Deep sequencing and transcriptome analyses to identify genes involved in secoiridoid biosynthesis in the Tibetan medicinal plant Swertia mussotii

Regulation of gene expression in the secondary metabolic synthesis pathway of Lonicera japonica Flos by yeast polysaccharides

Lonicera japonica Flos is a valuable herb in the Lonicerae family. While transcriptomic studies on L. japonica have focused on different tissues (stems, leaves, flowers) or flowering stages, few have investigated the molecular mechanisms underlying chemical composition synthesis influenced by exogenous factors, such as foliar fertilization. Moreover, most transcriptomic studies on L. Japonica have been conducted on chlorogenic acid and luteoloside, and the molecular synthesis mechanism of the overall chemical composition has not been analyzed. Methods: We conducted a single-factor, four-level foliar fertilization experiment using yeast polysaccharides. Different yeast polysaccharides concentrations were sprayed on L. japonica for six consecutive days with dynamic sampling. High-performance liquid chromatography determined the active ingredients in each group. The two groups exhibiting the most significant differences were selected for transcriptomic analysis to identify key synthetic genes responsible for L. japonica's active ingredients. Key results: Principal component analysis conducted on samples collected on September 8 revealed significant differences in the active ingredient amounts between the 0.1 g/L yeast polysaccharides treatment group and the control group. Transcriptome sequencing analysis identified 218 significantly differentially expressed genes, including 60 upregulated and 158 downregulated genes. Twelve differential genes involved in the chemical components synthesis pathway of L. japonica under yeast polysaccharides treatment were identified: PAL1, PAL2, PAL3, 4CL1, 4CL, CHS1, CHS2, CHS, CHI1, CHI2, F3H, and SOH. Conclusions: This study contributes to the theoretical understanding of essential synthetic genes associated with L. japonica's active ingredients. It offers data support for further gene exploration and sheds light on the molecular mechanisms underlying L. japonica quality formation. These findings hold significant implications for enhancing the content of secondary metabolites of L. japonica.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01482-1.

Integrative metabolomic and transcriptomic analyses reveals the accumulation patterns of key metabolites associated with flavonoids and terpenoids of Gynostemma pentaphyllum (Thunb.) Makino

Gynostemma pentaphyllum (Thunb.) Makino (G. pentaphyllum) is a medicinal and edible plant with multiple functions of liver protection, anti-tumor, anti-inflammation, balancing blood sugar and blood lipids. The nutritional value of the G. pentaphyllum plant is mainly due to its rich variety of biologically active substances, such as flavonoids, terpenes and polysaccharides. In this study, we performed a comprehensive analysis combining metabolomics and root, stem and leaf transcriptomic data of G. pentaphyllum. We used transcriptomics and metabolomics data to construct a dynamic regulatory network diagram of G. pentaphyllum flavonoids and terpenoids, and screened the transcription factors involved in flavonoids and terpenoids, including basic helix-loop-helix (bHLH), myb-related, WRKY, AP2/ERF. Transcriptome analysis results showed that among the DEGs related to the synthesis of flavonoids and terpenoids, dihydroflavonol 4-reductase (DFR) and geranylgeranyl diphosphate synthases (GGPPS) were core genes. This study presents a dynamic image of gene expression in different tissues of G. pentaphyllum, elucidating the key genes and metabolites of flavonoids and terpenoids. This study is beneficial to a deeper understanding of the medicinal plants of G. pentaphyllum, and also provides a scientific basis for further regulatory mechanisms of plant natural product synthesis pathways and drug development.

mRNA-Seq and miRNA-Seq Analyses Provide Insights into the Mechanism of Pinellia ternata Bulbil Initiation Induced by Phytohormones

Pinellia ternata (Thunb.) Breit (abbreviated as P. ternata) is a plant with an important medicinal value whose yield is restricted by many factors, such as low reproductive efficiency and continuous cropping obstacles. As an essential breeding material for P. ternata growth and production, the bulbils have significant advantages such as a high survival rate and short breeding cycles. However, the location effect, influencing factors, and molecular mechanism of bulbil occurrence and formation have not been fully explored. In this study, exogenously applied phytohormones were used to induce in vitro petiole of P. ternata to produce bulbil structure. Transcriptome sequencing of mRNA and miRNA were performed in the induced petiole (TCp) and the induced bulbil (TCb). Gene Ontology (GO) term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed for the identification of key genes and pathways involved in bulbil development. A total of 58,019 differentially expressed genes (DEGs) were identified. The GO and KEGG analysis indicated that DEGs were mainly enriched in plant hormone signal transduction and the starch and sucrose metabolism pathway. The expression profiles of miR167a, miR171a, and miR156a during bulbil induction were verified by qRT-PCR, indicating that these three miRNAs and their target genes may be involved in the process of bulbil induction and play an important role. However, further molecular biological experiments are required to confirm the functions of the identified bulbil development-related miRNAs and targets.

