Fig. 4: Transcriptional responses to microgravity of WT, gi mutant, 35S:CO and FG plants.

a Numbers of differentially expressed genes (DEGs) identified in WT, gi, 35S:CO and FG (p < 0.01) in response to spaceflight. FC, fold change. b Venn diagram of transcriptomic data (FC ≥ 5), showing the spaceflight responses of DEGs between gi, 35S:CO and FG in comparison with WT, respectively. Red arrows indicate upregulation and downregulation. Density scatter plots show comparisons of the spaceflight microgravity response (sp vs. gr) between gi, 35S:CO, FG and WT. The log₂ fold changes (FCs) are plotted for both the x and y variables. The grey dotted lines represent y = x, and the black dotted lines represent the regression of the data for the gi (y = 0.72x + 0.69, r² = 0.54), the 35S:CO (y = 0.51x + 0.80, r² = 0.40), the FG (y = 0.53x + 1.13, r² = 0.46). The differences in fold changes (sp vs gr) between the gi, 35S:CO or FG and WT, respectively, are indicated by red dots (>5 fold) and grey dots (≤5 fold). sp, spaceflight, gr, ground control. c Principal component analysis (PCA) was done with R package (https://bio-cloud.aptbiotech.com/) and demonstrated a strong difference between transcriptomes of the sp- and the gr-samples. The horizontal axis represents the contribution of principal component 1 (PC1) to distinguishing samples in the two-dimensional graph, whereas the vertical axis represents the contribution of principal component 2 (PC2). d PCA of four different genotypes, WT, gi, 35S:CO and FG, with distance based on fold changes of DEGs in space samples (top-500 genes) in comparison with their controls on ground. sp spaceflight condition, gr ground condition.