De novo sequencing of Bletilla striata (Orchidaceae) transcriptome and identification of genes involved in polysaccharide biosynthesis

Combined metabolome and transcriptome analyses reveal the pivotal role of mycorrhizal fungi Tulasnella sp. BJ1 in the growth and accumulation of secondary metabolites in Bletilla striata (Thunb.) Reiehb.f

The orchids usually coexist with mycorrhizal fungi during their growth and development. Numerous studies have substantiated the pivotal regulatory role of Tulasnella sp. mycorrhizal fungi in the germination and growth of orchid seeds. However, there remains a dearth of research elucidating the effects and underlying mechanisms of Tulasnella sp. on the growth, development, and metabolite accumulation in Bletilla striata seedlings. In the current study, metabolomics and transcriptomic analysis were used to reveal the key role of the mycorrhizal fungus Tulasnella sp.BJ1 in the growth and accumulation of secondary metabolites in B. striata. The results demonstrated that the application of BJ1 significantly enhanced the growth and development of B. striata seedlings. In September, the plant weight, tuber diameter, and tuber weight in the BJ1 treatment group reached 44.27 ± 6.79 g, 6.13 ± 0.53 cm, and 23.35 ± 3.06 g, respectively, surpassing those in the control group. The polysaccharide content in the BJ1 treatment group and control group peaked in June, reaching 14.91 ± 2.26 % and 14.38 ± 0.25 %, respectively. Total phenol content in both groups decreased in May and June, and the total phenol content in BJ1 treatment group was significantly lower than that in control group. The significant decrease observed in total phenol content during May and June may be attributed to an increase in proportion of polysaccharides promoted by BJ1. The transcriptome results showed that BJ1 upregulated polysaccharide biosynthesis-related genes, such as mannose phosphatase, transferase, mannose 6-phosphate isomerase, hexokinase, fructose kinase, and glucose 6-phosphate isomerase, as well as genes involved in stilbenes biosynthesis, including hydroxycinnamyltransferase and transcinnamate 4-monooxygenase. Metabolomics data indicated that the content of mannose and seven stilbene compounds in the tubers increased significantly after BJ1 treatment. Interestingly, the accumulation of these compounds corresponds to the pathway of upregulated genes. These findings suggest that an upregulation in mannose synthesis may facilitate the accumulation of polysaccharides in B. striata. Therefore, the current study uncovered that the mycorrhizal fungus Tulasnella sp. BJ1 can not only promote the growth and development of B. striata seedlings and increase tuber yield but also promote the accumulation of polysaccharides and stilbenes.

Effect of different origins on genes encoding key enzymes involved in the polysaccharide biosynthetic pathway in Hedysarum polybotrys Hand.-Mazz

Radix Hedysari (HP) is a traditional Chinese medicine that has gained widespread attention for its tonic effects. Environmental factors significantly influence the active components in HP, notably Radix Hedysari polysaccharides (HPS), which are the principal active constituents. To date, no studies have reported on the environmental impact on the accumulation and biosynthesis of HPS. This research aims to evaluate the HPS accumulation and its biosynthetic pathways across different environments. We measured the HPS levels in samples from the core geographic area (geo-authentic product region) in Wudu, Gansu Province (WD), and a non-core geographic area (non-geo-authentic product region) in Tanchang, Gansu Province (TC), and conducted transcriptomic analyses. The HPS content in HP from WD (HP-WD, 12.14 ± 0.17 mg/g) was significantly higher than that in HP from TC (HP-TC, 5.48 ± 0.29 mg/g). Our investigation into the biosynthetic pathways of HPS showed that 21 enzymes, encoded by 198 unigenes, are involved. We identified 50 unigenes encoding 15 enzymes as differentially expressed genes (DEGs), indicating that approximately 71.4% of these enzymes are substantially affected by environmental factors. Heat map analysis of these 50 DEGs clearly differentiates HP-WD from HP-TC. Pearson correlation analysis revealed that the regulatory genes for 11 key enzymes have a significant positive correlation with HPS content (P <  0.05, r >  0.8). Consequently, the HP-WD is more likely to accumulate polysaccharides than HP-TC, potentially due to the activity of the aforementioned 11 key enzymes. This study provides theoretical support for the enhanced HPS content and quality assessment of HP sourced from the geo-authentic product region.

