Multi-omics analysis of the bioactive constituents biosynthesis of glandular trichome in Perilla frutescens

Micromorphology and Molecular Insights Into Glandular Trichomes in Two Different Thymes: Glandular Trichomes Formation Process and the Function of the Main Regulator TqHD1

Thyme is widely distributed in the worldwild. In China, there are 15 species, 2 varieties and 1 variant. Thymus quinquecostatus which contains abundant bioactive terpenoids is an important wild medicinal and aromatic plant in Chinese native thymes. Thymus vulgaris 'Elsbeth' comes from Europe and is known for its medicinal properties. The terpenoids exist in the glandular trichomes (GTs), a special epidemal structure. In Lamiaceae, glandular trichomes usually include peltate glandular trichomes (PGTs) and capitate glandular trichomes (CGTs). In previous study, we had analysed the molecular mechanisms of GTs but the formation process was not revealed. In this study, we observed the formation of PGTs and CGTs in thyme. The PGT underwent the complex process, including the basal, stalk, and head cells, there were 8-12 head cells. The CGT also had three cells, but its head cell only had one cell. Meanwhile, molecular biology research was carried out and we identified 68 HD-ZIP proteins and selected several key genes related to the formation of GTs according to the expression levels. Then, we cloned an HD-ZIP IV transcription factor TqHD1 from T. quinquecostatus and characterised it. TqHD1 not only can promote the formation of GTs but also can lead to the changes of volatile components and some relative genes levels. These findings complete the study of cell micromorphology of thyme and lay the foundation for characterisation of factors in epidermis-related functions in thyme.

Comprehensive Review of Perilla frutescens: Chemical Composition, Pharmacological Mechanisms, and Industrial Applications in Food and Health Products

Perilla frutescens (L.) Britt., a multifunctional herbaceous plant, is widely used in traditional medicine and cuisine due to its rich array of bioactive compounds. To date, many key phytochemicals in P. frutescens have been identified, including volatile terpenoids (perillaldehyde, limonene,), flavonoids (luteolin, apigenin), and phenolic acids (rosmarinic acid derivatives), which exhibit significant antioxidant, anti-inflammatory, antiviral, anticancer, antibacterial, and blood sugar-lowering effects. Studies have shown that volatile oils, flavonoids, and phenolic acids in P. frutescens exert their effects in various experimental models. In food and industrial applications, P. frutescens shows innovative potential in functional foods, natural preservatives, and novel food additives, effectively extending food shelf life and providing antimicrobial protection. Moreover, research on the biology and genetic improvement of P. frutescens has provided new approaches to enhance its yield and bioactive content. Finally, this paper also discusses the safety and standardization issues of the plant, providing theoretical support for its widespread application.

Rapid discrimination and quantification of chemotypes in Perillae folium using FT-NIR spectroscopy and GC-MS combined with chemometrics

Perillae Folium (PF) is a well-known food and herb containing different chemotypes, which affect its quality. Herein, a method was proposed to classify and quantify PF chemotypes using gas chromatography-mass spectrometry (GC-MS) and Fourier transform-near infrared spectroscopy (FT-NIR). GC-MS results revealed that PF contains several chemotypes, including perilla ketone (PK) type, α-asarone (PP-as) type, and dillapiole (PP-dm) type, with the PK type being the predominant chemotype. Based on FT-NIR data, different chemotypes were accurately classified. The random forest algorithm achieved >90 % accuracy in chemotype classification. Furthermore, the main components of perilla ketone and isoegomaketone in PF were successfully quantified using partial least squares regression models, with prediction to deviation values of 3.76 and 2.59, respectively. This method provides valuable insights and references for the quality supervision of PF and other foods.

