22R- but not 22S-hydroxycholesterol is recruited for diosgenin biosynthesis

The biosynthesis of trillin 6'-O-glucoside: A low-abundance yet pharmacologically active polyphyllin from Paris polyphylla

Natural products from medicinal plants serve as an invaluable resource for drug discovery and development. However, low-abundance natural products are often understudied due to the challenges of obtaining sufficient quantities for pharmacological testing in cells or animals. Additionally, their complex stereochemistry and functional groups make chemical synthesis and purification difficult. In this study, we showcased the power of biosynthetic approaches to explore these underexplored compounds, using the low-abundance polyphyllin trillin 6'-O-glucoside from Paris polyphylla as an example. We identified two trillin 6'-O-glucosyltransferases required for its biosynthesis and successfully reconstructed the entire pathway in Nicotiana benthamiana. We demonstrated that trillin 6'-O-glucoside exhibits anti-bacterial activity comparable to major polyphyllins like polyphyllins I, II, and VII. Notably, it also showed much lower hemolytic activity, a common side effect of those major polyphyllins. Together, our study underscores the advantages of employing biosynthetic approaches to explore natural products that exist in low or trace abundances yet possess equally important pharmacological activities.

Characterization of a 4'-O-rhamnosyltransferase and de novo biosynthesis of bioactive steroidal triglycosides from Paris polyphylla

Steroidal saponins in Paris polyphylla featuring complicated sugar chains exhibit notable biological activities, but their sugar-chain biosynthesis is still not fully understood. Here, we identified a 4'-O-rhamnosyltransferase (UGT73DY2) from P. polyphylla, which catalyzes the 4'-O-rhamnosylation of polyphyllins V and VI, producing dioscin and pennogenin 3-O-β-chacotrioside, respectively. UGT73DY2 exhibits strict substrate specificity toward steroidal diglycosides and UDP-rhamnose, and a new steroidal triglycoside can be synthesized through enzyme catalysis. A mutation library was generated based on semi-rational design, identifying three mutants, I358T, A342V, and A132T, which displayed approximately two-fold enhanced enzyme activity. Molecular dynamics simulations revealed that shortened distances between the 4'-OH group of the sugar acceptor and either the crucial residue H20 or the donor UDP-Rha contribute to the enhanced enzyme activity. Moreover, subcellular localization analysis of UGT73DY2 and other biosynthetic enzymes indicated that dioscin biosynthesis predominantly occurs in the endoplasmic reticulum of plant cells. By co-expressing 14 biosynthetic genes in Nicotiana benthamiana, optimizing HMGR subcellular localization and cytochrome P450 gene sets, and engineering UGT73DY2, we successfully established a dioscin biosynthesis system with a yield of 3.12 ± 0.11 μg/g dry weight. This study not only clarifies the 4'-O-rhamnosylation process in steroidal saponin biosynthesis but also presents an alternative approach for the production of steroidal saponins in P. polyphylla through synthetic biology and metabolic engineering.

Genomics of sterols biosynthesis in plants: Current status and future prospects

Sterols produced by bacteria and all eukaryotic organisms are essential for membrane functionality and stability. They play a vital role in growth, development and in abiotic stress tolerance. They are involved in diverse responses to biotic and abiotic stresses that lead to providing resistance against multiple diseases. Additionally, sterols serve as defensive compounds against herbivorous insects and animals. Phytosterols derived from plants, improve human nutrition and health and cure different ailments. The biosynthetic pathways for sterols and triterpenes exhibit similarities until the synthesis of 2,3-oxidosqualene. The complexity of sterol pathways increases during the advanced stages of polycyclic structure synthesis, and remain poorly comprehended in plants. This review explores the various omics techniques used to unveil the functions of genes associated with the phytosterol pathways. The study investigates the biosynthetic gene clusters to clarify the structural arrangements of genes linked to metabolic pathways. Both the upstream and downstream genes associated with these pathways, as well as their evolutionary connections and interrelations within the pathways were brought to the forefront. Moreover, developing strategies to unravel the biosynthesis completely and their multi-layered regulation are crucial to comprehend the global roles that sterols play in plant growth, development, stress tolerance and in imparting defence against pathogens.

