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Diosgenin is a spiroketal steroidal natural product extracted from plants and used as the single most important precursor for the world steroid hormone industry. The sporadic occurrences of diosgenin in distantly related plants imply possible independent biosynthetic origins. The characteristic 5,6-spiroketal moiety in diosgenin is reminiscent of the spiroketal moiety present in anthelmintic avermectins isolated from actinomycete bacteria. How plants gained the ability to biosynthesize spiroketal natural products is unknown. Here, we report the diosgenin-biosynthetic pathways in himalayan paris ( Paris polyphylla ), a monocot medicinal plant with hemostatic and antibacterial properties, and fenugreek ( Trigonella foenum–graecum ), an eudicot culinary herb plant commonly used as a galactagogue. Both plants have independently recruited pairs of cytochromes P450 that catalyze oxidative 5,6-spiroketalization of cholesterol to produce diosgenin, with evolutionary progenitors traced to conserved phytohormone metabolism. This study paves the way for engineering the production of diosgenin and derived analogs in heterologous hosts. Diosgenin is a spiroketal natural product that is used as a precursor in the industrial synthesis of steroids. Here, the authors identified key cytochrome P450 enzymes responsible for the conversion of cholesterol to diosgenin from two phylogenetical distinct diosgenin-producing plant species.

Paris is famous in China for its medicinal value and has been included in the Chinese Pharmacopoeia. Inaccurate identification of these species could confound their effective exploration, conservation, and domestication. Due to the plasticity of the morphological characteristics, correct identification among Paris species remains problematic. In this regard, we report the complete chloroplast genome of P . thibetica and P . rugosa to develop highly variable molecular markers. Comparing three chloroplast genomes, we sought out the most variable regions to develop the best cpDNA barcodes for Paris . The size of Paris chloroplast genome ranged from 162,708 to 163,200 bp. A total of 134 genes comprising 81 protein coding genes, 45 tRNA genes and 8 rRNA genes were observed in all three chloroplast genomes. Eight rapidly evolving regions were detected, as well as the difference of simple sequence repeats (SSR) and repeat sequence. Two regions of the coding gene ycf1 , ycf1a and ycf1b , evolved the quickest and were proposed as core barcodes for Paris . The complete chloroplast genome sequences provide more integrated and adequate information for better understanding the phylogenetic pattern and improving efficient discrimination during species identification.

Background Paris polyphylla ( P. polyphylla ), a medicinal herb valued in traditional Chinese medicine, struggles with slow growth rate and long maturation periods, hindering sustainable cultivation and commercial production—especially for polyphyllins, its key bioactive compounds. Although plant growth-promoting rhizobacteria (PGPR) have shown potential in enhancing crop productivity and secondary metabolite accumulation, their application in slow-growing medicinal plants like P. polyphylla remains underexplored.  Results In this study, 25 strains with inorganic phosphorus-dissolving, potassium-solubilizing and nitrogen-fixing abilities were isolated from the rhizosphere soil of P. polyphylla , mainly belonging to Bacillus , Pseudomonas , and Rhizobium . Among them, the strain Pseudomonas palleroniana P6 exhibited the best growth-promoting effect on grass. The whole genome analysis demonstrated that P. palleroniana P6 could promote forage growth by secreting phosphatases, organic acids, and producing substances like IAA and siderophore. Field experiments were carried out to further validate the impact of P. palleroniana P6 on the growth of P. polyphylla . The results revealed that P. palleroniana P6 remarkably enhanced the biomass of P. polyphylla root and the content of polyphyllin I, II, and VII, and significantly increased the soil available potassium content. The transcriptome results indicated that the application of P. palleroniana P6 considerably increased the expression of genes related to the plant hormone signal transduction pathway involved in growth regulation, cholesterol synthesis, terpenoid backbone synthesis and the energy metabolism pathway associated with polyphyllins synthesis in P. polyphylla .  Conclusions This study systematically investigated the growth-promoting effects and secondary metabolic regulation mechanisms of the bacterial inoculant P. palleroniana P6 on the endangered medicinal plant P. polyphylla. The findings highlight the potential of P. palleroniana P6 in promoting plant growth and enhancing polyphenol accumulation in P. polyphylla , providing valuable insights for the application of microbial inoculants in enhancing the growth and bioactive compound production of perennial medicinal plants. 