Multi-omics analysis uncovers the transcriptional regulatory mechanism of magnesium Ions in the synthesis of active ingredients in Sophora tonkinensis

Magnesium (Mg) plays a pivotal role as an essential component of plant chlorophyll and functions as a critical coenzyme. However, research exploring the regulatory mechanisms of magnesium ions on the synthesis of secondary metabolites is still in its early stages. Sophora tonkinensis is a widely utilized medicinal plant in China, recognized for its diverse secondary metabolites with active properties. This study investigates variations in these ingredients in tissue-cultured seedlings under varying magnesium concentrations. Simultaneously, an omics data analysis was conducted on tissue-cultured seedlings subjected to treatments with magnesium and low magnesium. These comprehensive omics analyses aimed to elucidate the mechanisms through which magnesium influences active components, growth, and development. Magnesium exerts a pervasive influence on various metabolic pathways, forming an intricate network. Research findings indicate that magnesium impacts diverse metabolic processes, including the absorption of potassium and calcium, as well as photosynthetic activity. Consequently, these influences lead to discernible changes in the levels of pharmacologically active compounds and the growth and developmental status.This study is the first to employ a multi-omics data analysis in S. tonkinensis. This methodology allows us to uncover the overarching impact of metabolic networks on the levels of various active ingredients and specific phenotypes.

Integrated multi-omics analysis reveals genes involved in flavonoid biosynthesis and trichome development of Artemisia argyi

Artemisia argyi is an herbaceous plant of the genus Artemisia. Its young and mature leaves are used as food and medicine, respectively. Glandular trichomes (GTs) are distributed on the leaf surface in A. argyi and are generally considered the location of flavonoid biosynthesis and accumulation. However, the mechanism of flavonoid biosynthesis and accumulation in A. argyi remains unclear. In this study, the coregulatory genes involved in flavonoid biosynthesis and trichome development in this species were screened and evaluated, and the biosynthetic pathways for key flavonoids in A. argyi were uncovered. AaMYB1 and AaYABBY1 were screened using weighted gene co-expression network analysis, and both genes were then genetically transformed into Nicotiana tabacum L. cv. K326 (tobacco). Simultaneously, AaYABBY1 was also genetically transformed into Arabidopsis thaliana. The total flavonoid and rutin contents were increased in tobacco plants overexpressing AaMYB1 and AaYABBY1, and the expression levels of genes participating in the flavonoid synthesis pathway, such as PAL, FLS, and F3H, were significantly up-regulated in plants overexpressing these genes. These results indicated that AaMYB1 and AaYABBY1 promote flavonoid biosynthesis in tobacco. Furthermore, compared to that in the wild-type, the trichome density was significantly increased in tobacco and A. thaliana plants overexpressing AaYABBY1. These results confirm that AaYABBY1 might be involved in regulating trichome formation in A. argyi. This indicates the potential genes involved in and provides new insights into the development of trichome cellular factories based on the "development-metabolism" interaction network and the cultivation of high-quality A. argyi.

Transcriptome and metabolome analysis revealed the dynamic change of bioactive compounds of Fructus Ligustri Lucidi

BACKGROUND

The Fructus Ligustri Lucidi, the fruit of Ligustrum lucidum, contains a variety of bioactive compounds, such as flavonoids, triterpenoids, and secoiridoids. The proportions of these compounds vary greatly during the different fruit development periods of Fructus Ligustri Lucidi. However, a clear understanding of how the proportions of the compounds and their regulatory biosynthetic mechanisms change across the different fruit development periods of Fructus Ligustri Lucidi is still lacking.

RESULTS

In this study, metabolite profiling and transcriptome analysis of six fruit development periods (45 DAF, 75 DAF, 112 DAF, 135 DAF, 170 DAF, and 195 DAF) were performed. Seventy compounds were tentatively identified, of which secoiridoids were the most abundant. Eleven identified compounds were quantified by high performance liquid chromatography. A total of 103,058 unigenes were obtained from six periods of Fructus Ligustri Lucidi. Furthermore, candidate genes involved in triterpenoids, phenylethanols, and oleoside-type secoiridoid biosynthesis were identified and analyzed. The in vitro enzyme activities of nine glycosyltransferases involved in salidroside biosynthesis revealed that they can catalyze trysol and hydroxytyrosol to salidroside and hydroxylsalidroside.

CONCLUSIONS

These results provide valuable information to clarify the profile and molecular regulatory mechanisms of metabolite biosynthesis, and also in optimizing the harvest time of this fruit.