The genus Paris: a fascinating resource for medicinal and botanical studies

The genus Paris, comprising a series of distinctive medicinal plants, has been utilized globally for its therapeutic properties over centuries. Modern pharmacological studies have demonstrated that secondary metabolites from Paris species exhibit significant pharmacological activities, including anticancer, hemostatic, anti-inflammatory, antimicrobial, and other effects. Additionally, the unique morphological traits and large genome size of Paris species have continuously captured the interest of botanists and horticulturalists. Nonetheless, the conservation of wild Paris populations is threatened due to the lengthy reproductive cycle and overexploitation, posing considerable challenges to their development and sustainable use. This review provides a comprehensive overview of the botanical characteristics, historical medicinal uses, pharmacological effects, and toxicity evaluation of secondary metabolites in Paris species. It also covers the molecular biological research conducted on the genus Paris and proposes key research questions and important directions for future solutions. We advocate the expansion and implementation of multi-omics approaches, as well as molecular and genetic technologies recently advanced in model plant research, to intensively study Paris species. This will facilitate the comprehensive understanding of gene function and molecular mechanisms underlying specialized metabolite formation in Paris.

An independent biosynthetic route to frame a xanthanolide-type sesquiterpene lactone in Asteraceae

Xanthanolides, also described as seco-guaianolides, are unique sesquiterpene lactones (STLs) with diverse bioactivities. Most of xanthanolides are 12,8-olides based on the position of their lactone ring. The biosynthetic pathway leading to xanthanolides has hitherto been elusive, especially how nature creates the xanthane skeleton is a long-standing question. This study reports the elucidation of a complete biosynthetic pathway to the important 12,8-xanthanolide 8-epi-xanthatin. The xanthane-type backbone is directly derived from the central precursor germacrene-type sesquiterpene, germacrene A acid, via oxidative rearrangement, catalyzed by an unusual cytochrome P450. Subsequently, a 12,8-lactone ring is formed within this xanthane-type backbone resulting in xanthanolides. The biosynthetic pathway for xanthanolides contrasts with the previously unified biosynthetic route for diverse 12,6-guaianolides, in which a 12,6-lactone ring formation precedes the transformation of a germacrene-type skeleton into a guaiane-type structure. The discovery of the full biosynthetic pathway of 8-epi-xanthantin opens new opportunities for producing xanthanolides in microbial organisms using synthetic biology strategies.

A cellulose synthase-like protein governs the biosynthesis of Solanum alkaloids

Decades of research on the infamous antinutritional steroidal glycoalkaloids (SGAs) in Solanaceae plants have provided deep insights into their metabolism and roles. However, engineering SGAs in heterologous hosts has remained a challenge. We discovered that a protein evolved from the machinery involved in building plant cell walls is the crucial link in the biosynthesis of SGAs. We show that cellulose synthase-like M [GLYCOALKALOID METABOLISM15 (GAME15)] functions both as a cholesterol glucuronosyltransferase and a scaffold protein. Silencing GAME15 depletes SGAs, which makes plants more vulnerable to pests. Our findings illuminate plant evolutionary adaptations that balance chemical defense and self-toxicity and open possibilities for producing steroidal compounds in heterologous systems for food, cosmetics, and pharmaceuticals.

Comparative transcriptomic and metabolomic analyses reveal key regulatory gene for methyl jasmonate-induced steroidal saponins synthesis in Dioscorea composita

Dioscorea composita (D. composita) is a perennial herb with abundant steroidal saponins that have gained worldwide attention for their remarkable efficacy in cardiovascular diseases. However, few studies have been worked on the regulatory network of steroidal saponins biosynthesis under phytohormone induced. In this study, we combined the transcriptome and metabolome analysis to reveal the variation of diosgenin and steroidal saponins in transcriptional and metabolism levels under methyl-jasmonate (MeJA) treatment. Although the application of MeJA indeed significantly increased the accumulation of diosgenin of D. composita, different types of steroidal saponins exhibited different accumulation patterns. Consistently, the expression levels of UDP-glycosyltransferases and Cytochrome P450 monooxygenases genes that highly related to the accumulation of steroidal saponins were either up- or down-regulated. Correlation analyses of transcription factors (TFs)-steroidal saponins and structural genes-TFs were further to identified the TFs potentially involved in the regulation of steroidal saponins biosynthesis. Silencing of DcWRKY11 in Dioscorea composita decreases the accumulation of steroidal saponins by regulating the expression steroidal saponins synthesis genes, suggesting that DcWRKY11 is a positive regulator in the regulation of steroidal saponins biosynthesis. Our findings take a deeper understanding of the regulatory network of MeJA-mediated steroidal saponins biosynthesis in D. composita.

