## 2 Results
### Transcription Factor Genes  
Transcription factors (TFs) were not only involved in a wide range of plant growth, development, and response to environmental stresses, but also involved in the regulation of the biosynthesis of active ingredients in medicinal plants [26; 27; 28]. To identify transcription factors involved in the regulation of catalpol and acetoside accumulation in tuberous root, we analyzed transcription factor genes, whose expression was positively or negatively related to catalpol and acetoside content. A total of 4461 unigenes encoding TFs were classified into 59 TF families (Figure S6). The largest gene family was the MYB family, followed by the MYB-related family, the C3H family, the AP2-EREBP family, the bHLH family, the WRKY family, and the ARF family of transcription factors. We compared the number of differentially expressed TFs between different groups (Table 2). In all cultivars, the number of differentially expressed TFs was the largest when comparing radial striation to non-radial striation of 1706 for both upregulated and downregulated TFs, while the lowest number of DETs, with 33 upregulated and 50 downregulated TFs, was found for the W85_RS vs. W85_nRS comparison. In total, the DETs of TFs were divided into 27 subfamilies, including WRKY, AP2-EREBP, bHLH, MYB, and so on. The TFs belonging to WRKY, bHLH, MYB, and AP2- EREBP families execute key roles in the regulation of the biosynthesis of secondary metabolites [29; 30; 31; 32]. We identified many differentially expressed WRKY, bHLH, and MYB genes in four comparisons, where only _CL8654.Contig3_ (WRKY), _CL15084.Contig2_ (DHLH), _CL12833.Contig2_ (MYB), _CL9048.Contig2_ (MYB), _CL9048.Contig3_ (MYB), and _CL1177.Contig4_ (C3H) were the upregulated genes, whose expression was significantly higher in non-radial striation than in radial striation (Table S11, Figure 9A). Interestingly, all differentially \begin{table}
\begin{tabular}{c c c c c c c c c c c c} \hline \hline \multirow{2}{*}{**Transcription Factor**} & \multirow{2}{*}{**Total of**} & \multicolumn{3}{c}{**1706**} & \multicolumn{3}{c}{**BJ1**} & \multicolumn{3}{c}{**QH1**} & \multicolumn{3}{c}{**W85**} & \multicolumn{3}{c}{**All**} \\ \cline{3-11}  & & **Up** & **Down** & **Up** & **Down** & **Up** & **Down** & **Up** & **Down** & **Up** & **Down** \\ \hline WRKY & 184 & 17 & 11 & 11 & 10 & 6 & 8 & 4 & 11 & 1 & 2 \\ TCP & 39 & 2 & 2 & 1 & 2 & 1 & 0 & 1 & 1 & 0 & 0 \\ MADS & 119 & 3 & 2 & 0 & 2 & 1 & 3 & 0 & 1 & 0 & 1 \\ C2C2-GATA & 62 & 2 & 1 & 1 & 0 & 0 & 0 & 1 & 0 & 0 & 0 \\ AP2-EREBP & 286 & 35 & 9 & 17 & 8 & 6 & 2 & 2 & 1 & 0 & 0 \\ C2H2 & 93 & 4 & 5 & 1 & 2 & 0 & 2 & 1 & 1 & 0 & 0 \\ bHLH & 235 & 17 & 28 & 9 & 25 & 3 & 16 & 5 & 8 & 1 & 6 \\ MYB & 513 & 19 & 21 & 15 & 24 & 9 & 6 & 8 & 3 & 3 & 1 \\ Trihelix & 104 & 0 & 2 & 0 & 2 & 0 & 1 & 0 & 1 & 0 & 1 \\ HSF & 53 & 1 & 1 & 1 & 1 & 0 & 0 & 1 & 0 & 0 & 0 \\ C2C2-CO-like & 26 & 1 & 2 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & 0 \\ NAC & 141 & 2 & 16 & 1 & 3 & 1 & 0 & 0 & 8 & 0 & 0 \\ C3H & 299 & 10 & 2 & 2 & 1 & 3 & 0 & 2 & 0 & 1 & 0 \\ C2C2-Dof & 94 & 2 & 2 & 0 & 7 & 1 & 0 & 0 & 1 & 0 & 0 \\ ARF & 155 & 0 & 15 & 0 & 9 & 0 & 8 & 0 & 5 & 0 & 3 \\ FAR1 & 139 & 1 & 0 & 0 & 0 & 3 & 0 & 0 & 2 & 0 & 0 \\ SBP & 91 & 9 & 0 & 1 & 1 & 1 & 0 & 3 & 0 & 0 & 0 \\ ABI3 VP1 & 120 & 1 & 1 & 0 & 0 & 0 & 0 & 1 & 1 & 0 & 0 \\ LOB & 49 & 0 & 6 & 0 & 7 & 0 & 6 & 0 & 3 & 0 & 2 \\ FHA & 61 & 0 & 1 & 0 & 0 & 0 & 1 & 0 & 0 & 0 & 0 \\ BES1 & 47 & 1 & 2 & 1 & 5 & 1 & 3 & 0 & 0 & 0 & 0 \\ zf-HD & 45 & 0 & 2 & 0 & 1 & 0 & 1 & 0 & 0 & 0 & 0 \\ EIL & 22 & 0 & 2 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & 0 \\ OFP & 30 & 8 & 1 & 4 & 0 & 0 & 0 & 3 & 0 & 0 & 0 \\ GRAS & 154 & 8 & 2 & 0 & 3 & 0 & 1 & 0 & 2 & 0 & 1 \\ Bzip & 40 & 0 & 2 & 0 & 4 & 0 & 0 & 0 & 1 & 0 & 0 \\ TCP & 39 & 2 & 1 & 1 & 0 & 1 & 0 & 1 & 0 & 0 & 0 \\ Total of DET & 145 & 139 & 66 & 119 & 37 & 58 & 33 & 50 & 6 & 17 \\ \hline \hline \end{tabular}
\end{table} 
Table 2: Regulated transcription factors (TFs) between radial striation and non-radial striation in four _R. glutinosa_ cultivars.