We previously analyzed the expression of genes associated with Paris polyphylla var. yunnanensis seed maturation and dormancy release; however, we were unable to clarify the relationship between gene expression levels and these processes. To reveal the molecular mechanisms underlying P. polyphylla var. yunnanensis seed dormancy release during a warm stratification, the transcriptomes of dormant and germinating P. polyphylla var. yunnanensis seeds were separately analyzed by RNA sequencing and were also compared with the transcriptomes of stem-leaf and root tissues harvested during the seed maturation stage. The RNA sequencing of five tissues generated 234,331 unigenes, of which 10,137 (4.33%) were differentially expressed among the analyzed tissues. The 6,619 unigenes whose expression varied among mature dormant, sprouted, and germinated seeds included 95 metabolic and 62 signaling genes related to abscisic acid, gibberellin, auxin, brassinosteroid, cytokinin, ethylene, jasmonic acid and salicylic acid. Additionally, 243 differentially expressed genes were annotated as known seed dormancy/germination-related genes. Among these genes, 109 were regulated by hormones or involved in hormone signal transduction. Finally, 310 transcription factor unigenes, including 71 homologs of known seed dormancy/ germination-related genes, were observed to be differentially expressed during a warm stratification. These results confirm that multiple hormones and transcription factors influence P. polyphylla var. yunnanensis seed dormancy release and germination during a warm stratification. This study identified candidate genes (e.g., ABI5) that should be cloned and functionally characterized regarding their effects on the release of P. polyphylla var. yunnanensis seed morphophysiological dormancy.

Origin traceability is important for controlling the effect of Chinese medicinal materials and Chinese patent medicines. Paris polyphylla var. yunnanensis is widely distributed and well-known all over the world. In our study, two spectroscopic techniques (Fourier transform mid-infrared (FT-MIR) and near-infrared (NIR)) were applied for the geographical origin traceability of 196 wild P. yunnanensis samples combined with low-, mid-, and high-level data fusion strategies. Partial least squares discriminant analysis (PLS-DA) and random forest (RF) were used to establish classification models. Feature variables extraction (principal component analysis—PCA) and important variables selection models (recursive feature elimination and Boruta) were applied for geographical origin traceability, while the classification ability of models with the former model is better than with the latter. FT-MIR spectra are considered to contribute more than NIR spectra. Besides, the result of high-level data fusion based on principal components (PCs) feature variables extraction is satisfactory with an accuracy of 100%. Hence, data fusion of FT-MIR and NIR signals can effectively identify the geographical origin of wild P. yunnanensis.

Paris polyphylla var. yunnanensis is a widely cultivated rhizomatous perennial woody plant known for producing highly valued steroidal saponins. Steroidal saponins serve as the primary active components and exhibit a variety of pharmacological effects. Their production is closely correlated with the growth environment and developmental stages of P. polyphylla . However, the medicinal value of P. polyphylla cultivated for varying durations remains unclear. In this study, we collected samples of P. polyphylla aged 3 to 8 years for metabolome and transcriptome sequencing analysis. The total saponin content was found to be significantly higher in 8-year-old P. polyphylla compared to younger plants. A total of 1,510 metabolites and 270.65 Gb of clean data were identified from these samples. This study provides insights into the medicinal values of P. polyphylla at different growth stages and elucidates the metabolic pathways for specific steroidal saponins.

Background Paris (Melanthiaceae) is an economically important but taxonomically difficult genus, which is unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships within Paris have long been controversial. Based on complete plastomes and nuclear ribosomal DNA (nrDNA) sequences, this study aims to reconstruct a robust phylogenetic tree and explore historical biogeography and clade diversification in the genus. Results All 29 species currently recognized in Paris were sampled. Whole plastomes and nrDNA sequences were generated by the genome skimming approach. Phylogenetic relationships were reconstructed using the maximum likelihood and Bayesian inference methods. Based on the phylogenetic framework and molecular dating, biogeographic scenarios and historical diversification of Paris were explored. Significant conflicts between plastid and nuclear datasets were identified, and the plastome tree is highly congruent with past interpretations of the morphology. Ancestral area reconstruction indicated that Paris may have originated in northeastern Asia and northern China, and has experienced multiple dispersal and vicariance events during its diversification. The rate of clade diversification has sharply accelerated since the Miocene/Pliocene boundary. Conclusions Our results provide important insights for clarifying some of the long-standing taxonomic debates in Paris . Cytonuclear discordance may have been caused by ancient and recent hybridizations in the genus. The climatic and geological changes since the late Miocene, such as the intensification of Asian monsoon and the rapid uplift of Qinghai-Tibet Plateau, as well as the climatic fluctuations during the Pleistocene, played essential roles in driving range expansion and radiative diversification in Paris . Our findings challenge the theoretical prediction that large genome sizes may limit speciation.