Metabolomic and transcriptomic analyses reveal the mechanism of polysaccharide and secondary metabolite biosynthesis in Bletilla striata tubers in response to shading

Polysaccharides and various secondary metabolites are the major bioactive ingredients in Bletilla striata tubers and their biosynthesis and accumulation are influenced by light intensity. However, the mechanisms underlying shading effects remain largely unknown. In the present study, we used a combined analysis of the physiology, metabolome, and transcriptome to investigate the physiological activities and bioactive component accumulation of B. striata under different shading treatments (S0, S50, S70, and S90). The dry weight of shoots and tubers, net photosynthetic rate, and polysaccharide content were highest in S50 and lowest in S90. The content of precursors (sucrose, Glucose-6P, and Mannose-6P) for polysaccharide synthesis significantly increased in S50. However, the expression levels of genes involved in starch biosynthesis decreased in S50. Several structural genes involved in secondary metabolism, including cinnamic acid 4-hydroxylase (C4H), chalcone synthase (CHS), and 1-Deoxy-D-xylulose-5-phosphate synthase (DXS), showed decreased expression in S50. However, the shading effect on the biosynthesis of secondary metabolites (phenylpropanoids, flavonoids, and terpenoids) was inconsistent. Our study provides the molecular mechanisms underlying the effects of shading on the biosynthesis of polysaccharides and secondary metabolites in B. striata and offers a theoretical basis for the artificial cultivation and industrial production of bioactive ingredients.

Combined metabolomics and transcriptomics reveal the secondary metabolite networks in different growth stages of Bletilla striata (Thunb.) Reichb.f

BACKGROUND

Bletilla striata (Thunb.) Reichb.f. (B. striata) is a traditional Chinese medicinal herb. B. striata polysaccharides (BSP), stilbenes and 2-isobutyl malic acid glucosoxy-benzyl ester compounds are the main active ingredients in B. striata. However, there is limited report on the changes of medicinal components and their biosynthesis regulation mechanisms in the tubers of B. striata at different stages.

METHOD

The tubers of B. striata were collected during the flowering period, fruiting period, and harvest period to determine the total polysaccharide content using the phenol sulfuric acid method. The changes in secondary metabolites in the tubers at these stages were analyzed by ultra performance liquid chromatography tandem mass spectrometry (UPLC-MS), and transcriptomics was conducted for further exploration of their biosynthetic pathways.

RESULT

The BSP content gradually increases from the flowering period to the fruiting period as the tubers develop, reaching its peak, but subsequently decreases at harvest time, which may be associated with the germination of B. striata buds in later stage. A total of 294 compounds were identified in this study. Among them, a majority of the compounds, such as 2-isobutyl malate gluconoxy-benzyl ester, exhibited high content during the fruit stage, while stilbenes like coelonin, 3'-O-methylbatatasin III, and blestriarene A accumulated during the harvesting period. The transcriptome data also revealed a substantial number of differentially expressed genes at various stages, providing a partial explanation for the complex changes in metabolites. We observed a correspondence between the expression pattern of GDP-Man biosynthesis-related enzyme genes and cumulative changes in BSP. And identified a positive correlation between 9 transcription factors and genes associated with polysaccharide biosynthesis, while 5 transcription factors were positively correlated with accumulation of 2-isobutyl malate gluconoxy-benzyl ester compounds and 5 transcription factors exhibited negative correlated with stilbene accumulation.

CONCLUSION

It is imperative to determine the appropriate harvesting period based on the specific requirements of different active ingredients and the accumulation patterns of their metabolites. Considering the involvement of multiple transcription factors in the biosynthesis and accumulation of its active ingredients, a comprehensive investigation into the specific regulatory mechanisms that facilitate high-quality cultivation of B. striata is imperative.