Comparative transcriptome analysis to identify putative genes involved in carvacrol biosynthesis pathway in two species of Satureja, endemic medicinal herbs of Iran

Satureja is rich in phenolic monoterpenoids, mainly carvacrol, that is of interest due to diverse biological activities including antifungal and antibacterial. However, limited information is available regarding the molecular mechanisms underlying carvacrol biosynthesis and its regulation for this wonderful medicinal herb. To identify the putative genes involved in carvacrol and other monoterpene biosynthesis pathway, we generated a reference transcriptome in two endemic Satureja species of Iran, containing different yields (Satureja khuzistanica and Satureja rechingeri). Cross-species differential expression analysis was conducted between two species of Satureja. 210 and 186 transcripts related to terpenoid backbone biosynthesis were identified for S. khuzistanica and S. rechingeri, respectively. 29 differentially expressed genes (DEGs) involved in terpenoid biosynthesis were identified, and these DEGs were significantly enriched in monoterpenoid biosynthesis, diterpenoid biosynthesis, sesquiterpenoid and triterpenoid biosynthesis, carotenoid biosynthesis and ubiquinone and other terpenoid-quinone biosynthesis pathways. Expression patterns of S. khuzistanica and S. rechingeri transcripts involved in the terpenoid biosynthetic pathway were evaluated. In addition, we identified 19 differentially expressed transcription factors (such as MYC4, bHLH, and ARF18) that may control terpenoid biosynthesis. We confirmed the altered expression levels of DEGs that encode carvacrol biosynthetic enzymes using quantitative real-time PCR (qRT-PCR). This study is the first report on de novo assembly and transcriptome data analysis in Satureja which could be useful for an understanding of the main constituents of Satureja essential oil and future research in this genus.

Co-Expression Analysis Reveals Differential Expression of Homologous Genes Associated with Specific Terpenoid Biosynthesis in Rehmannia glutinosa

Terpenoids are naturally occurring compounds involved in respiration, photosynthesis, membrane fluidity, and pathogen interactions and are classified according to the structure of their carbon skeleton. Although most terpenoids possess pharmacological activity, knowledge about terpenoid metabolism in medicinal plants is insufficient. Rehmannia glutinosa (R. glutinosa) is a traditional herb that is widely used in East Asia and has been reported to contain various terpenoids. In this study, we performed a comprehensive transcriptome analysis of terpenoid metabolism in R. glutinosa using two RNA sequencing platforms: Illumina and PacBio. The results show that the sterol, saponin, iridoid, and carotenoid pathways are active in R. glutinosa. Sterol and saponin biosynthesis were mevalonate pathway dependent, whereas iridoid and carotenoid biosynthesis were methylerythritol 4-phosphate pathway dependent. In addition, we found that the homologous genes of key enzymes involved in terpenoid metabolism were expressed differentially and that the differential expression of these genes was associated with specific terpenoid biosynthesis. The different expression of homologous genes encoding acetyl-CoA acetyltransferase, 3-hydroxy-3-methylglutaryl-CoA reductase, mevalonate kinase, mevalonate diphosphate decarboxylase, farnesyl pyrophosphate synthase, squalene synthase, and squalene epoxidase was associated with sterol and saponin biosynthesis. Homologous genes encoding 1-deoxy-D-xylulose 5-phosphate synthase were also differentially expressed and were associated with carotenoid and iridoid biosynthesis. These results suggest that the biosynthesis of specific terpenoids can be regulated by the homologous of key enzymes involved in plant terpenoid metabolism.

Global gene expression profiling under nitrogen stress identifies key genes involved in nitrogen stress adaptation in maize (Zea mays L.)

Maize is a heavy consumer of fertilizer nitrogen (N) which not only results in the high cost of cultivation but may also lead to environmental pollution. Therefore, there is a need to develop N-use efficient genotypes, a prerequisite for which is a greater understanding of N-deficiency stress adaptation. In this study, comparative transcriptome analysis was performed using leaf and root tissues from contrasting inbred lines, viz., DMI 56 (tolerant to N stress) and DMI 81 (susceptible to N stress) to delineate the differentially expressed genes (DEGs) under low-N stress. The contrasting lines were grown hydroponically in modified Hoagland solution having either sufficient- or deficient-N, followed by high-throughput RNA-sequencing. A total of 8 sequencing libraries were prepared and 88–97% of the sequenced raw reads were mapped to the reference B73 maize genome. Genes with a p value ≤ 0.05 and fold change of ≥ 2.0 or ≤ − 2 were considered as DEGs in various combinations performed between susceptible and tolerant genotypes. DEGs were further classified into different functional categories and pathways according to their putative functions. Gene Ontology based annotation of these DEGs identified three different functional categories: biological processes, molecular function, and cellular component. The KEGG and Mapman based analysis revealed that most of the DEGs fall into various metabolic pathways, biosynthesis of secondary metabolites, signal transduction, amino acid metabolism, N-assimilation and metabolism, and starch metabolism. Some of the key genes involved in N uptake (high-affinity nitrate transporter 2.2 and 2.5), N assimilation and metabolism (glutamine synthetase, asparagine synthetase), redox homeostasis (SOD, POX), and transcription factors (MYB36, AP2-EREBP) were found to be highly expressed in the tolerant genotype compared to susceptible one. The candidate genes identified in the present study might be playing a pivotal role in low-N stress adaptation in maize and hence could be useful in augmenting further research on N metabolism and development of N-deficiency tolerant maize cultivars.

Application of High-Throughput Sequencing on the Chinese Herbal Medicine for the Data-Mining of the Bioactive Compounds

The Chinese Herbal Medicine (CHM) has been used worldwide in clinic to treat the vast majority of human diseases, and the healing effect is remarkable. However, the functional components and the corresponding pharmacological mechanism of the herbs are unclear. As one of the main means, the high-throughput sequencing (HTS) technologies have been employed to discover and parse the active ingredients of CHM. Moreover, a tremendous amount of effort is made to uncover the pharmacodynamic genes associated with the synthesis of active substances. Here, based on the genome-assembly and the downstream bioinformatics analysis, we present a comprehensive summary of the application of HTS on CHM for the synthesis pathways of active ingredients from two aspects: active ingredient properties and disease classification, which are important for pharmacological, herb molecular breeding, and synthetic biology studies.

