suppl. Fig. 1. Experimental design of the P starvation RNAseq experiment. Suppl. Fig. 2. KEGG pathway enrichment for induced (A) and repressed (B) DEGs in tomato roots upon P starvation and P replenishment. Suppl. Fig. 3. Heatmap showing fold change of SL related genes in RNAseq dataset and RT-qPCR validation of SL biosynthetic and P starvation marker genes. A, heatmap showing fold change of genes involved in the SL biosynthetic and signaling pathway under P starvation for different time periods and P replenishment in WT tomato and CCD8 RNAi line. A fold change in bold indicates significance (P<0.05). B-D, relative expression of D27 (B), CCD8 (C) and LePS2 (D) upon P starvation (and P replenishment) (n = 3). The gene expression level in 2-day control wild‐type plants (YP2) was set to 1. Error bars represent standard error of the mean. **, 0.01>P; *, 0.01 < P < 0.05; NG, not significant. E, comparison of RT-qPCR and RNA-seq data. A Pearson correlation coefficient of 0.9761 (P < 0.01) is observed between the RNA-seq and RT-qPCR data of three genes (D27, CCD8 and LePS2). Suppl. Fig. 4. PCA of tomato root transcript profiles using RPKM. YP4 and NP4 represent 4 days control P and P starvation treatment in WT, respectively. CCD8.YP4 and CCD8.NP4 represent control P and P starvation treatment in CCD8, respectively. Suppl. Fig. 5. Heatmap showing a selection of strongest induced and repressed DEGs in the roots of WT tomato and CCD8 RNAi line under different P starvation treatment times. The RPKM value of the top 10 strongest P starvation induced DEGS (at 2, 3, 4 and 5 days of P starvation) and their repression by P replenishment in WT, and DEGs at 4 days of P starvation in CCD8 RNAi line. Suppl. Fig. 6. Secondary metabolism visualization of PS induced DEGs, PS repressed and SL-dependent DEGs with iPath 3.0 [53, 54]. A, secondary metabolite biosynthesis visualization of P starvation repressed DEGs (4 days) in WT. B, secondary metabolite biosynthesis visualization of P starvation repressed and SL-dependent DEGs. Suppl. Fig. 7. Expression profiles of steroid and brassinosteroid pathway in the root of tomato under normal P and P starvation. A, schematic representation of steroid biosynthesis and schematic representation of brassinosteroid biosynthesis (from KEGG) [54]. B, hierarchical clustering diagram of brassinosteroid biosynthesis related genes (H1 and H2 represent homolog 1 and 2, respectively). YP4 and NP4 represent tomato WT at 4 days of control P and P starvation, respectively. CCD8.YP4 and CCD8.NP4 represent the CCD8 RNAi line at 4 days of control P and P starvation, respectively. SMT, STEROL 24-C-METHYLTRANSFERASE; STE, DELTA(7)-STEROL-C5(6)-DESATURASE; DWF, DELTA (24)-STEROL REDUCTASE; SMO, C-4Α-STEROL-METHYLOXIDASE2; DET, STEROID 5-ALPHA-REDUCTASE. Suppl. Table 1. Gene list and go enrichment of 48 DEGs (common P starvation induced DEGs). Suppl. Table 2. Summary of Go enrichment of P starvation repressed DEGs. Suppl. Table 3. The fold change of 108 DEGs (SL dependent P starvation induced genes) after 4 days P starvation in WT and CCD8. Suppl. Table 4. The KO of P starvation induced DEGs. Suppl. Table 5. The KO of P starvation repressed DEGs. Suppl. Table 6. The KO of 31 DEGs (P starvation repressed and SL dependent DEGs). Suppl. Table 7. The KO of 108 DEGs (P starvation induced and SL dependent DEGs). Suppl. Table 8. An overview of raw read numbers, and trimming and mapping statistics. Suppl. Table 9. Primers used in this study. Suppl. Data set 1. The DEGs of 2 days P starvation in wild type. Suppl. Data set 1. S1, significant DEGs after 2 days P starvation in wild type. Suppl. Data set 1. S2, GO enrichment of 2 days P starvation significantly induced genes in PlantRegMap (P value <=0.01). Suppl. Data set 2. The DEGs of 3 days P starvation in wild type. Suppl. Data set 2. S1, significant DEGs after 3 days P starvation in wild type. Suppl. Data set 2. S2, GO enrichment of 3 days P starvation significantly induced genes in PlantRegMap (P value <=0.01). Suppl. Data set 2. S3, GO enrichment of 3 days P starvation significantly repressed genes in PlantRegMap (P value <=0.01). Suppl. Data set 3. The DEGs of 4 days P starvation in wild type. Suppl. Data set 3. S1, significant DEGs after 4 days P starvation in wild type. Suppl. Data set 3. S2, GO enrichment of 4 days P starvation significantly induced genes in PlantRegMap (P value <=0.01). Suppl. Data set 3. S3, GO enrichment of 4 days P starvation significantly repressed genes in PlantRegMap (P value <=0.01). Suppl. Data set 4. The DEGs of 5 days P starvation in wild type. Suppl. Data set 4. S1, significant DEGs after 5 days P starvation in wild type. Suppl. Data set 4. S2, GO enrichment of 5 days P starvation significantly induced genes in PlantRegMap (P value <=0.01). Suppl. Data set 4. S3, GO enrichment of 5 days P starvation significantly repressed genes in PlantRegMap (P value <=0.01). Suppl. Data set 5. The DEGs of one day P replenishment in wild type. Suppl. Data set 5. S1, significant DEGs of one day P replenishment after 4 days P starvation in wild type. Suppl. Data set 5. S2, GO enrichment of one day P replenishment after 4 days P starvation significantly induced genes in PlantRegMap (P value <=0.01). Suppl. Data set 5. S3, GO enrichment of one day P replenishment after 4 days P starvation significantly repressed genes in PlantRegMap (P value <=0.01). Suppl. Data set 6. The DEGs of 4 days P starvation in CCD8 RNAi line. Suppl. Data set 6. S1, significant DEGs after 4 days P starvation in CCD8 RNAi line. Suppl. Data set 6. S2, GO enrichment of 4 days P starvation significantly induced genes in PlantRegMap (P value <=0.01). Suppl. Data set 6. S3, GO enrichment of 4 days P starvation significantly repressed genes in PlantRegMap (P value <=0.01). Suppl. Data set 7. The DEGs in CCD8 RNAi line compared with wild type under P starvation condition. Suppl. Data set 7. S1, significant DEGs in CCD8 RNAi line compared with wild type after 4 days P starvation. Suppl. Data set 7. S2, GO enrichment of significant induced DEGs in CCD8 RNAi line compared with wild type after 4 days P starvation (P value <=0.01). Suppl. Data set 7. S3, GO enrichment of significant repressed DEGs in CCD8 RNAi line compared with wild type after 4 days P starvation (P value <=0.01).