Leaf morpho-anatomical adjustments in a Quercus pubescens forest after 10 years of partial rain exclusion in the field

In the Mediterranean region, a reduction of annual precipitation and a longer and drier summer season are expected with climate change by the end of the century, eventually endangering forest survival. To cope with such rapid changes, trees may modulate their morpho-anatomical and physiological traits. In the present study, we focused on the variation in leaf gas exchange and different leaf morpho-anatomical functional traits of Quercus pubescens Willd. in summer using a long-term drought experiment in natura consisting of a dynamic rainfall exclusion system where trees have been submitted to amplified drought (AD) (~-30% of annual precipitation) since April 2012 and compared them with trees under natural drought (ND) in a Mediterranean forest. During the study, we analyzed net CO2 assimilation (An), stomatal conductance (gs), transpiration (E), water-use efficiency (WUE), stomatal size and density, density of glandular trichomes and non-glandular trichomes, thickness of the different leaf tissues, specific leaf area and leaf surface. Under AD, tree functioning was slightly impacted, since only An exhibited a 49% drop, while gs, E and WUE remained stable. The decrease in An under AD was regulated by concomitant lower stomatal density and reduced leaf thickness. Trees under AD also featured leaves with a higher non-glandular trichome density and a lower glandular trichome density compared with ND, which simultaneously limits transpiration and production costs. This study points out that Q. pubescens exhibits adjustments of leaf morpho-anatomical traits which can help trees to acclimate to AD scenarios as those expected in the future in the Mediterranean region.

Effect of Salvia sclarea L. extract on growth performance, antioxidant capacity, and immune function in lambs

The aim of this experiment is to explore the effects of salvia sclarea extract on the growth performance, apparent nutrient digestibility, antioxidant capacity, and immune function of lambs. Sixty female lambs (Chinese Merino sheep) aged 2 months and weighing 20 ± 2 kg were selected and randomly divided into five groups of twelve lambs in each. While the control group (CK) received only basal feed, the experimental group was supplemented with different concentrations of salvia sclarea extract in the basal feed at 0.04 mL/kg (group CL1), 0.08 mL/kg (group CL2), 0.12 mL/kg (group CL3), and 0.16 mL/kg (group CL4). The feeding period was 85 days, including 15 days of pre-feeding and 70 days of regular feeding. Body weight and feed intake were recorded during the test period, and blood was collected at the end of the test for the determination of immune and antioxidant indices. The results showed that the average daily gain and average daily feed intake of lambs were significantly increased in CL3 group compared to CK group (p < 0.05). Also, the apparent nutrient digestibility of crude protein and neutral detergent fiber was significantly increased (p < 0.05). The Dry matter, acid detergent fiber and Ether extract were not significantly different (p > 0.05). The serum levels of superoxide dismutase, catalase, glutathione peroxidase, and antioxidant capacity were significantly higher in the CL2, CL3, and CL4 groups compared to CK group, while malondialdehyde levels were significantly lower (p < 0.05). The serum levels of immune globulin A, immune globulin G, immune globulin M, interferon-γ, and interleukin-10 were significantly higher and the levels of tumor necrosis factor-α and interleukin-1β were significantly lower in the CL2, CL3, and CL4 groups (p < 0.05). In conclusion, the addition of salvia sclarea extract to the ration promotes growth performance and nutrient digestion in lambs. Improvement of immune response by increasing immunoglobulin and cytokine concentrations. And it enhances the antioxidant status by increasing the antioxidant enzyme activity in lambs.

Introduction

This study aimed to explore the effects of Salvia sclarea extract on the growth performance, apparent nutrient digestibility, antioxidant capacity, and immune function of the lambs.

Methods

Sixty female lambs (Chinese Merino sheep) aged 2 months and weighing 20 ± 2 kg were selected and randomly divided into five groups of 12 lambs each. The control group (CK) received only basal feed, whereas the experimental group was supplemented with different concentrations of salvia sclarea extract in the basal feed at 0.04, 0.08, 0.12, and 0.16 mL/kg (CL1, CL2, CL3, and CL4, respectively). The feeding period was 85 days, including 15 days of pre-feeding and 70 days of regular feeding. Body weight and feed intake were recorded during the test period, and blood was collected at the end of the test to determine immune and antioxidant indices.