The rhizosphere microbiome and its influence on the accumulation of metabolites in Bletilla striata (Thunb.) Reichb. f

BACKGROUND

Bletilla striata (Thunb.) Reichb. f. (B. striata) is a perennial herbaceous plant in the Orchidaceae family known for its diverse pharmacological activities, such as promoting wound healing, hemostasis, anti-inflammatory effects, antioxidant properties, and immune regulation. Nevertheless, the microbe-plant-metabolite regulation patterns for B. striata remain largely undetermined, especially in the field of rhizosphere microbes. To elucidate the interrelationships between soil physics and chemistry and rhizosphere microbes and metabolites, a comprehensive approach combining metagenome analysis and targeted metabolomics was employed to investigate the rhizosphere soil and tubers from four provinces and eight production areas in China.

RESULTS

Our study reveals that the core rhizosphere microbiome of B. striata is predominantly comprised of Paraburkholderia, Methylibium, Bradyrhizobium, Chitinophaga, and Mycobacterium. These microbial species are recognized as potentially beneficial for plants health. Comprehensive analysis revealed a significant association between the accumulation of metabolites, such as militarine and polysaccharides in B. striata and the composition of rhizosphere microbes at the genus level. Furthermore, we found that the soil environment indirectly influenced the metabolite profile of B. striata by affecting the composition of rhizosphere microbes. Notably, our research identifies soil organic carbon as a primary driving factor influencing metabolite accumulation in B. striata.

CONCLUSION

Our fndings contribute to an enhanced understanding of the comprehensive regulatory mechanism involving microbe-plant-metabolite interactions. This research provides a theoretical basis for the cultivation of high-quality traditional Chinese medicine B. striata.

Cytochemical localization and synthesis mechanism of the glucomannan in pseudobulbs of Bletilla striata Reichb. f

The dried pseudobulbs of Bletilla striata, an important traditional Chinese medicine named BaiJi, have an extraordinary polysaccharide content and excellent prospects for medicinal effects. However, the distribution and molecular mechanism underlying biosynthesis are poorly understood. In this study, chemical and immunologic analyses were performed in representative tissues of B. striata, and the results showed that what are conventionally termed Bletilla striata polysaccharides (BSPs) are water-soluble polysaccharides deposited only in pseudobulbs. The structural component of BSPs is glucomannan, with a mannose:glucose mass ratio of ~3:2. BSPs are present in the parenchyma of the pseudobulbs in cells known as glucomannan idioblasts and distributed in the cytoplasm within cellular membranes, but are not contained in the vacuole. Comparative transcriptomics and bioinformatics analyses mapped the pathway from sucrose to BSP and identified BsGPI, BsmanA, and BsCSLAs as the key genes of BSP biosynthesis, suggesting that the functional differentiation of the cellulose synthase-like family A (CSLA) may be critical for the flow of glucomannan to the BSP or cell wall. Subsequently, virus-mediated gene silencing showed that silencing of two CSLAs (Bs03G11846 and Bs03G11849) led to a decrease in BSP content, and yeast two-hybrid and luciferase complementation experiments confirmed that four CSLAs (Bs03G11846, Bs03G11847, Bs03G11848, and Bs03G11849) can form homo- or heterodimers, suggesting that multiple CSLAs may form a large complex that functions in BSP synthesis. Our results provide cytological evidence of BSP and describe the isolation and characterization of candidate genes involved in BSP synthesis, laying a solid foundation for further research on its regulation mechanisms and the genetic engineering breeding of B. striata.

Identification of Bletilla striata and related decoction pieces: a data fusion method combining electronic nose, electronic tongue, electronic eye, and high-performance liquid chromatography data