Toward understanding of the methoxylated flavonoid biosynthesis pathway in Dracocephalum kotschyi Boiss

Nowadays, with the development and advancement of next-generation sequencing technologies, a new path has been provided for transcriptomic studies. In this study, the transcriptome of Dracocephalum kotschyi Boiss., as an endemic and endangered plant which is contained a large amount of valuable secondary metabolites with antioxidant and anticancer properties, was sequenced. Then functional annotation and gene ontology analysis for 165,597 assembled transcripts were performed, most were associated with the metabolic pathways. This might be because there are various active biochemical pathways in this plant. Furthermore, after comprehensive transcript annotation, the putative genes involved in the main metabolic pathways of D. kotschyi were identified. Then, the biosynthetic pathway of its valuable methoxylated flavones was proposed. Finally, the accumulations of important methoxylated-flavone metabolites in three different tissues were quantified by HPLC. The relative expression of the genes involved in the proposed pathway was investigated by qRT-PCR, which indicated high expression levels in the bud tissue. The present results may lead to the design strategies to preserve the genetic diversity of endangered D. kotschyi plants and apply the new methods for engineering its valuable methoxylated-flavones pathway.

Metabolomics integrated with transcriptomics reveals the distribution of iridoid and crocin metabolic flux in Gardenia jasminoides Ellis

Gardenia jasminoides Ellis (G. jasminoides) fruits are used as a resource for obtaining natural colorants and in traditional Chinese herbal medicine. However, G. jasminoides presents a relatively long flowering period and different ripening periods, so there are significant differences in the accumulation of metabolites in fruits of different colors. In addition, the complete metabolic pathways of iridoidsand crocins, which are used as medicinal composition of G. jasminoides, are poorly understood at present. In this research, we comprehensively compared the transcriptome and metabolites profiles of the developmental stages and locations of iridoid and crocin biosynthesis. A large number of differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were detected in four groups of samples, and clear variation in the pattern of metabolite abundance and gene expression were observed among different fruit colors and parts. Geniposide and gardenoside mainly accumulated in the sarcocarp of green fruit (GFS) and the sarcocarp of red fruit (FS), respectively. Crocin mainly accumulated in the peel and sarcocarp of red fruits. In the iridoid pathway, we hypothesized that there was a transport mechanism from the sarcocarp to the peel of G. jasminoides because of the inconsistent expression of G8O, 10-HGO and IS associated with differences in fruit ripening. UGTs play an important role in the biosynthesis of the active components of G. jasminoides. Combined transcriptome and metabonomics analysis showed a negative correlation between the biosynthesis of geniposide and crocin. The redirection of the metabolic flux and the regulation of key enzymes may be the main reasons for the changes in the biosynthesis of iridoid and crocin in G. jasminoides fruit. Our study expended valuable information for functional genomic library and provided new insights for metabolic engineering of secondary metabolite in G. Jasminoides.

Full-length transcriptome analysis provides new insights into the early bolting occurrence in medicinal Angelica sinensis

Angelica sinensis (Oliv.) Diels root part is an integral component of traditional Chinese medicine, widely prescribed to improve blood circulation and blood stasis. However, early bolting of A. sinensis compromises the quality of the roots and hence is a major limitation for yield of medicinal materials. To date, little information about the molecular mechanisms underlying bolting is available for this important medicinal plant. To identify genes putatively involved in early bolting, we have conducted the transcriptome analysis of the shoot tips of the early-bolting plants and non-bolting (normal) plants of A. sinensis, respectively, using a combination of third-generation sequencing and next-generation sequencing. A total of 43,438 non-redundant transcripts were collected and 475 unique differentially expressed genes (DEGs) were identified. Gene annotation and functional analyses revealed that DEGs were highly involved in plant hormone signaling and biosynthesis pathways, three main flowering pathways, pollen formation, and very-long-chain fatty acids biosynthesis pathways. The levels of endogenous hormones were also changed significantly in the early bolting stage of A. sinensis. This study provided new insights into the transcriptomic control of early bolting in A. sinensis, which could be further applied to enhance the yield of medicinally important raw materials.

Biotechnological interventions and genetic diversity assessment in Swertia sp.: a myriad source of valuable secondary metabolites

