Additional file 1 of Temporal transcriptomic differences between tolerant and susceptible genotypes contribute to rice drought tolerance
Creators: name: Xia, Hui
name: Ma, Xiaosong
name: Xu, Kai
name: Wang, Lei
name: Liu, Hongyan
name: Chen, Liang
name: Luo, Lijun
Publisher: name: figshare
Year: 2020
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Mental Health

description: Additional file 1: Supplementary Figure S1. Soil water contents monitored during the experimental period. The grey dot and dashed line indicate coefficient of variance (C.V.). Supplementary Figure S2. Venn diagram of DEGs detected during drought period, DEGs detected at recovery, and function-studied drought-tolerant (DT) genes. Supplementary Figure S3. Overlap of DEGs detected among genotypes or between the tolerant and the susceptible groups. Supplementary Figure S4. Mean absolute Log2(fold changes) of DEGs of different frequencies detected at among 12 rice genotypes from time points D1 to R (a-f). Supplementary Figure S5. Cluster analysis of 12 rice genotypes in drought (D) and well-watered (W) fields based on expressions levels of total expressed genes from time points D1 to R (a-f). Supplementary Figure S6. Cluster analysis of 12 rice genotypes in drought (D) and well-watered (W) fields based on expressions levels of DEGs from time points D1 to R (a-f). Supplementary Figure S7. Cluster analysis of 12 rice genotypes by SNP called from total transcripts (a) and transcripts of DEGs (b). Supplementary Figure S8. Results of principal component analysis of the tolerant and the susceptible groups at six time points (D1-D5 and R) based on their DEGs (a) and enriched GO biological processes (b). Supplementary Figure S9. Venn diagram of drought-responsive genes (DRG) and recovery related genes (RRG) in the tolerant and the susceptible groups. Supplementary Figure S10. Distributions of enriched GO biological processes in various GO classifications by tolerant (T)-specific, susceptible (S)-specific, and T-S different DRGs. Supplementary Figure S11. Time-series clusters based on Log2(fold change) in the tolerant groups during drought period. Supplementary Figure S12. Time-series clusters based on Log2(fold change) in the susceptible groups during drought period. Supplementary Figure S13. Regulation modes of recovery related genes (RRGs) and their differences between the tolerant and the susceptible groups. Supplementary Figure S14. A heatmap describing temporal differences of enriched GO biological processes (Bonferroni corrected p &lt; 0.05) between the tolerant and the susceptible groups at six time points (D1-D5 and R). Supplementary Figure S15. A heatmap describing temporal differences of enriched GO biological processes (p &lt; 0.05) in the GO classification of carbohydrate metabolic process (GO:0005975) between the tolerant and the susceptible groups at six time points (D1-D5 and R). Supplementary Figure S16. A heatmap describing temporal differences of enriched GO biological processes (p &lt; 0.05) in the GO classification of lipid metabolic process (GO:0006629) between the tolerant and the susceptible groups at six time points (D1-D5 and R). Supplementary Figure S17. A heatmap describing temporal differences of enriched GO biological processes (p &lt; 0.05) in the GO classification of protein metabolic process (GO:0019538) between the tolerant and the susceptible groups at six time points (D1-D5 and R). Supplementary Figure S18. A heatmap describing temporal differences of enriched GO biological processes (p &lt; 0.05) in the GO classification of nucleobase, nucleoside, nucleotide, and nucleic acid metabolic process (GO:0006139) between the tolerant and the susceptible groups at six time points (D1-D5 and R). Supplementary Figure S19. A heatmap describing temporal differences of enriched GO biological processes (p &lt; 0.05) in the GO classification of transporter (GO:0006810) between the tolerant and the susceptible groups at six time points (D1-D5 and R). Supplementary Figure S20. A heatmap describing temporal differences of enriched GO biological processes (p &lt; 0.05) in the GO classification of secondary metabolic process (GO:0019748) between the tolerant and the susceptible groups at six time points (D1-D5 and R). Supplementary Figure S21. Cluster analyses of rice genotypes in the drought field (D) at time points D1 to D5 (a-e) and recovery stage (R) (f) based on expressions of photosynthesis-relevant genes. Supplementary Figure S22. Cluster analyses of rice genotypes in the well-watered field (W) at time points W1 to W5 (a-e) based on expressions of photosynthesis-relevant genes. Supplementary Figure S23. A heatmap of regulations of photosynthesis-relevant DRGs during drought period (D1-D5) and at recovery (R) by mean log2(fold changes) in tolerant (T) and susceptible (S) groups. Supplementary Figure S24. A heatmap of regulations of phytohormone-relevant DRGs during drought period (D1-D5) and at recovery (R) by mean log2(fold changes) in tolerant (T) and susceptible (S) groups. Supplementary Figure S25. The matrix of mean Pearson’s correlation coefficients (PCCs) calculated from DRGs among eight phytohormones. The above matrix is of tolerant genotypes while the below one is of susceptible genotypes. Supplementary Figure S26. Venn diagram of (a) osmolality- and H2O2- correlated drought-responsive genes and (b) DTIB- and biomass- correlated drought-responsive genes. Supplementary Figure S27. Comparisons of absolute values of Log2(Fold change) of osmolality- (a) and H2O2-correlated (b) drought-responsive genes (DRGs) between the tolerant and the susceptible groups at six time points. Bars indicate standard errors. “*”, “**”, and “***” indicate significant differences at p &lt; 0.05, p &lt; 0.01, and p &lt; 0.001 by independent t test between the tolerant and the susceptible groups.