Introduction: We here describe a new method for distinguishing authentic Bletilla striata from similar decoctions (namely, Gastrodia elata, Polygonatum odoratum, and Bletilla ochracea schltr). Methods: Preliminary identification and analysis of four types of decoction pieces were conducted following the Chinese Pharmacopoeia and local standards. Intelligent sensory data were then collected using an electronic nose, an electronic tongue, and an electronic eye, and chromatography data were obtained via high-performance liquid chromatography (HPLC). Partial least squares discriminant analysis (PLS-DA), support vector machines (SVM), and back propagation neural network (BP-NN) models were built using each set of single-source data for authenticity identification (binary classification of B. striata vs. other samples) and for species determination (multi-class sample identification). Features were extracted from all datasets using an unsupervised approach [principal component analysis (PCA)] and a supervised approach (PLS-DA). Mid-level data fusion was then used to combine features from the four datasets and the effects of feature extraction methods on model performance were compared. Results and Discussion: Gas chromatography-ion mobility spectrometry (GC-IMS) showed significant differences in the types and abundances of volatile organic compounds between the four sample types. In authenticity determination, the PLS-DA and SVM models based on fused latent variables (LVs) performed the best, with 100% accuracy in both the calibration and validation sets. In species identification, the PLS-DA model built with fused principal components (PCs) or fused LVs had the best performance, with 100% accuracy in the calibration set and just one misclassification in the validation set. In the PLS-DA and SVM authenticity identification models, fused LVs performed better than fused PCs. Model analysis was used to identify PCs that strongly contributed to accurate sample classification, and a PC factor loading matrix was used to assess the correlation between PCs and the original variables. This study serves as a reference for future efforts to accurately evaluate the quality of Chinese medicine decoction pieces, promoting medicinal formulation safety.

Overexpression of phosphomannomutase increases the production and bioactivities of Ganoderma exopolysaccharides

In this study, we explored a novel approach to enhancing the production and bioactivities of Ganoderma exopolysaccharides. The homologous phosphomannomutase gene (PMM1) was cloned and overexpressed in Ganoderma for the first time. As a result, the maximum production of exopolysaccharides by the PMM1 transformant was 1.53 g/L, which was 1.41-fold higher than of a wild-type (WT) strain in a 5-L bioreactor. The transcription levels of PMM1 and PMM2 increased 40.5- and 2.4-fold, respectively, whereas the value of the GDP-D-mannose pyrophosphorylase gene did not change significantly in this transgenic strain. Furthermore, the major exopolysaccharide fractions from PMM1 transformants contained higher amounts of mannose (56.5 % and 21.1 %) than those from a WT strain (26.7 % and 9.3 %). Moreover, the major fractions from PMM1 transformants exhibited stronger regulation effects on macrophage. In conclusion, this study is helpful for the efficient production and application of Ganoderma exopolysaccharides and facilitates an understanding of polysaccharide biosynthesis regulation.

Comparative transcriptome analysis of different tissues of Rheum tanguticum Maxim. ex Balf. (Polygonaceae) reveals putative genes involved in anthraquinone biosynthesis

Rheum tanguticum is a perennial herb and an important medicinal plant, with anthraquinones as its main bioactive compounds. However, the specific pathway of anthraquinone biosynthesis in rhubarb is still unclear. The accumulation of anthraquinones in different tissues (root, leaf, stem and seed) of R. tanguticum revealed considerable variation, suggesting possible differences in metabolite biosynthetic pathways and accumulation among various tissues. To better illustrate the biosynthetic pathway of anthraquinones, we assembled transcriptome sequences from the root, leaf, stem and seed tissues yielding 157,564 transcripts and 88,142 unigenes. Putative functions could be assigned to 56,911 unigenes (64.57%) based on BLAST searches against annotation databases, including GO, KEGG, Swiss-Prot, NR, and Pfam. In addition, putative genes involved in the biosynthetic pathway of anthraquinone were identified. The expression profiles of nine unigenes involved in anthraquinone biosynthesis were verified in different tissues of R. tanguticum by qRT-PCR. Various transcription factors, including bHLH, MYB_related, and C2H2, were identified by searching unigenes against plantTFDB. This is the first transcriptome analysis of different tissues of R. tanguticum and can be utilized to describe the genes involved in the biosynthetic pathway of anthraquiones, understanding the molecular mechanism of active compounds in R. tanguticum.