The genus Swertia (Family: Gentianaceae) has cosmopolitan distribution which is present in almost all the continents except South America and Australia. Swertia genus has been renowned as one of the potent herbal drugs in the British, American, and Chinese Pharmacopeias as well as well-documented in the Indian traditional medicinal systems, viz. Ayurveda, Siddha, and Unani. Many species of this genus have therapeutic properties and have been used traditionally in the treatment of a number of health ailments viz. hepatitis, diabetes, inflammation, bacillary dysentery, cancer, malaria, fever etc. This genus is industrially important medicinal plant that has been used as a principal component in numerous marketed herbal/ polyherbal formulations. Medicinal usage of Swertia is endorsed to the miscellaneous compounds viz. xanthones, irridoids, seco-irridoids, and triterpenoids. A chain of systematic isolation of bio-active compounds and their diverse range of pharmacological effects during last 15-20 years proved this genus as industrially important plant. Due to the various practices of the Swertia species, annual demand is more than 100 tons per year for this important herb which is continuously increasing 10% annually. The market value rises 10% by the year as there is increased demand in national and international market resulted in adulteration of many Swertia spp. due to paucity of agricultural practices, exomorphological, phytochemical, and molecular characterization. Thus, efficient biotechnology methods are prerequisite for the mass production of authentic species, sustainable production of bio-active compounds and ex situ conservation. A chain of systematic biotechnological interventions in Swertia herb during last 20 years cover the assessment of genetic diversity, in vitro sustainable production of bio-active compounds and mass propagation of elite genotypes via direct and indirect organogenesis. This review attempts to present the comprehensive assessment on biotechnological process made in Swertia over the past few years. KEY POINTS: • Critical and updated assessment on biotechnological aspects of Swertia spp. • In vitro propagation and genetic diversity assessment in Swertia spp. • Biosynthesis and sustainable production of secondary metabolites in Swertia spp.

Full-Length Transcriptome Sequencing Provides Insights into Flavonoid Biosynthesis in Fritillaria hupehensis

One of the most commonly utilized medicinal plants in China is Fritillaria hupehensis (Hsiao et K.C. Hsia). However, due to a lack of genomic resources, little is known about the biosynthesis of relevant compounds, particularly the flavonoid biosynthesis pathway. A PacBio RS II sequencing generated a total of 342,044 reads from the bulb, leaf, root, and stem, of which 316,438 were full-length (FL) non-redundant reads with an average length of 1365 bp and a N50 of 1888 bp. There were also 38,607 long non-coding RNAs and 7914 simple sequence repeats detected. To improve our understanding of processes implicated in regulating secondary metabolite biosynthesis in F. hupehensis tissues, we evaluated potential metabolic pathways. Overall, this study provides a repertoire of FL transcripts in F. hupehensis for the first time, and it will be a valuable resource for marker-assisted breeding and research into bioactive compounds for medicinal and pharmacological applications.

Full-length transcriptome analysis and identification of genes involved in asarinin and aristolochic acid biosynthesis in medicinal plant Asarum sieboldii

Asarum sieboldii, a well-known traditional Chinese medicinal herb, is used for curing inflammation and ache. It contains both the bioactive ingredient asarinin and the toxic compound aristolochic acid. To address further breeding demand, genes involved in the biosynthetic pathways of asarinin and aristolochic acid should be explored. Therefore, the full-length transcriptome of A. sieboldii was sequenced using PacBio Iso-Seq to determine the candidate transcripts that encode the biosynthetic enzymes of asarinin and aristolochic acid. In this study, 63 023 full-length transcripts were generated with an average length of 1371 bp from roots, stems, and leaves, of which 49 593 transcripts (78.69%) were annotated against public databases. Furthermore, 555 alternative splicing (AS) events, 10 869 long noncoding RNAs (lncRNAs) as well as their 11 291 target genes, and 17 909 simple sequence repeats (SSRs) were identified. The data also revealed 97 candidate transcripts related to asarinin metabolism, of which six novel genes that encoded enzymes involved in asarinin biosynthesis were initially reported. In addition, 56 transcripts related to aristolochic acid biosynthesis were also identified, including CYP81B. In summary, these transcriptome data provide a useful resource to study gene function and genetic engineering in A. sieboldii.

Transcriptomics of the Rooibos (Aspalathus linearis) Species Complex

Rooibos (Aspalathus linearis), widely known as a herbal tea, is endemic to the Cape Floristic Region of South Africa (SA). It produces a wide range of phenolic compounds that have been associated with diverse health promoting properties of the plant. The species comprises several growth forms that differ in their morphology and biochemical composition, only one of which is cultivated and used commercially. Here, we established methodologies for non-invasive transcriptome research of wild-growing South African plant species, including (1) harvesting and transport of plant material suitable for RNA sequencing; (2) inexpensive, high-throughput biochemical sample screening; (3) extraction of high-quality RNA from recalcitrant, polysaccharide- and polyphenol rich plant material; and (4) biocomputational analysis of Illumina sequencing data, together with the evaluation of programs for transcriptome assembly (Trinity, IDBA-Trans, SOAPdenovo-Trans, CLC), protein prediction, as well as functional and taxonomic transcript annotation. In the process, we established a biochemically characterized sample pool from 44 distinct rooibos ecotypes (1–5 harvests) and generated four in-depth annotated transcriptomes (each comprising on average ≈86,000 transcripts) from rooibos plants that represent distinct growth forms and differ in their biochemical profiles. These resources will serve future rooibos research and plant breeding endeavours.

