Transcriptome changes of tomato internode elongation induced by far-red light 3 63 Additionally, our PCA analysis (Figure S3.1) unveiled a discernible contrast between morning and afternoon timepoints, indicating a robust response linked to the diurnal cycle, which was also reported in Arabidopsis (Franklin, 2020; Fraser et al., 2021). Figure 3.5. Differentially expressed genes (DEGs) upon FR treatment from RNA-seq on tomato SAS internode elongation. (a) First internode FR-responsive DEGs at the four timepoints. (b) First internode and pith FR-responsive DEGs at 30 and 48 hours of FR treatment. (c) Pith and internode diurnal-responsive DEGs, analysed by grouping the morning or afternoon timepoints. Figure 3.6. Overlap between DEGs. Venn diagram showing the overlap in FR-responsive DEGs in (a) first internode over time, and (b) in the two tissues, first internode or pith, at 30h and 48h. To conduct a detailed examination of the DEGs, we looked at the overlap in upregulated genes in the internode over time (Figure 3.6). It’s worth noting that at the 6-hour timepoint, a substantial number of DEGs are uniquely present. Additionally, when
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