Medicinal Plant Research 2024, Vol.14, No.1, 31-44 http://hortherbpublisher.com/index.php/mpr 37 high repetitive sequence content, polyploidy, and large genomes, which hinder comprehensive whole-genome sequencing and analysis. Moreover, the complexity and diversity of medicinal components make it difficult to infer biosynthetic pathways, posing challenges for in-depth research. In particular, genes in major secondary metabolism pathways, such as those in the phenylpropane metabolism pathway, are often multi-copied, and enzymes encoded by different gene copies may participate in different metabolic branches. Systematic exploration and analysis of these gene family members provide valuable references for accurately locating enzymes catalyzing these steps in further functional studies. Moreover, comparative genomic studies with other Dioscorea species have highlighted the evolutionary aspects of these biosynthetic pathways. For example, the genome of Dioscorea zingiberensis, a closely related species, has shed light on the origin and evolution of diosgenin saponin biosynthesis (Figure 2), suggesting that similar mechanisms may be at play in yam (Wang et al., 2020). These genomic insights not only enhance our understanding of the plant's medicinal properties but also open up possibilities for metabolic engineering to optimize the production of valuable bioactive compounds. Figure 2 Diosgenin distributions and gene expression levels in different tissues of D. zingiberensis (Adopted from Li et al., 2022) Image caption: (a) Diosgenin contents in different tissues of D. zingiberensis during the development period of 7 months. (b-f) Immunohistochemical localization of diosgenin in stem (b), leaf (c, d), and rhizome (e, f) tissues. Blue color in sections represents the diosgenin signal. Diosgenin is detected in the epidermis (Ep), ground tissue (Gt), and phloem (Ph) of the stem cross-section. Blue signals localized in the phloem are observed. The diosgenin signal is concentrated in palisade tissue (Pat), spongy tissue (Spt), and phloem in the leaf. Xy represents the xylem. Scale bar = 100 μm. (g) Schematic diagram of the transport assay. The aerial part of the plant with leaves attached (exp1), stem connected to the rhizome (exp2), and stem of the aerial part with leaves detached were immersed in flasks containing deionized water (exp3). The aerial part with leaves attached was also inserted into a flask containing 1.5 mM dinitrophenol (exp4). The diosgenin content secreted into the water in each treatment is shown in the histogram. (h) Expression profiles of pathway genes based on RNA-seq data from three tissues (leaves, stems, and rhizomes). Gene expression values (FPKM) were normalized by log2, and the expression pattern was visualized using the R package pheatmap. Three biological replicates for each sample were collected in this study, and the error bar represents the standard error (Adopted from Li et al., 2022)
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