Study on Quality Response to Environmental Factors and Geographical Traceability of Wild Gentiana rigescens Franch

Gentiana rigescens Franch. ex Hemsl. is an important medicinal plant in China and the over exploitation of wild resources has affected its quality and clinical efficacy. The accumulation of plant secondary metabolites is not only determined by their genetic characteristics but also influenced by environmental factors. At present, many studies on evaluating the environmental conditions of its planting area are still in the qualitative stage. Therefore, it is necessary to establish a systematic evaluation method to deeply analyze the impact of environmental factors on the quality of medicinal materials and quickly verify the geographical origin. In this study, the contents of five iridoids (loganic acid, swertiamarin, sweroside, gentiopicroside and 6'-O-β-D-glucopyranosylgentiopicroside) of G. rigescens from 45 different origins (including 441 individuals) of Yunnan Province in China were analyzed by high performance liquid chromatography. Analytical procedures of one-way analysis of variance, correlation analysis, principal components analysis, and hierarchical cluster analysis were employed to interpret the correlation of iridoid content and environmental factors. Fourier transform infrared spectroscopy (FT-IR) combined with two multivariate analysis methods (partial least squares discriminant analysis; support vector machines, SVM) was used to discriminate four major producing areas (158 individuals). The combination of SVM with grid search algorithm achieved an accuracy of 100% in the test set. One-way analysis of variance showed that the contents of five iridoids in root tissues of G. rigescens varied significantly among different origins, which was also verified by the chemometrics analysis results of hierarchical cluster analysis. The results of correlation analysis indicated that the high value of altitude and precipitation were unfavorable for the accumulation of these five iridoids. A correlation between increase of temperature and iridoid accumulation was observed. This study provided a certain theoretical basis for the resource protection and development of G. rigescens based on the correlation analysis between the ecological environment factors and quality.

Cross-Species Annotation of Expressed Genes and Detection of Different Functional Gene Modules Between 10 Cold- and 10 Hot-Propertied Chinese Herbal Medicines

According to the traditional Chinese medicine (TCM) system, Chinese herbal medicines (HMs) can be divided into four categories: hot, warm, cold, and cool. A cool nature usually is categorized as a cold nature, and a warm nature is classified as a hot nature. However, the detectable characteristics of the gene expression profile associated with the cold and hot properties have not been studied. To address this question, a strategy for the cross-species annotation of conserved genes was established in the present study by using transcriptome data of 20 HMs with cold and hot properties. Functional enrichment analysis was performed on group-specific expressed genes inferred from the functional genome of the reference species (i.e., Arabidopsis). Results showed that metabolic pathways relevant to chrysoeriol, luteolin, paniculatin, and wogonin were enriched for cold-specific genes, and pathways of inositol, heptadecane, lauric acid, octanoic acid, hexadecanoic acid, and pentadecanoic acid were enriched for hot-specific genes. Six functional modules were identified in the HMs with the cold property: nucleotide biosynthetic process, peptidy-L-cysteine S-palmitoylation, lipid modification, base-excision repair, dipeptide transport, and response to endoplasmic reticulum stress. For the hot HMs, another six functional modules were identified: embryonic meristem development, embryonic pattern specification, axis specification, regulation of RNA polymerase II transcriptional preinitiation complex assembly, mitochondrial RNA modification, and cell redox homeostasis. The research provided a new insight into HMs’ cold and hot properties from the perspective of the gene expression profile of plants.

De novo transcriptome analysis unravels tissue-specific expression of candidate genes involved in major secondary metabolite biosynthetic pathways of Plumbago zeylanica: implication for pharmacological potential

KEY MESSAGE

The present study provides comparative transcriptome analysis, besides identifying functional secondary metabolite genes of Plumbago zeylanica with pharmacological potential for future functional genomics, and metabolomic engineering of secondary metabolites from this plant towards diversified biomedical applications.

ABSTRACT

Plumbago zeylanica is a widely used medicinal plant of the traditional Indian system of medicine with wide pharmacological potential to treat several disorders. The present study aimed to carry out comparative transcriptome analysis in leaf and root tissue of P. zeylanica using Illumina paired end sequencing to identify tissue-specific functional genes involved in the biosynthesis of secondary metabolites, contributing to its therapeutic efficacy. De novo sequencing assembly resulted in the identification of 62,321 "Unigenes" transcripts with an average size of 1325 bp. Functional annotation using BLAST2GO resulted in the identification of 50,301 annotated transcripts (80.71%) and GO assigned to 18,814 transcripts. KEGG pathway annotation of the "Unigenes" revealed that 2465 transcripts could be assigned to 242 KEGG pathway maps wherein the number of transcripts involved in secondary metabolism was distinct in root and leaf transcriptome. Among the secondary metabolite biosynthesis pathways, the cluster of "Unigenes" encoding enzymes of 'Phenylpropanoid biosynthesis pathway' represents the largest group (84 transcripts) followed by 'Terpenoid Backbone biosynthesis' (48 transcripts). The transcript levels of the candidate unigenes encoding key enzymes of phenylpropanoid (PAL, TAL) and flavanoid biosynthesis (CHS, ANS, FLS) pathways were up-regulated in root, while the expression levels of candidate "Unigenes" transcript for monoterpenoid (DXS, ISPF), diterpenoid biosynthesis (SPS, SDS) and indole alkaloid pathways (STR) were significantly higher in leaf of P. zeylanica. Interestingly, validation of differential gene expression profile by qRT-PCR also confirmed that candidate "Unigenes" enzymes of phenylpropanoid and flavonoid biosynthesis were highly expressed in the root, while the key regulatory enzymes of terpenoid and indole alkaloid compounds were up-regulated in the leaf, suggesting that (differences in) the levels of these functional genes could be attributed to the (differential) pharmacological activity (between root and leaf) in tissues of P. zeylanica.