Efficient production of 22(R)-hydroxycholesterol via combination optimization of Saccharomyces cerevisiae

22(R)-hydroxycholesterol (22(R)-HCHO) is a crucial precursor of steroids biosynthesis with various biological functions. However, the production of 22(R)-HCHO is expensive and unsustainable due to chemical synthesis and extraction from plants or animals. This study aimed to construct a microbial cell factory to efficiently produce 22(R)-HCHO through systems metabolic engineering. First, we tested 7-dehydrocholesterol reductase (Dhcr7s) and cholesterol C22-hydroxylases from different sources in Saccharomyces cerevisiae, and the titer of 22(R)-HCHO reached 128.30 mg L-1 in the engineered strain expressing Dhcr7 from Columba livia (ClDhcr7) and cholesterol 22-hydroxylase from Veratrum californicum (VcCyp90b27). Subsequently, the 22(R)-HCHO titer was significantly increased to 427.78 mg L-1 by optimizing the critical genes involved in 22(R)-HCHO biosynthesis. Furthermore, hybrid diploids were constructed to balance cell growth and 22(R)-HCHO production and to improve stress tolerance. Finally, the engineered strain produced 2.03 g L-1 of 22(R)-HCHO in a 5-L fermenter, representing the highest 22(R)-HCHO titer reported to date in engineered microbial cell factories. The results of this study provide a foundation for further applications of 22(R)-HCHO in various industrially valuable steroids.

Fenugreek derived diosgenin as an emerging source for diabetic therapy

Diabetes is a chronic metabolic disease that endangers the entire body's tissues and organs. Diabetes impairs glucose and insulin regulation in the human body by causing pancreatic cell damage. Diabetes modifies pathways such as serine/threonine protein kinase (Akt) and Protein kinase C (PKC)/- glucose transporter 4 (GLUT4), peroxisome proliferator-activated receptor (PPAR) glucose absorption, and inhibits α-amylase and α-glucosidase, Sodium/glucose cotransporter 1 (SGLT-1), and Na+-K+-ATPase activity. Diabetes may also be caused by a decrease in the expression of sterol regulatory element binding protein 1 (SREBP-1) and its target genes, fatty acid synthase (FAS), stearoyl-CoA desaturase-1 (SCD-1), and acetyl-CoA carboxylase α (ACC), as well as a decrease in the levels of C/EBP homologous protein (CHOP), Caspase12, and Caspase3 proteins. Diabetes has long been linked to diseases of the cardiovascular, nervous, skeletal, reproductive, hepatic, ocular, and renal systems. Diosgenin, a steroidal compound derived from fenugreek, aids in the prevention of diabetes by altering cellular pathways in favor of healthy bodily functions. Diosgenin is a new nutraceutical on the market that claims to cure diabetes in particular. This article focuses on diosgenin extraction and purification, fenugreek bioactive compounds, pharmacological properties of diosgenin, mode of action of diosgenin to cure diabetes, and dosages.

Diosgenin biosynthesis pathway and its regulation in Dioscorea cirrhosa L

Dioscorea cirrhosa L. (D. cirrhosa) tuber is a traditional medicinal plant that is abundant in various pharmacological substances. Although diosgenin is commonly found in many Dioscoreaceae plants, its presence in D. cirrhosa remained uncertain. To address this, HPLC-MS/MS analysis was conducted and 13 diosgenin metabolites were identified in D. cirrhosa tuber. Furthermore, we utilized transcriptome data to identify 21 key enzymes and 43 unigenes that are involved in diosgenin biosynthesis, leading to a proposed pathway for diosgenin biosynthesis in D. cirrhosa. A total of 3,365 unigenes belonging to 82 transcription factor (TF) families were annotated, including MYB, AP2/ERF, bZIP, bHLH, WRKY, NAC, C2H2, C3H, SNF2 and Aux/IAA. Correlation analysis revealed that 22 TFs are strongly associated with diosgenin biosynthesis genes (-r2- > 0.9, P < 0.05). Moreover, our analysis of the CYP450 gene family identified 206 CYP450 genes (CYP450s), with 40 being potential CYP450s. Gene phylogenetic analysis revealed that these CYP450s were associated with sterol C-22 hydroxylase, sterol-14-demethylase and amyrin oxidase in diosgenin biosynthesis. Our findings lay a foundation for future genetic engineering studies aimed at improving the biosynthesis of diosgenin compounds in plants.

