Exploring conservation of cellular-level traits in shade avoidance syndrome among species 5 185 To also benefit from existing Arabidopsis gene expression data, we examined the expression patterns of homologs AT5G51910, AT2G45050, AT2G45680, and AT2G42380 in Arabidopsis using the eFP browser (Winter et al., 2007)(Figures S5.45.8). The homolog of Solyc08g080150 in Arabidopsis, AT5G51910, reveals heightened expression in inflorescence and seed, hinting at a role in later developmental stages. AT2G45680 shows high expression in leaves and second internode of inflorescence stem. Then, the homolog of Solyc01g090760 in Arabidopsis, AT2G45050, displays its peak expression in petals, while the homolog of Solyc07g053450, AT2G42380, shows strong expression in mature pollen. Together, these distinct expression patterns suggest specific involvement of each homolog in later stages of Arabidopsis development. Additionally, AT2G45050, AT2G45680, and AT2G42380 were also reported to be upregulated in FR response in Arabidopsis leaf tip (Küpers et al., 2023), these three genes were found in differentially expressed in hypocotyl after FR seedling treatment (Kohnen et al., 2016b), indicating that they have FR-responsive regulation in other parts of Arabidopsis than what we profiled. This lack of conservation of FR-responsive expression patterns between the Solanaceae and Brassicaceae/Fabaceae families sparks intriguing questions about the underlying genetics and evolution of the FR-response. This disparity prompts the hypothesis that the observed transcription factor behaviors—upregulation in Solanaceae and downregulation in Brassicaceae/Fabaceae—may signify a family-specific FR-induced function for these TFs. An alternative hypothesis would be these transcription factors are not functionally related to shade avoidance it is very specific upregulated in our qPCR and RNA-seq results due to tissue/timepoint limitations. This finding opens avenues for deeper investigation into the unique regulators in shade avoidance syndrome in Solanaceae family compared to other diverse families. When TF expression is not conserved across different species, it indicates that the regulatory mechanisms inducing these TFs may have diverged during evolution, resulting in differences in gene expression patterns. Studies have shown that the conservation of TF binding events is associated with the conservation of gene expression at the individual gene level (Hemberg and Kreiman, 2011). However, it is important to note that the conservation of TF binding events and gene expression can vary across different species and tissues (Diehl and Boyle, 2018). Therefore, the lack of conservation in TF expression across species suggests that the regulatory control of gene expression by these TFs has evolved differently, potentially leading to species-specific or tissue-specific gene expression patterns.
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