Optimization of salicylic acid and chitosan treatment for bitter secoiridoid and xanthone glycosides production in shoot cultures of Swertia paniculata using response surface methodology and artificial neural network

BACKGROUND

In this study, response surface methodology (RSM) and artificial neural network (ANN) was used to construct the predicted models of linear, quadratic and interactive effects of two independent variables viz. salicylic acid (SA) and chitosan (CS) for the production of amarogentin (I), swertiamarin (II) and mangiferin (III) from shoot cultures of Swertia paniculata Wall. These compounds are the major therapeutic metabolites in the Swertia plant, which have significant role and demand in the pharmaceutical industries.

RESULTS

Present study highlighted that different concentrations of SA and CS elicitors substantially influenced the % yield of (I), (II) and (III) compounds in the shoot culture established on modified ½ MS medium (supplemented with 2.22 mM each of BA and KN and 2.54 mM NAA). In RSM, different response variables with linear, quadratic and 2 way interaction model were computed with five-factor-three level full factorial CCD. In ANN modelling, 13 runs of CCD matrix was divided into 3 subsets, with approximate 8:1:1 ratios to train, validate and test. The optimal enhancement of (I) (0.435%), (II) (4.987%) and (III) (4.357%) production was achieved in 14 days treatment in shoot cultures of S. paniculata elicited by 9 mM and 12 mg L^- 1 concentrations (SA) and (CS).

CONCLUSIONS

In optimization study, (I) show 0.170-0.435%; (II) display 1.020-4.987% and (III) upto 2.550-4.357% disparity with varied range of SA (1-20 mM) and CS (1-20 mg L^- 1). Overall, optimization of elicitors to promote secoiridoid and xanthone glycoside production with ANN modeling (r² = 100%) offered more significant results as compared to RSM (r² = 99.8%).

Mining genes associated with furanocoumarin biosynthesis in an endangered medicinal plant, Glehnia littoralis

The endangered medicinal plant Glehnia littoralis is one of the important natural source of furanocoumarin, which has been used as mucolytic, antitussive, antitumour and antibacterial. However, the genetic information of furanocoumarin biosynthesis in G. littoralis is scarce at present. The objective of this study was to mine the putative candidate genes involved in the biosynthesis pathwayof furanocoumarin and provide references for gene identification, and functional genomics of G. littoralis. We carried out the transcriptome analysis of leaves and roots in G. littoralis, which provided a dataset for gene mining. Psoralen, imperatorin and isoimperatorin were detected in G. littoralis by high performance liquid chromatography analysis. Candidate key genes were mined based on the annotations and local BLAST with homologous sequences using BioEdit software. The relative expression of genes was analysed using quantitative real-time polymerase chain reaction. Further, the CYP450 genes were mined using phylogenetic analyses using MEGA 6.0 software. Atotal of 156,949 unigenes were generated, of which 9021 were differentially-expressed between leaves and roots. A total of 82 unigenes encoding eight enzymes in furanocoumarin biosynthetic pathway were first obtained. Seven genes that encoded key enzymes in the downstream furanocoumarin biosynthetic pathway and expressed more in roots than leaves were screened. Twenty-six candidate CYP450 unigenes expressed abundantly in roots and were chiefly concentrated in CYP71, CYP85 and CYP72 clans. Finally, we filtered 102 differentially expressed transcription factors (TFs) unigenes. The transcriptome of G. littoralis was characterized which would help to elucidate the furanocoumarin biosynthetic pathway in G. littoralis and provide an invaluable resource for further study of furanocoumarin.

Exploration of the Hepatoprotective Effect and Mechanism of Swertia mussotii Franch in an Acute Liver Injury Rat Model

Background and Objective:

Swertia mussotii Franch, also known as “Zangyinchen”, is one of a Tibetan traditional herb used for treatment of liver diseases over thousands of years at Qinghai-Tibet Plateau, has been confirmed to be hepatoprotective. However, the underlying mechanism is largely unknown.

Materials and Method:

In this study, we evaluated the effect of S. mussotii treatment in a carbon tetrachloride-induced acute liver injury rat model by examining the serum alanine aminotransferase, aspartate aminotransferase, total bilirubin levels and performing histological observations of the liver tissues. Meanwhile, the metabolomics analysis was used to explore the molecular mechanism of S. mussotii treatment by high performance liquid chromatography tandem mass spectrometry.

Results:

The results showed that S. mussotii treatment could effectively improve the serum alanine aminotransferase, aspartate aminotransferase, total bilirubin in acute liver injury rat model. Histological observation showed that S. mussotii treatment could effectively alleviate liver injury. Moreover, the metabolomics analysis showed that S. mussotii treatment could normalize the levels of many fatty acid metabolism related metabolites. And the results of pathway analysis showed that these metabolites significantly enriched in fatty acid biosynthesis pathway (myristic acid, dodecanoic acid and capric acid) and linoleic acid metabolism pathway (13-OxoODE).

Conclusion:

The results indicated that S. mussotii treatment could significantly improve acute liver injury through affecting the pathways related to lipid metabolism.

Full-length transcriptome analysis of shade-induced promotion of tuber production in Pinellia ternata

BACKGROUND

Pinellia ternata is native to China and has been used as a traditional herb due to its antiemetic, antitussive, analgesic, and anxiolytic effects. When exposed to strong light intensity and high temperature during the reproductive growth process, P. ternata withers in a phenomenon known as "sprout tumble", which largely limits tuber production. Shade was previously found to delay sprout tumble formation (STF); however, no information exists regarding this process at the molecular level. Hence, we determined the genes involved in tuber development and STF in P. ternata.

