Plant Gene and Trait 2025, Vol.16, No.5, 225-233 http://genbreedpublisher.com/index.php/pgt 227 frequently used for the expression and validation of specific enzymes. Hairy root culture and transgenic root systems are also feasible. The saponin content of some transgenic roots even exceeds that of common cultivated roots (Binh et al., 2023). Figure 1 The proposed pathway for de novo biosynthesis of ginsenosides Rg2 and Re in engineered yeast strains (Adopted from Li et al., 2022a) Image caption: Bluish green arrows represent glycosylation steps using UDP-glucose as a sugar donor, blue arrows represent the biosynthetic pathway of UDP-rhamnose and glycosylation steps using UDP-rhamnose as a sugar donor. Multi-step conversions were presented as multi arrows. Bluish green marked genes represented previous reported genes and the bule marked gene represented the identified one in this study. PPD protopanaxadiol, PPT protopanaxatriol (Adopted from Li et al., 2022a) 4 Omics-Guided Metabolic Engineering 4.1 Genomics and gene mining of biosynthetic enzymes The analysis of the ginseng genome has laid the foundation for the study of functional metabolites. Whole-genome sequencing has revealed the complex tetraploid genomic structure of ginseng, annotating over 59000 genes. Researchers discovered important enzyme genes related to saponin synthesis, such as DDS and SQE, in the reconstruction of metabolic networks and revealed their evolutionary characteristics. These results provide targets for gene editing and synthetic biology (Kim et al., 2018; Yu et al., 2024). In addition, the amplification and diversity of the UDP-glycosyltransferase (UGT) family are closely related to the diversity of saponin structures. The functional verification and structural research of related genes have provided molecular basis for the directed synthesis of saponins. 4.2 Transcriptomics and co-expression networks for regulatory insights Transcriptomics studies have revealed the dynamic changes and regulatory networks of key genes in the saponin synthesis pathway by analyzing gene expression profiles under different tissues, developmental stages and environmental conditions. The gene co-expression network helps researchers identify transcription factors and signaling pathways that may regulate saponin synthesis, deepening the understanding of the regulatory mechanism (Wei et al., 2024; Yu et al., 2024). For example, the combined analysis of transcriptome and metabolome can identify the gene modules related to saponin accumulation, which provides a reference for achieving multi-gene synergistic regulation in metabolic engineering (Kim et al., 2018; Yuan et al., 2023). 4.3 Metabolomics for pathway flux analysis and bottleneck identification Metabolomics utilizes high-throughput mass spectrometry and other techniques to conduct systematic analysis of metabolites in different tissues, at different growth stages, and under different processing conditions of ginseng. Studies have revealed the dynamic changes of metabolites such as saponins and their flow distribution in
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