Integrated evolutionary pattern analyses reveal multiple origins of steroidal saponins in plants

Steroidal saponins are a class of specialized metabolites essential for plant's response to biotic and abiotic stresses. They are also important raw materials for the industrial production of steroid drugs. Steroidal saponins are present in some monocots, such as Dioscorea and Paris, but their distribution, origin, and evolution in plants remain poorly understood. By reconstructing the evolutionary history of the steroidal saponin-associated module (SSAM) in plants, we reveal that the steroidal saponin pathway has its origin in Asparagus and Dioscorea. Through evaluating the distribution and evolutionary pattern of steroidal saponins in angiosperms, we further show that steroidal saponins originated multiple times in angiosperms, and exist in early diverged lineages of certain monocot lineages including Asparagales, Dioscoreales, and Liliales. In these lineages, steroidal saponins are synthesized through the high copy and/or high expression mechanisms of key genes in SSAM. Together with shifts in gene evolutionary rates and amino acid usage, these molecular mechanisms shape the current distribution and diversity of steroidal saponins in plants. Consequently, our results provide new insights into the distribution, diversity and evolutionary history of steroidal saponins in plants, and enhance our understanding of plants' resistance to abiotic and biotic stresses. Additionally, fundamental understanding of the steroidal saponin biosynthesis will facilitate their industrial production and pharmacological applications.

Unraveling the serial glycosylation in the biosynthesis of steroidal saponins in the medicinal plant Paris polyphylla and their antifungal action

Sugar-sugar glycosyltransferases play important roles in constructing complex and bioactive saponins. Here, we characterized a series of UDP-glycosyltransferases responsible for biosynthesizing the branched sugar chain of bioactive steroidal saponins from a widely known medicinal plant Paris polyphylla var. yunnanensis. Among them, a 2'-O-rhamnosyltransferase and three 6'-O-glucosyltrasferases catalyzed a cascade of glycosylation to produce steroidal diglycosides and triglycosides, respectively. These UDP-glycosyltransferases showed astonishing substrate promiscuity, resulting in the generation of a panel of 24 terpenoid glycosides including 15 previously undescribed compounds. A mutant library containing 44 variants was constructed based on the identification of critical residues by molecular docking simulations and protein model alignments, and a mutant UGT91AH1Y187A with increased catalytic efficiency was obtained. The steroidal saponins exhibited remarkable antifungal activity against four widespread strains of human pathogenic fungi attributed to ergosterol-dependent damage of fungal cell membranes, and 2'-O-rhamnosylation appeared to correlate with strong antifungal effects. The findings elucidated the biosynthetic machinery for their production of steroidal saponins and revealed their potential as new antifungal agents.

Identification of P450 Candidates Associated with the Biosynthesis of Physalin-Class Compounds in Physalis angulata

The Physalis genus has long been used as traditional medicine in the treatment of various diseases. Physalins, the characteristic class of compounds in this genus, are major bioactive constituents. To date, the biogenesis of physalins remains largely unknown, except for the recently established knowledge that 24-methyldesmosterol is a precursor of physalin. To identify the genes encoding P450s that are putatively involved in converting 24-methyldesmosterol to physalins, a total of 306 P450-encoding unigenes were retrieved from our recently constructed P. angulata transcriptome. Extensive phylogenetic analysis proposed 21 P450s that might participate in physalin biosynthesis. To validate the candidates, we developed a virus-induced gene silencing (VIGS) system for P. angulata, and four P450 candidates were selected for the VIGS experiments. The reduction in the transcripts of the four P450 candidates by VIGS all led to decreased levels of physalin-class compounds in the P. angulata leaves. Thus, this study provides a number of P450 candidates that are likely associated with the biosynthesis of physalin-class compounds, forming a strong basis to reveal the unknown physalin biosynthetic pathway in the future.

