Transcriptome changes of tomato internode elongation induced by far-red light 3 67 typically relies on energetically favourable non-covalent interactions (Dang, 2022). Pyruvate metabolism involves energy consumption: the input of energy in the form of ATP and NADH during the conversion of pyruvate to acetyl-CoA in the mitochondria (McCommis and Finck, 2015; Bispo and Vieira, 2022). These energy exchange activities are instrumental in sustaining vital cellular functions, such as energy storage and signalling processes (McCommis and Finck, 2015; Lim et al., 2017; Dang, 2022). This result is consistent with the previous finding in FR pre-treatment of 4-week-old tomato (Courbier et al., 2020), where it was observed that in WL there was a downregulation of genes associated with glucan-related structural processes, potentially indicating carbohydrate reallocation for energy production in response to a fungal pathogen. 3.2.7 Examining pith-specific expression in comparison to the whole internode under far-red light conditions Delving into the significance of pith as a tissue understudied, we examined enriched GO categories to unravel its roles and functions. In all pith-specific GO enrichments (Figure 3.9), transmembrane transport was highly upregulated. This may indicate that the movement of nutrients and/or metabolites was active in pith cells, and it is a typical stress adaptive strategy in abiotic stress due to ionic balance and sugar supply change (Gill et al., 2021). At the same time, multiple photosynthesis-related GO terms were enriched in the downregulated DEGs at the beginning of FR treatment. From 6 hours until 48 hours, the sugar-related transfer pathway was enriched in the downregulated DEGs, with the most drastic response happening at 6 hours and gradually soothing down. Enriched GO categories highlighted the heightened activity of transmembrane transport in pith cells, suggesting an adaptive strategy in response to abiotic stress. Concurrently, the downregulation of photosynthesis-related GO terms and the sugar-related transfer pathway indicated dynamic shifts in cellular processes over the course of the far-red light treatment. 3.2.8 DNA-binding is enriched in FR-upregulated DEGs The second most enriched pathway in upregulated DEGs, which consistently appeared at multiple timepoints in response to far-red light (FR), is associated with DNA binding (Figure 3.7). DNA-binding proteins include transcription factors, which control the expression of genes by binding to specific DNA sequences in the promoter region of genes, and chromatin-modifying enzymes, which modify the structure of the DNA molecule and its associated proteins to regulate gene expression (Luscombe et al., 2000). This DNA-
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