Chapter 6 218 SAUR upregulation was the main component of the auxin response Gene Ontology (GO) category enrichment, and we also assumed SAUR upregulation reflected IAA signaling. However, our findings revealed that while IAA alone had a limited effect on stem elongation and we observed no IAA change in the stem in response to FR. GA and BR, on the other hand, had a more pronounced impact on stem elongation compared to IAA. It might be that SAUR upregulation was not a reflection of IAA, but instead either GA or BR signaling. These findings highlight the restrictions of GO annotations and the complications coming from the multifaceted regulatory networks, in this case, of SAUR regulation by IAA, BR and GA pathways. 6.2.4 Limitations of GO annotation in tomato To investigate the limitations of the GO analysis in tomato, we carried out a comparative analysis, to identify ratios of genes belonging to different categories in the well-annotated Arabidopsis and our model tomato (Table 6.1). With a focus on Brassinosteroid (BR), Gibberellic Acid (GA), auxin and far-red GO categories, it is clear that tomato annotations are severely lacking. Arabidopsis currently has annotations for 63 BR genes and 23 GA genes, while S. lycopersicum lacked BR annotations and had 5 GA annotations. The ratios highlighted the absence of BR annotations in tomato (0) and minimal GA annotations in both species. Poor GO annotation in S. lycopersicum will be a key limitation to our GO enrichment in Chapter 3, which we then overcame by plotting the FR-responsive behavior of tomato homologs of known hormone-related and -responsive genes (Figure 4.2, S4.1, S4.2). Also, should SAURs be only annotated as response to auxin? Since Auxin and BR signaling pathways are hugely overlapped, we assume the annotation might need to expand. Based on our experimental results from Chapter 4, we now assume that SAUR upregulation is not only from IAA signaling, but can be an outcome of GA, BR and IAA crosstalk in response to FR. Table 6.1. Annotation ratio (GO category : total number of genes) in Arabiodopsis and S. lycopersicum for GO categories of interest. Arabidopsis (TAIR10 genome) S. lycopersicum (ITAG4.0,) Total number of genes 25500 34075 Brassinosteroid 63 0 GA 23 5 Auxin 124 115 Far-red light 7 0 Ratio of BR annotation 0.25% 0.00% Ratio of GA annotation 0.09% 0.01% Ratio of Auxin annotation 0.49% 0.34% Ratio of far-red light annotation 0.03% 0.00%
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