RESULTS

Compared to that with natural sun-light (control), shade significantly induced chlorophyll accumulation, increased chlorophyll fluorescence parameters including initial fluorescence, maximal fluorescence, and qP, and dramatically repressed chlorophyll a:b and NPQ. Catalase (CAT) activity was largely induced by shade, and tuber products were largely increased in this environment. Transcriptome profiles of P. ternata grown in natural sun-light and shaded environments were analyzed by a combination of next generation sequencing (NGS) and third generation single-molecule real-time (SMRT) sequencing. Corrections of SMRT long reads based on NGS short reads yielded 136,163 non-redundant transcripts, with an average N50 length of 2578 bp. In total, 6738 deferentially-expressed genes (DEGs) were obtained from the comparisons, specifically D5S vs D5CK, D20S vs D20CK, D20S vs D5S, and D20CK vs D5CK, of which, 6384 DEGs (94.8%) were generated from the D20S vs D20CK comparison. Gene annotation and functional analyses revealed that these genes were related to auxin signal transduction, polysaccharide and sugar metabolism, phenylpropanoid biosynthesis, and photosynthesis. Moreover, the expression of genes enriched in photosynthesis appeared to be significantly altered by shade. The expression patterns of 16 candidate genes were consistent with changes in their transcript abundance as identified by RNA-Seq, and these might contribute to STF and tuber production.

CONCLUSION

The full-length transcripts identified in this study have provided a more accurate depiction of P. ternata gene transcription. Further, we identified potential genes involved in STF and tuber growth. Such data could serve as a genetic resource and a foundation for further research on this important traditional herb.

Secoiridoids Metabolism Response to Wounding in Common Centaury (Centaurium erythraea Rafn) Leaves

Centaurium erythraea Rafn produces and accumulates various biologically active specialized metabolites, including secoiridoid glucosides (SGs), which help plants to cope with unfavorable environmental conditions. Specialized metabolism is commonly modulated in a way to increase the level of protective metabolites, such as SGs. Here, we report the molecular background of the wounding-induced changes in SGs metabolism for the first time. The mechanical wounding of leaves leads to a coordinated up-regulation of SGs biosynthetic genes and corresponding JA-related transcription factors (TFs) after 24 h, which results in the increase of metabolic flux through the biosynthetic pathway and, finally, leads to the elevated accumulation of SGs 96 h upon injury. The most pronounced increase in relative expression was detected for secologanin synthase (CeSLS), highlighting this enzyme as an important point for the regulation of biosynthetic flux through the SG pathway. A similar expression pattern was observed for CeBIS1, imposing itself as the TF that is prominently involved in wound-induced regulation of SGs biosynthesis genes. The high degree of positive correlations between and among the biosynthetic genes and targeted TFs expressions indicate the transcriptional regulation of SGs biosynthesis in response to wounding with a significant role of CeBIS1, which is a known component of the jasmonic acid (JA) signaling pathway.

Analysis of Centranthera grandiflora Benth Transcriptome Explores Genes of Catalpol, Acteoside and Azafrin Biosynthesis

Cardiovascular diseases (CVDs) are a major cause of health loss in the world. Prevention and treatment of this disease by traditional Chinese medicine is a promising method. Centranthera grandiflora Benth is a high-value medicinal herb in the prevention and treatment of CVDs; its main medicinal components include iridoid glycosides, phenylethanoid glycosides, and azafrin in roots. However, biosynthetic pathways of these components and their regulatory mechanisms are unknown. Furthermore, there are no genomic resources of this herb. In this article, we provide sequence and transcript abundance data for the root, stem, and leaf transcriptome of C. grandiflora Benth obtained by the Illumina Hiseq2000. More than 438 million clean reads were obtained from root, stem, and leaf libraries, which produced 153,198 unigenes. Based on databases annotation, a total of 557, 213, and 161 unigenes were annotated to catalpol, acteoside, and azafrin biosynthetic pathways, respectively. Differentially expressed gene analysis identified 14,875 unigenes differentially enriched between leaf and root with 8,054 upregulated genes and 6,821 downregulated genes. Candidate MYB transcription factors involved in catalpol, acteoside, and azafrin biosynthesis were also predicated. This work is the first transcriptome analysis in C. grandiflora Benth which will aid the deciphering of biosynthesis pathways and regulatory mechanisms of active components.

De novo transcriptome assembly of the Chinese pearl barley, adlay, by full-length isoform and short-read RNA sequencing

Adlay (Coix lacryma-jobi) is a tropical grass that has long been used in traditional Chinese medicine and is known for its nutritional benefits. Recent studies have shown that vitamin E compounds in adlay protect against chronic diseases such as cancer and heart disease. However, the molecular basis of adlay's health benefits remains unknown. Here, we generated adlay gene sets by de novo transcriptome assembly using long-read isoform sequencing (Iso-Seq) and short-read RNA-Sequencing (RNA-Seq). The gene sets obtained from Iso-seq and RNA-seq contained 31,177 genes and 57,901 genes, respectively. We confirmed the validity of the assembled gene sets by experimentally analyzing the levels of prolamin and vitamin E biosynthesis-associated proteins in adlay plant tissues and seeds. We compared the screened adlay genes with known gene families from closely related plant species, such as rice, sorghum and maize. We also identified tissue-specific genes from the adlay leaf, root, and young and mature seed, and experimentally validated the differential expression of 12 randomly-selected genes. Our study of the adlay transcriptome will provide a valuable resource for genetic studies that can enhance adlay breeding programs in the future.