Background Polyphyllins are significant medicinal compounds found in Paris species, with different polyphyllins fulfilling distinct medicinal roles. Although some genes involved in polyphyllin synthesis have been identified, further exploration of the genes in the polyphyllin synthesis pathway is necessary due to the extensive genome of Paris species. The content and composition of polyphyllins vary among different Paris species, and the variations in specific polyphyllin levels across these plants make them promising candidates for identifying metabolites and genes associated with the biosynthesis of specific polyphyllins. Results In this study, we investigate the global metabolic and transcriptomic profiles of three types of Paris polyphylla var. yunnanensis (Franch.) Hand.-Mazz, one Paris fargesii Franch, and one Paris forrestii (Takht.) H. Li. The rhizome of P. polyphylla is rich in polyphyllin I and II, while P. forrestii is abundant in polyphyllin III, and P. fargesii contains high levels of polyphyllin VI, VII and H. The three Paris species exhibit distinct metabolomic and transcriptomic profiles. Through an integrated analysis of metabolic and transcriptomic data, along with a phylogenetic analysis of genes related to polyphyllin synthesis in Pari s, we annotated a total of six 2,3-oxidosqualene cyclases (OSCs), 120 cytochrome P450s (CYPs), and 138 UDP glycosyltransferases (UGTs). Phylogenetic tree analysis of the obtained data assisted in refining the candidate gene pool for OSC , CYP , and UGT . Subsequently, we identified 6, 12, and 26 candidate genes for OSC , CYP , and UGT , respectively. Finally, by combining the analyses of metabolic and genetic differences, we identified a total of 17 candidate genes, including 2 CAS , 4 CYP , and 11 UGT . Conclusions P. fargesii and P. forrestii are candidate medicinal plants for the development and application of specific polyphyllins. Transcripts from the UGT91 subfamily in Paris may play dual roles, contributing to both the synthesis of polyphyllin II and the catabolism of polyphyllin V and VI. The homologous genes of PpUGT73CE1 may regulate the synthesis of polyphyllin VI in P. fargesii . This study provides new insights into the investigation of biosynthetic pathways in medicinal plants that lack gene clusters.

Background  Paris polyphylla Sm. is a precious medicinal plant rich in various active ingredients. In addition to the well-known saponins, the flavonoids it contains have unique pharmacological potential in antioxidant, neuroprotective, and metabolic regulation. However, the flavonoids in Paris polyphylla Sm. have not been fully researched and developed yet. In this work, we conducted a comprehensive metabolomics and transcriptomics analysis to reveal the metabolic differences and biosynthetic mechanisms of flavonoids in the leaves, stems, and roots of Paris polyphylla Sm. Results Non-targeted metabolomics analysis detected a total of 332 metabolites in Paris polyphylla Sm., among which flavonoids accounted for 19.49%. The diversity and abundance of flavonoids in leaves are the highest, followed by stems and roots. By comparing the metabolites of the roots, stems, and leaves in Paris polyphylla Sm., it was found that there were 45 differential metabolites (DMs) between the leaves and roots, of which flavonoids accounted for 35%. There are 38 DMs between leaves and stems, of which flavonoids account for 45.45%. And there are 52 DMs in stems and roots, among which flavonoids account for 25.53%. A total of 62,766 genes were detected by transcriptomics, and pairwise comparison showed that there were tens of thousands of differentially expressed genes (DEGs) between each group. Afterwards, we selected 39 flavonoids and related metabolites (e.g., kaempferol-3-O-glucoside, quercetin 3-β-D-glucoside, rutin) for targeted metabolomics validation and performed RT-qPCR validation on 29 key flavonoid synthesis genes (e.g., C4H, CHS, FLS, F3’H) to verify the reliability of non-targeted metabolomics and transcriptomics. Conclusions This work indicated that leaves are the main site for the biosynthesis of flavonoids in Paris polyphylla Sm. Among them, kaempferol-3-O-glucoside, quercetin 3-β-D-glucoside, rutin, and other flavonoids are present in higher contents in leaves ( P  < 0.05). Further research on its biosynthetic mechanism indicates that naringenin chalcone is converted to naringenin by chalcone isomerase (CHI). Among them, CHI may be the rate-limiting enzyme in the biosynthesis of flavonoids in Paris polyphylla Sm. The expression of FLS is higher in leaves ( P  < 0.05) and tends to promote the synthesis of flavonols. This work promotes the utilization of non-medicinal parts of Paris polyphylla Sm. and enhances the sustainable development of this precious traditional Chinese medicine resource.

Pairs polyphylla var. yunnanensis (Paris L.) is a valuable medicinal plant used in traditional Chinese medicine. The market demand for P. polyphylla has increased over time, but it has slow growth and a low natural propagation rate. Endophytic bacteria are bioactive microorganisms that form a mutualistic relationship with host plants in long-term coordinated evolution, and they can promote the growth and accumulation of effective components in host plants. The aims of this study were to identify endophytic bacteria of P. polyphylla and to characterize their properties in promoting plant growth. A total of 10 endophytic bacteria were isolated from rhizomes of P. polyphylla. The isolated endophytes exhibited a variable capacity for indole acetic acid production, phosphate solubilization and nitrogen fixation. To investigate the effects of the endophytes on plant growth, four endophyte strains, G5, J2, G20, and Y2, were selected to compare their ability to promote plant growth. The results indicated that microbial endophytes isolated from P. polyphylla rhizomes play a vital role in improving P. polyphylla plant growth and could be used as inoculants to establish a sustainable crop production system.