The Functional Characterization of DzCYP72A12-4 Related to Diosgenin Biosynthesis and Drought Adaptability in Dioscorea zingiberensis

Dioscorea zingiberensis is a perennial herb famous for the production of diosgenin, which is a valuable initial material for the industrial synthesis of steroid drugs. Sterol C26-hydroxylases, such as TfCYP72A616 and PpCYP72A613, play an important role in the diosgenin biosynthesis pathway. In the present study, a novel gene, DzCYP72A12-4, was identified as C26-hydroxylase and was found to be involved in diosgenin biosynthesis, for the first time in D. zingiberensis, using comprehensive methods. Then, the diosgenin heterogenous biosynthesis pathway starting from cholesterol was created in stable transgenic tobacco (Nicotiana tabacum L.) harboring DzCYP90B71(QPZ88854), DzCYP90G6(QPZ88855) and DzCYP72A12-4. Meanwhile, diosgenin was detected in the transgenic tobacco using an ultra-performance liquid chromatography system (Vanquish UPLC 689, Thermo Fisher Scientific, Bremen, Germany) tandem MS (Q Exactive Hybrid Quadrupole-Orbitrap Mass Spectrometer, Thermo Fisher Scientific, Bremen, Germany). Further RT-qPCR analysis showed that DzCYP72A12-4 was highly expressed in both rhizomes and leaves and was upregulated under 15% polyethylene glycol (PEG) treatment, indicating that DzCYP72A12-4 may be related to drought resistance. In addition, the germination rate of the diosgenin-producing tobacco seeds was higher than that of the negative controls under 15% PEG pressure. In addition, the concentration of malonaldehyde (MDA) was lower in the diosgenin-producing tobacco seedlings than those of the control, indicating higher drought adaptability. The results of this study provide valuable information for further research on diosgenin biosynthesis in D. zingiberensis and its functions related to drought adaptability.

Steroidal saponin profiles and their key genes for synthesis and regulation in Asparagus officinalis L. by joint analysis of metabolomics and transcriptomics

BACKGROUND

Asparagus officinalis L. is a worldwide cultivated vegetable enrichened in both nutrient and steroidal saponins with multiple pharmacological activities. The upstream biosynthetic pathway of steroidal saponins (USSP) for cholesterol (CHOL) synthesis has been studied, while the downstream pathway of steroidal saponins (DSSP) starting from cholesterol and its regulation in asparagus remains unknown.

RESULTS

Metabolomics, Illumina RNAseq, and PacBio IsoSeq strategies were applied to different organs of both cultivated green and purple asparagus to detect the steroidal metabolite profiles & contents and to screen their key genes for biosynthesis and regulation. The results showed that there is a total of 427 compounds, among which 18 steroids were detected with fluctuated concentrations in roots, spears and flowering twigs of two garden asparagus cultivars. The key genes of DSSP include; steroid-16-hydroxylase (S16H), steroid-22-hydroxylase (S22H) and steroid-22-oxidase-16-hydroxylase (S22O-16H), steroid-26-hydroxylase (S26H), steroid-3-β-glycosyltransferase (S3βGT) and furostanol glycoside 26-O-beta-glucosidases (F26GHs) which were correlated with the contents of major steroidal saponins were screened, and the transcriptional factors (TFs) co-expressing with the resulted from synthetic key genes, including zinc fingers (ZFs), MYBs and WRKYs family genes were also screened.

CONCLUSIONS

Based on the detected steroidal chemical structures, profiles and contents which correlated to the expressions of screened synthetic and TFs genes, the full steroidal saponin synthetic pathway (SSP) of asparagus, including its key regulation networks was proposed for the first time.

Characterization and Biological Activities of Four Biotransformation Products of Diosgenin from Rhodococcus erythropolis

Diosgenin (DSG), a steroidal sapogenin derived from the tuberous roots of yam, possesses multiple biological properties. DSG has been widely used as a starting material for the industrial production of steroid drugs. Despite its significant pharmacological activities, moderate potency and low solubility hinder the medicinal application of DSG. Biotransformation is an efficient method to produce valuable derivatives of natural products. In this work, we performed the biotransformation of DSG using five Rhodococcus strains. Compounds 1–4 were isolated and identified from Rhodococcus erythropolis. Compounds 1 and 2 showed potent cytotoxicity against the A549, MCF-7, and HepG2 cell lines. Compounds 3 and 4 are novel entities, and each possesses a terminal carboxyl group attached to the spiroacetal ring. Remarkably, 4 exhibited significant cell protective effects for kidney, liver, and vascular endothelial cells, suggesting the therapeutic potential of this compound in chronic renal diseases, atherosclerosis, and hypertension. We further optimized the fermentation conditions aiming to increase the titer of compound 4. Finally, the yield of compound 4 was improved by 2.9-fold and reached 32.4 mg/L in the optimized conditions. Our study lays the foundation for further developing compound 4 as a cell protective agent.

