*2.8. DEGs Related to Hormone Signaling*

Plant hormones (IAA, abscisic acid, ethylene, brassinosteroids, etc.) play a direct role in the biosynthesis of anthocyanins [31,32]. KEGG analysis showed that there were differences in phytohormone signaling transduction in the three pairwise comparisons. To thoroughly analyze the molecular mechanism of anthocyanin transformation, we investigated the gene expression differences in hormone signaling in the three pairwise groups. The results show that most of the genes involved in phytohormone metabolic pathways were downregulated in the A sample relative to the B, C, and D samples. In the D vs. A comparison, 42 hormone-signaling-related DEGs were up-regulated and 17 DEGs were down-regulated. Meanwhile, 38 DEGs were screened in the C vs. A comparison, with 22 up-regulated and 16 down-regulated. For the comparison of B vs. A, 52 DEGs revealed differences, including 30 up-regulated and 22 down-regulated genes. (Table S6).

The overlapping DEGs among the three pairwise comparisons were screened using a Venn diagram (Figure S4). The results indicate that 21 genes were differentially expressed, and we found that the genes involved in auxin (IAA) or brassinosteroid (BR) signaling were the most enriched (Table S6). Three DEGs (*RhsimUnG0255100*, *Rhsim06G0190800*, *Rhsim13G0033000*) involved in IAA signaling were identified, and the abundance of these transcripts was significantly decreased in the A sample relative to the B, C, and D samples (Table S6). Moreover, one (*Rhsim07G022810*) and eight DEGs (*Rhsim09G0181000*, *Rhsim07G0028200*, *RhsimUnG0200100*, etc.) involved in ABA and BR signaling, respectively, were found in the three comparison groups. Interestingly, these genes were more lowly expressed in the A sample relative to the B, C, and D samples.