Integrated Metabolites and Transcriptomics at Different Growth Stages Reveal Polysaccharide and Flavonoid Biosynthesis in Cynomorium songaricum

Cynomorium songaricum is a perennial parasitic herb, and its stem is widely used as a traditional Chinese medicine, which largely relies on bioactive compounds (e.g., polysaccharides, flavonoids, and triterpenes). To date, although the optimum harvest time of stems has been demonstrated at the unearthed stage (namely the early flowering stage, EFS), the accumulation mechanism of polysaccharides and flavonoids during growth stages is still limited. In this study, the physiological characteristics (stem fresh weight, contents of soluble sugar and flavonoids, and antioxidant capacity) at four different growth stages (germination stage (GS), vegetative growth stage (VGS), EFS, and flowering stage (FS)) were determined, transcriptomics were analyzed by illumina sequencing, and expression levels of key genes were validated by qRT-PCR at the GS, VGS, and EFS. The results show that the stem biomass, soluble sugar and total flavonoids contents, and antioxidant capacity peaked at EFS compared with GS, VGS, and FS. A total of 6098 and 13,023 differentially expressed genes (DEGs) were observed at VGS and EFS vs. GS, respectively, with 367 genes co-expressed. Based on their biological functions, 109 genes were directly involved in polysaccharide and flavonoid biosynthesis as well as growth and development. The expression levels of key genes involved in polysaccharides (e.g., GLCs, XTHs and PMEs), flavonoids (e.g., 4CLLs, CYPs and UGTs), growth and development (e.g., AC58, TCPs and AP1), hormones biosynthesis and signaling (e.g., YUC8, AIPT and ACO1), and transcription factors (e.g., MYBs, bHLHs and WRKYs) were in accordance with changes of physiological characteristics. The combinational analysis of metabolites with transcriptomics provides insight into the mechanism of polysaccharide and flavonoid biosynthesis in C. songaricum during growth stages.

Haplotype-resolved genome assembly of Bletilla striata (Thunb.) Reichb.f. to elucidate medicinal value

Bletilla striata, commonly known as baiji, is a species used in traditional Chinese medicine; it is highly regarded for its medicinal applications and therefore has high economic value. Here, we report a high-quality haplotype-resolved genome of B. striata, haplotype A (2.37 Gb, with a scaffold N50 of 146.39 Mb and a contig N50 of 1.65 Mb) and haplotype B (2.43 Gb, with a scaffold N50 of 150.22 Mb and a contig N50 of 1.66 Mb), assembled from high-fidelity (HiFi) reads and chromosome conformation capture (Hi-C) reads. We find evidence that B. striata has undergone two whole-genome duplication (WGD) events: an ancient WGD event shared by most monocots and a recent WGD event unique to all orchids. We also reconstructed the ancestral orchid karyotype (AOK) of 18 ancient chromosomes and the evolutionary trajectories of 16 modern B. striata chromosomes. Comparative genomic analysis suggests that the expanded gene families of B. striata might play important roles in secondary metabolite biosynthesis and environmental adaptation. By combining genomic and transcriptomic data, we identified the 10 core members from nine gene families that were probably involved in B. striata polysaccharide (BSP) biosynthesis. Based on virus-induced gene silencing (VIGS) and yeast two-hybrid experiments, we present an MYB transcription factor (TF), BsMYB2, that can regulate BSP biosynthesis by directly interacting with eight key BSP-related genes: sacA1, HK1, scrK1, scrK2, GPI1, manA1, GMPP1 and UGP2_1. Our study will enhance the understanding of orchid evolution and accelerate the molecular-assisted breeding of B. striata for improving traits of medicinal value.

Phenotype correlation analysis and excellent germplasm screening of herb Bletilla Rchb. f. based on comprehensive evaluation from thirty-three geographic populations

BACKGROUND

The Bletilla genus of Orchidaceae includes plants with great economic value, among which B. striata is the main traditional medicinal plant, and its pseudobulb, known as BaiJi, was first recorded in Shennong's Classic of Materia Medica. However, there has been little systemic evaluation of the germplasm quality of Bletilla plants in China. In order to comprehensive evaluate the Bletilla resources in China and screen out the candidate phenotypic traits determining yield and/or quality of Bletilla, the variation of phenotypic indicators (pseudobulb, leaf, stem, inflorescence, flower) and active ingredients contents (polysaccharide, total phenolics and militarine) in different populations of B. striata and B. ochracea were investigated through 4 years' common-garden experiment.

