Genome-Wide Transcriptional Excavation of Dipsacus asperoides Unmasked both Cryptic Asperosaponin Biosynthetic Genes and SSR Markers

Full-length transcriptome, proteomics and metabolite analysis reveal candidate genes involved triterpenoid saponin biosynthesis in Dipsacus asperoides

Dipsacus asperoides is a traditional medicinal herb widely used in inflammation and fracture in Asia. Triterpenoid saponins from D. asperoides are the main composition with pharmacological activity. However, the biosynthesis pathway of triterpenoid saponins has not been completely resolved in D. asperoides. Here, the types and contents of triterpenoid saponins were discovered with different distributions in five tissues (root, leaf, flower, stem, and fibrous root tissue) from D. asperoides by UPLC-Q-TOF-MS analysis. The discrepancy between five tissues in D. asperoides at the transcriptional level was studied by combining single-molecule real-time sequencing and next- generation sequencing. Meanwhile, key genes involved in the biosynthesis of saponin were further verified by proteomics. In MEP and MVA pathways, 48 differentially expressed genes were identified through co-expression analysis of transcriptome and saponin contents, including two isopentenyl pyrophosphate isomerase and two 2,3-oxidosqualene β-amyrin cyclase, etc. In the analysis of WGCNA, 6 cytochrome P450s and 24 UDP- glycosyltransferases related to the biosynthesis of triterpenoid saponins were discovered with high transcriptome expression. This study will provide profound insights to demonstrate essential genes in the biosynthesis pathway of saponins in D. asperoides and support for the biosynthetic of natural active ingredients in the future.

Transcriptome analysis reveals that jasmonic acid biosynthesis and signaling is associated with the biosynthesis of asperosaponin VI in Dipsacus asperoides

Dipsacus asperoides is a perennial herb, the roots of which are abundant in asperosaponin VI, which has important medicinal value. However, the molecular mechanism underlying the biosynthesis of asperosaponin VI in D. asperoides remains unclear. In present study, a comprehensive investigation of asperosaponin VI biosynthesis was conducted at the levels of metabolite and transcript during root development. The content of asperosaponin VI was significantly accumulated in two-leaf stage roots, and the spatial distribution of asperosaponin VI was localized in the xylem. The concentration of asperosaponin VI gradually increased in the root with the development process. Transcriptome analysis revealed 3916 unique differentially expressed genes (DEGs) including 146 transcription factors (TFs) during root development in D. asperoides. In addition, α-linolenic acid metabolism, jasmonic acid (JA) biosynthesis, JA signal transduction, sesquiterpenoid and triterpenoid biosynthesis, and terpenoid backbone biosynthesis were prominently enriched. Furthermore, the concentration of JA gradually increased, and genes involved in α-linolenic acid metabolism, JA biosynthesis, and triterpenoid biosynthesis were up-regulated during root development. Moreover, the concentration of asperosaponin VI was increased following methyl jasmonate (MeJA) treatment by activating the expression of genes in the triterpenoid biosynthesis pathway, including acetyl-CoA acetyltransferase (DaAACT), 3-hydroxy-3-methylglutaryl coenzyme A synthase (DaHMGCS), 3-hydroxy-3-methylglutaryl coenzyme-A reductase (DaHMGCR). We speculate that JA biosynthesis and signaling regulates the expression of triterpenoid biosynthetic genes and facilitate the biosynthesis of asperosaponin VI. The results suggest a regulatory network wherein triterpenoids, JA, and TFs co-modulate the biosynthesis of asperosaponin VI in D. asperoides.

Comparative Proteomic Analysis of Dipsacus asperoides Roots from Different Habitats in China

Dipsacus asperoides is a kind of Chinese herbal medicine with beneficial health properties. To date, the quality of D. asperoides from different habitats has shown significant differences. However, the molecular differences in D. asperoides from different habitats are still unknown. The aim of this study was to investigate the differences in protein levels of D. asperoides from different habitats. Isobaric tags for relative and absolute quantification (iTRAQ) and 2DLC/MS/MS were used to detect statistically significant changes in D. asperoides from different habitats. Through proteomic analysis, a total of 2149 proteins were identified, of which 42 important differentially expressed proteins were screened. Through in-depth analysis of differential proteins, the protein metabolism energy and carbohydrate metabolism of D. asperoides from Hubei Province were strong, but their antioxidant capacity was weak. We found that three proteins, UTP-glucose-1-phosphate uridylyltransferase, allene oxide cyclase, and isopentyl diphosphate isomerase 2, may be the key proteins involved in dipsacus saponin VI synthesis. Eight proteins were found in D. asperoides in response to environmental stress from different habitats. Quantitative real-time PCR analysis confirmed the accuracy and authenticity of the proteomic analysis. The results of this study may provide the basic information for exploring the cause of differences in secondary metabolites in different habitats of D. asperoides and the protein mechanism governing differences in quality.

Association between dipsacus saponin VI level and diversity of endophytic fungi in roots of Dipsacus asperoides

Dipsacus asperoides contains multiple pharmacologically active compounds. The principal are saponins. The plant can be cultivated, but it contains lower levels of bioactive compounds than the plant in the wild. It may be the reason to exploit the endophytic fungi that colonize the plant roots in order to produce bioactive compounds. However, the endophytic fungi of D. asperoides have not been analyzed in detail. In this study, we isolated and identified 46 endophytic fungal strains from the taproots, lateral roots and leaves, and we used morphological and molecular biological methods to assign them into 15 genera: Fusarium sp., Ceratobasidium sp., Chaetomium sp., Penicillium sp., Aspergillus sp., Talaromyces sp., Cladosporium sp., Bionectria sp., Mucor sp., Trichoderma sp., Myrothecium sp., Clonostachys sp., Ijuhya sp., Leptosphaeria sp. and Phoma sp. Taproots contained abundant endophytic fungi, the numbers of which correlated positively with level of dipsacus saponin VI. Primary fermentation of several endophytic fungal strains from taproots showed that Fusarium, Leptosphaeria, Ceratobasidium sp. and Phoma sp. can produce the triterpenoid saponin. These results may guide efforts to sustainably produce bioactive compounds from D. asperoides.

Comparative transcriptomics provides novel insights into the mechanisms of selenium tolerance in the hyperaccumulator plant Cardamine hupingshanensis

Selenium (Se) is an essential mineral element for animals and humans. Cardamine hupingshanensis (Brassicaceae), found in the Wuling mountain area of China, has been identified as a novel Se hyperaccumulator plant. However, the mechanism for selenium tolerance in Cardamine plants remains unknown. In this study, two cDNA libraries were constructed from seedlings of C. hupingshanensis treated with selenite. Approximately 100 million clean sequencing reads were de novo assembled into 48,989 unigenes, of which 39,579 and 33,510 were expressed in the roots and leaves, respectively. Biological pathways and candidate genes involved in selenium tolerance mechanisms were identified. Differential expression analysis identified 25 genes located in four pathways that were significantly responsive to selenite in C. hupingshanensis seedlings. The results of RNA sequencing (RNA-Seq) and quantitative real-time PCR (RT-qPCR) confirmed that storage function, oxidation, transamination and selenation play very important roles in the selenium tolerance in C. hupingshanensis. Furthermore, a different degradation pathway synthesizing malformed or deformed selenoproteins increased selenium tolerance at different selenite concentrations. This study provides novel insights into the mechanisms of selenium tolerance in a hyperaccumulator plant, and should serve as a rich gene resource for C. hupingshanensis.