Transcriptome changes of tomato internode elongation induced by far-red light 3 79 06h In 24h In 30h In 48h In 30h Pith 48h Pith Solyc00g500025 Solyc00g500058 Solyc00g500064 Solyc00g500072 Solyc00g500131 Solyc00g500137 Solyc00g500140 Solyc00g160190 Solyc00g500207 Solyc00g500209 Solyc00g500297 Solyc00g500320 Solyc00g500330 Solyc02g031900 Solyc02g031970 Solyc03g118150 Solyc06g071370 Solyc07g041930 Solyc07g052950 Solyc10g005100 Log FC -0.5 0 0.5 1.0 Figure 3.16. Hub gene expression heatmap. The heatmap colors indicate average fold change in response to FR treatment, red indicating upregulation in FR and blue indicating downregulation. 3.2.11 TF identification identified well-recognized motifs that regulate cell fate Next, we wanted to explore the possible transcriptional regulators of the gene expression changes we observed. With a list of tomato transcription factors (ITAG 3.2 annotation) obtained from Plant Cistrome Database (http://neomorph.salk.edu/dap_web/pages/ index.php)(O’Malley et al., 2016), we identified the DEGs which are TFs (Table S3.2). Then, we looked for TFs whose Arabidopsis orthologs had functional annotations related to cell size, cell elongation and cell expansion. Our primary focus moving forward was centered on the transcription factors (TFs) that have already been identified and are known for their functions in cell or organ elongation. Many of these TFs have previously been studied in Arabidopsis and Solanaceae roots under stress conditions, where they play a role in regulating e.g. epidermis cell functions and anthocyanin biosynthesis, including basic-helix-loop-helix (bHLH) GLABRA3 (GL3), ENHANCER OF GLABRA3 (EGL3),) and MYB transcription factors (such as CAPRICE PAP1, PAP2, MYB113 or MYB114 in Arabidopsis and FER in tomato). MYBs, such AtMYB30 in Arabidopsis root
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