Transcriptome changes of tomato internode elongation induced by far-red light 3 65 3.2.4 Auxin signalling showed strong upregulation in afternoon timepoints To explore the response pathway governed by WL+FR treatment, we conducted a gene ontology (GO) enrichment analysis on up- and downregulated DEGs at different timepoints, utilizing ITAG 4.1 annotation data from Sol Genomics Network (solgenomics. net). We observed several enriched GO categories, with a notable concentration emerging at the 6-hour timepoint. Genes responsive to auxin exhibited a remarkable enrichment in upregulated genes, indicating a substantial 38-fold enrichment (Figure 3.7). What’s particularly interesting is that this enrichment in auxin response was exclusively observed during the afternoon timepoints throughout the entire internode and pith. This implies a synchronized regulation of auxin across all cell types, particularly prominently in the pith, suggesting a diurnal-related effect, a phenomenon previously documented in Arabidopsis (Covington and Harmer, 2007). Pith-30h M82 Pith-30h MM Pith-48h MM Pith-48h M82 copper ion binding serine-type endopeptidase inhibitor activity quinone binding chitin binding amine metabolic process primary amine oxidase activity hydrolase activity- acting on ester bonds catalytic activity trehalose biosynthetic process O-methyltransferase activity 3-beta-hydroxy-delta5-steroid dehydrogenase activity steroid biosynthetic process oxidoreductase activity- acting on the CH-OH group of donors- NAD or NADP as acceptor DNA binding response to auxin FAD binding oxidoreductase activity galactosyltransferase activity transferase activity- transferring alkyl or aryl (other than methyl) groups -log(q value) Pith treated hours and cultivar Up DEGs Down DEGs -4 -2 0 2 Figure 3.8. Gene ontology enrichment analysis of FR-responsive DEGs in pith of each cultivar. Heatmap of the -log of adjusted p-values (q-value) for each enriched GO category. Red color scheme for upregulated DEGs, and blue for downregulated. The DEG comparisons are made by comparing WL+FR to WL in a specific cultivar at a specific timepoint.
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