RESULTS

There were abundant phenotypic variations and significant differences among different populations in the morphological phenotypes, pseudobulb weight and main active ingredient contents. AHBZ, HBLT and HBSN populations showed good prospects for industrial development, presenting higher quality in terms of yield and main active ingredient content. Pseudobulb yield, polysaccharide and total phenol content are positively correlated with phenotypic traits. Militarine content is negatively correlated with almost all indexes. Plant height, leaf width and stem diameter may be important indicators of potential excellent germplasms.

CONCLUSIONS

Bletilla is not strictly geoauthentic medicinal plants. B. ochracea could be accepted as an alternative resource to B. striata. The best harvest period of Bletilla is the third year after cultivation. Plant height, leaf width and stem diameter may be important indicators of potential excellent germplasms. These results provide important information required for the efficient screening and utilization of Bletilla germplasm resources.

Screening of Bletilla striata, Bletilla ochracea, and Oreorchis foliosa differential metabolites based on metabolomics

As a representative medicinal plant in Orchidaceae, Bletilla striata plays a variety of pharmacological roles in the clinic. However, the emergence of counterfeit species affects the basic medicinal materials source identification process, of which Bletilla ochracea and Oreorchis foliosa of Orchidaceae are two representative species. For this study, 13 representative B. striata samples, 3 B. ochracea samples and 3 O. foliosa samples were selected for the systematic determination of polysaccharide yields and monosaccharide composition, and further detection of secondary metabolites by HPLC-MS. The results revealed that there was a significant difference in the yields of polysaccharides between B. striata and B. ochracea (P = 0.006). Although the polysaccharides of both species were composed of glucose and mannose, the molar ratio of the two monosaccharides was different suggested that the structures of the polysaccharide were different. The metabolomics results showed that there were no differences in the types of metabolites between B. striata and B. ochracea; however, there were differences in the content of these metabolites. Although there was no significant difference in the polysaccharide yields of B. striata and O. foliosa (P = 0.074) and the monosaccharide composition was the same (glucose and mannose), many different metabolites were screened out between them: 6 compounds such as C₃₆ H₃₄ O₁₁ existed only in B. striata, while substance C₃₉ H₅₄ O₂₂ was unique to O. foliosa. Therefore, based on the analysis of the polysaccharide content and monosaccharide composition, combined with phase metabolomics research, a preliminary distinction between B. striata, B. ochracea, and O. foliosa was achieved.

Organ-specific, integrated omics data-based study on the metabolic pathways of the medicinal plant Bletilla striata (Orchidaceae)

BACKGROUND

Bletilla striata is one of the important species belonging to the Bletilla genus of Orchidaceae. Since its extracts have an astringent effect on human tissues, B. striata is widely used for hemostasis and healing. Recently, some other beneficial effects have also been uncovered, such as antioxidation, antiinflammation, antifibrotic, and immunomodulatory activities. As a key step towards a thorough understanding on the medicinal ingredient production in B. striata, deciphering the regulatory codes of the metabolic pathways becomes a major task.

RESULTS

In this study, three organs (roots, tubers and leaves) of B. striata were analyzed by integrating transcriptome sequencing and untargeted metabolic profiling data. Five different metabolic pathways, involved in polysaccharide, sterol, flavonoid, terpenoid and alkaloid biosynthesis, were investigated respectively. For each pathway, the expression patterns of the enzyme-coding genes and the accumulation levels of the metabolic intermediates were presented in an organ-specific way. Furthermore, the relationships between enzyme activities and the levels of the related metabolites were partially inferred. Within the biosynthetic pathways of polysaccharides and flavonoids, long-range phytochemical transportation was proposed for certain metabolic intermediates and/or the enzymes.

CONCLUSIONS

The data presented by this work could strengthen the molecular basis for further studies on breeding and medicinal uses of B. striata.