Deciphering the network of cholesterol biosynthesis in Paris polyphylla laid a base for efficient diosgenin production in plant chassis

Cholesterol serves as a key precursor for many high-value chemicals such as plant-derived steroidal saponins and steroidal alkaloids, but a plant chassis for effective biosynthesis of high levels of cholesterol has not been established. Plant chassis have significant advantages over microbial chassis in terms of membrane protein expression, precursor supply, product tolerance, and regionalization synthesis. Here, using Agrobacterium tumefaciens-mediated transient expression technology, Nicotiana benthamiana, and a step-by-step screening approach, we identified nine enzymes (SSR1-3, SMO1-3, CPI-5, CYP51G, SMO2-2, C14-R-2, 8,7SI-4, C5-SD1, and 7-DR1-1) from the medicinal plant Paris polyphylla and established detailed biosynthetic routes from cycloartenol to cholesterol. Specfically, we optimized HMGR, a key gene of the mevalonate pathway, and co-expressed it with the PpOSC1 gene to achieve a high level of cycloartenol (28.79 mg/g dry weight, which is a sufficient amount of precursor for cholesterol biosynthesis) synthesis in the leaves of N. benthamiana. Subsequently, using a one-by-one elimination method we found that six of these enzymes (SSR1-3, SMO1-3, CPI-5, CYP51G, SMO2-2, and C5-SD1) were crucial for cholesterol production in N. benthamiana, and we establihed a high-efficiency cholesterol synthesis system with a yield of 5.63 mg/g dry weight. Using this strategy, we also discovered the biosynthetic metabolic network responsible for the synthesis of a common aglycon of steroidal saponin, diosgenin, using cholesterol as a substrate, obtaining a yield of 2.12 mg/g dry weight in N. benthamiana. Our study provides an effective strategy to characterize the metabolic pathways of medicinal plants that lack a system for in vivo functional verification, and also lays a foundation for the synthesis of active steroid saponins in plant chassis.

Cytochrome P450 monooxygenase-mediated tailoring of triterpenoids and steroids in plants

The cytochrome P450 monooxygenase (CYP) superfamily comprises hemethiolate enzymes that perform remarkable regio- and stereospecific oxidative chemistry. As such, CYPs are key agents for the structural and functional tailoring of triterpenoids, one of the largest classes of plant natural products with widespread applications in pharmaceuticals, food, cosmetics, and agricultural industries. In this review, we provide a full overview of 149 functionally characterised CYPs involved in the biosynthesis of triterpenoids and steroids in primary as well as in specialised metabolism. We describe the phylogenetic distribution of triterpenoid- and steroid-modifying CYPs across the plant CYPome, present a structure-based summary of their reactions, and highlight recent examples of particular interest to the field. Our review therefore provides a comprehensive up-to-date picture of CYPs involved in the biosynthesis of triterpenoids and steroids in plants as a starting point for future research.

The genome of Dioscorea zingiberensis sheds light on the biosynthesis, origin and evolution of the medicinally important diosgenin saponins

Diosgenin saponins isolated from Dioscorea species such as D. zingiberensis exhibit a broad spectrum of pharmacological activities. Diosgenin, the aglycone of diosgenin saponins, is an important starting material for the production of steroidal drugs. However, how plants produce diosgenin saponins and the origin and evolution of the diosgenin saponin biosynthetic pathway remain a mystery. Here we report a high-quality, 629-Mb genome of D. zingiberensis anchored on 10 chromosomes with 30 322 protein-coding genes. We reveal that diosgenin is synthesized in leaves ('source'), then converted into diosgenin saponins, and finally transported to rhizomes ('sink') for storage in plants. By evaluating the distribution and evolutionary patterns of diosgenin saponins in Dioscorea species, we find that diosgenin saponin-containing may be an ancestral trait in Dioscorea and is selectively retained. The results of comparative genomic analysis indicate that tandem duplication coupled with a whole-genome duplication event provided key evolutionary resources for the diosgenin saponin biosynthetic pathway in the D. zingiberensis genome. Furthermore, comparative transcriptome and metabolite analysis among 13 Dioscorea species suggests that specific gene expression patterns of pathway genes promote the differential evolution of the diosgenin saponin biosynthetic pathway in Dioscorea species. Our study provides important insights and valuable resources for further understanding the biosynthesis, evolution, and utilization of plant specialized metabolites such as diosgenin saponins.