Traditional Tibetan medicinal plants: a highlighted resource for novel therapeutic compounds

Around 70-80% of drugs used in traditional Tibetan medicine (TTM) come from Qinghai Tibet Plateau, the majority of which are plants. The biological and medicinal culture diversity on Qinghai Tibet Plateau are amazing and constitute a less tapped resource for innovative drug research and development. Meanwhile, the problem of the exhausting Tibetan medicine resources is worrying. Here, the latest awareness, as well as the gaps of the traditional Tibetan medicinal plant issues in drug development and clinical usage of TTM compounds, was systematically reviewed and highlighted. The TTM resource studies should be enhanced within the context of deeper and more extensive investigations of molecular biology and genomics of TTM plants, phytometabolites and metabolomics and ethnopharmacology-based bioactivity, thus enabling the sustainable conservation and exploitation of Tibetan medicinal resource.

Comparative transcriptome analysis of roots, stems and leaves of Isodon amethystoides reveals candidate genes involved in Wangzaozins biosynthesis

BACKGROUND

Isodon amethystoides (Ben-th) Cy Wu et Hsuan is an important traditional medicinal plant endowed with pharmacological properties effective in the treatment of various diseases, including pulmonary tuberculosis. The tetracyclic diterpenoids, Wangzaozins (Wangzaozin A, glaucocalyxin A, glaucocalyxin B), are the major bioactive compounds of I. amethystoides. However, the molecular information about the biosynthesis of these compounds still remains unclear.

RESULTS

An examination of the accumulated levels of Wangzaozins in I. amethystoides revealed considerable variations in the root, stem, and leaf tissues of this plant, indicating possible differences in metabolite biosynthesis and accumulation among various tissues. To better elucidate the tetracyclic diterpenoid biosynthesis pathway, we generated transcriptome sequences from the root, stem, and leaf tissues, and performed de novo sequence assembly, yielding 230,974 transcripts and 114,488 unigenes, with average N50 lengths of 1914 and 1241 bp, respectively. Putative functions could be assigned to 73,693 transcripts (31.9%) based on BLAST searches against annotation databases, including GO, KEGG, Swiss-Prot, NR, and Pfam. Moreover, the candidate genes involving in the diterpenoid biosynthesis, such as CPS, KSL, were also analyzed. The expression profiles of eight transcripts, involving the tetracyclic diterpenoid biosynthesis, were validated in different I. amethystoides tissues by qRT-PCR, unraveling the gene expression profile of the pathway. The differential expressions of ISPD, ISPF and ISPH (MEP pathway), and IaCPS and IaKSL (diterpenoid pathway) candidate genes in leaves and roots, may contribute to the high accumulation of Wangzaozins in I. amethystoides leaves.

CONCLUSION

The genomic dataset and analyses reported here lay the foundations for further research on this important medicinal plant.

Chemical and genomic diversity of six Lonicera species occurring in Korea

Lonicera spp. (Caprifoliaceae) are important not only as a common medicinal herb in East Asia but also as one of the most problematic invasive species in North America. In the present study, we performed a systemic analysis of genomic and chemical diversity among six Lonicera species occurring in Korea, L. japonica, L. maackii, L. insularis, L. sachalinensis, L. praeflorens, and L. vesicaria, using chloroplast DNA whole genome shotgun (WGS) sequencing and LC-MS analyses. The phylogenetic and phylochemical relationships did not coincide with each other, but partial consistency could be found among them. InDel-based cDNA marker for authentication was developed based on the genome sequences. Flavonoids, iridoids, and organic acids were identified in the LC-MS analyses, and their inter-species distribution and localization were also revealed.

Comprehensive Quality Assessment Based Specific Chemical Profiles for Geographic and Tissue Variation in Gentiana rigescens Using HPLC and FTIR Method Combined with Principal Component Analysis

Roots, stems, leaves, and flowers of Longdan (Gentiana rigescens Franch. ex Hemsl) were collected from six geographic origins of Yunnan Province (n = 240) to implement the quality assessment based on contents of gentiopicroside, loganic acid, sweroside and swertiamarin and chemical profile using HPLC-DAD and FTIR method combined with principal component analysis (PCA). The content of gentiopicroside (major iridoid glycoside) was the highest in G. rigescens, regardless of tissue and geographic origin. The level of swertiamarin was the lowest, even unable to be detected in samples from Kunming and Qujing. Significant correlations (p < 0.05) between gentiopicroside, loganic acid, sweroside, and swertiamarin were found at inter- or intra-tissues, which were highly depended on geographic origins, indicating the influence of environmental conditions on the conversion and transport of secondary metabolites in G. rigescens. Furthermore, samples were reasonably classified as three clusters along large producing areas where have similar climate conditions, characterized by carbohydrates, phenols, benzoates, terpenoids, aliphatic alcohols, aromatic hydrocarbons, and so forth. The present work provided global information on the chemical profile and contents of major iridoid glycosides in G. rigescens originated from six different origins, which is helpful for controlling quality of herbal medicines systematically.

Researches on Transcriptome Sequencing in the Study of Traditional Chinese Medicine

Due to its incomparable advantages, the application of transcriptome sequencing in the study of traditional Chinese medicine attracts more and more attention of researchers, which greatly promote the development of traditional Chinese medicine. In this paper, the applications of transcriptome sequencing in traditional Chinese medicine were summarized by reviewing recent related papers.