## 3 Results
### Identification of Putative Genes in the Pathway of Catalogl Biosynthesis  
We focused attention on the downstream steps to catalogl. According to the proposed biosynthetic pathway of catalogl shown in Figure 1, GPP was converted to 10-oxogeraniad by GES, G10H, and 10 HGO in sequence, which were common enzymes in _route I_ and _route II_. Subsequently, _epi_-repetalactol was formed from 10-oxogeraniad by _epi_-ISY protein, followed by its conversion into either 8-_epi_-deoxyloganetic acid or iridotrital by DLS-like enzyme. The candidate genes for these enzymes were screened by keyword searching, and a total of 51 sequences were found (Supplementary Table S6). Among them, several unigenes, including one for GES (Cluster-11149.40193), one for G10H (Cluster-11149.27919), four for 10 HGO (Cluster11149.19580, Cluster-11149.22551, Cluster-11149.34028, and Cluster-11149.31299), two for _epi_-ISY (Cluster-11149.20854 and Cluster-11149.27465), and two for DLS-like (Cluster-11149.30874 and Cluster-11149.34412), were selected as putative genes involved in catalogl biosynthesis, due to their similar expression to the accumulation pattern of catalogl. These putative candidate genes displayed their presence in all the Beijing No. 3, Huaifeng, and Jin No. 9 cultivars; meanwhile, their highest expression level was in the young leaves, followed by the tuberous roots and adventitious roots (Figure 5A). Discarding two unigenes for 10 HGO (Cluster-11149.31299 and Cluster-11149.19580) and one for DLS-like (Cluster-11149.34412), the others with complete open reading frames (ORFs) were selected for the qRT-PCR analysis. The expression levels of these unigenes were consistent between the qRT-PCR results and the FPKM data, except for Cluster-11149.40193 (Figure 5B). The qRT-PCR melting curves are shown in Supplementary Figure S4. Additionally, GES (AFD64744.1), G10H (CAC80883.1), 10 HGO (AHA82031.1), ISY (AFW98981.1), and DLS (AHX24370.1) from _C. roseus_ were used as the query sequences to conduct the tBLASTn searching, and the highest hits  
Figure 4: Number of DEGs (**A**) and KEGG enrichment analysis of up-regulated genes (**B**) between different parts of _R. glutinosa_; (**C**) Venn diagram of up-regulated unigenes in different tissues of _R. glutinosa_ (J9L vs. J9 AR, J9L vs. J9R, and J9R vs. J9 AR); (**D**) representative pathway of the common up-regulated genes from J9L vs. J9 AR, J9L vs. J9R, and J9R vs. J9 AR. in the _R. glutinosa_ transcriptomes were Cluster-11149.40193 (GES), Cluster-11149.27919 (G10H), Cluster-11149.22551 (10 HGO), Cluster-11149.27465 (_epi_-ISY), and Cluster-11149.11401 (DLS-like), respectively (Supplementary Table S6). As depicted in Figure 1, UGT catalyzed the conversion of 8-_epi_-deoxyloganeic acid and iridotrital into 8-_epi_-deoxyloganic acid and boschnaloside, respectively. A total of 167 UGT unigenes were discovered in the _R. glutinosa_ transcriptomes (Supplementary Table S7) while 8 of them (RgUGT1-8) satisfied our gene screening criteria. In addition, 21 sequences were annotated as UGT candidates related to the iridoid glucosides biosynthesis. The cluster analysis of all these UGT candidate genes revealed that RgUGT1-8 were assigned to the same cluster,  
Figure 5: Heatmap based on the FPKM data (**A**) and qRT-PCR analysis (**B**) of the putative common genes in route _Il_ from different parts of _R. glutinosa_. Asterisks indicate a significant difference (\({}^{**}p<0.01\); \({}^{***}p<0.001\)). which formed a separate group with other UGT candidates (Figure 6A). CrUGT8 (AB733667) from _C. roseus_, which glycosylated deoxylomagnetic acid to deoxylognatic acid in _route I_, was used as the query sequence to search in the _R. glutinosa_ transcriptomes. As a result, the highest hit was Cluster-11149.23607 (RgUGT9), which was highly expressed in the adventitious roots compared to the tuberous roots [10]. Previous studies have suggested that UGT genes involved in the production of iridoids usually belong to group G of the Family 1 plant secondary product glycosyltransferases (PSPGs).