Results

The results showed that the average daily weight gain and feed intake of the lambs were significantly higher in the CL3 group than in the CK group (p < 0.05). In addition, the apparent nutrient digestibility of crude protein and neutral detergent fiber increased significantly (p < 0.05). The dry matter, acid detergent fiber, and ether extract were not significantly different (p > 0.05). Serum levels of superoxide dismutase, catalase, and glutathione peroxidase and antioxidant capacity were significantly higher in the CL2, CL3, and CL4 groups than in the CK group, whereas malondialdehyde levels were significantly lower (p < 0.05). The serum levels of immune globulin immune globulin A, immune globulin G, immune globulin M, interferon-γ, and interleukin-10 were significantly higher and the levels of tumor necrosis factor-α and interleukin-1β were significantly lower in the CL2, CL3, and CL4 groups (p < 0.05).

Discussion

In conclusion, the addition of the S. sclarea extract to the diet promoted growth performance and nutrient digestion in lambs. Immune response was improved by increasing Ig and cytokine concentrations. It enhances antioxidant status by increasing antioxidant enzyme activity in lambs.

Metabolite profiling and transcriptomic analyses demonstrate the effects of biocontrol agents on alkaloid accumulation in Fritillaria thunbergii

BACKGROUND

During Fritillaria thunbergii planting, pests and diseases usually invade the plant, resulting in reduced yield and quality. Previous studies have demonstrated that using biocontrol agents can effectively control grubs and affect the steroid alkaloids content in F. thunbergii. However, the molecular regulatory mechanisms underlying the differences in the accumulation of steroid alkaloids in response to biocontrol agents remain unclear.

RESULTS

Combined transcriptomic and metabolic analyses were performed by treating the bulbs of F. thunbergii treated with biocontrol agents during planting. Otherwise, 48 alkaloids including 32 steroid alkaloids, 6 indole alkaloids, 2 scopolamine-type alkaloids, 1 isoquinoline alkaloid, 1 furoquinoline alkaloid, and 6 other alkaloids were identified. The content of steroidal alkaloids particularly peimine, peiminine, and veratramine, increased significantly in the group treated with the biocontrol agents. Transcriptome sequencing identified 929 differential genes using biocontrol agents, including 589 upregulated and 340 downregulated genes. Putative biosynthesis networks of steroid alkaloids have been established and combined with differentially expressed structural unigenes, such as acetyl-CoA C-acetyl-transferase, acelyl-CoAC-acetyltransferase3-hydroxy-3-methylglutaryl-coenzyme A synthase, 1-deoxy-D-xylulose-5-phosphate reductor-isomerase, 2-C-methyl-D-erythritol-4-phosphate cytidylyltransferase and 4-hydroxy-3-methylbut-2-enyl diphosphate reductase. In addition, biological processes such as amino acid accumulation and oxidative phosphorylation were predicted to be related to the synthesis of steroid alkaloids. Cytochrome P450 enzymes also play crucial roles in the steroid alkaloid synthesis. The transcription factor families MYB and bHLH were significantly upregulated after using biocontrol agents.

CONCLUSIONS

Biocontrol agents increased the steroid alkaloids accumulation of steroid alkaloids by affecting key enzymes in the steroid alkaloid synthesis pathway, biological processes of oxidative phosphorylation and amino acid synthesis, cytochrome P450 enzymes, and transcription factors. This study revealed the mechanism underlying the difference in steroidal alkaloids in F. thunbergii after using biocontrol agents, laying the groundwork for future industrial production of steroid alkaloids and ecological planting of medicinal materials in the future.

Applying quantitative spatial phenotypes analysis to the investigation of peltate glandular trichomes development pattern in Perilla frutescens

BACKGROUND

Glandular trichomes, often referred to as "phytochemical factories", plays a crucial role in plant growth and metabolism. As the site for secretion and storage, the development of glandular trichomes is related to the dynamic biosynthesis of specialised metabolites. The study aims to explore the relationship between spatial phenotype and dynamic metabolism of glandular trichomes, and establish a novel approach for the exploration and study of the regulatory mechanism governing the development of glandular trichomes.

RESULTS

In this study, we proposed a technical route based on the relative deviation value to distinguish the peltate glandular trichomes (PGTs) from the background tissues and extract their spatial phenotype. By defining glandular trichome developmental stages based on the leaf vein growth axis, we found that young PGTs were densely distributed near the proximal end of growth axis of the leaf veins, where perillaketone, a primary metabolite of PGTs, is predominantly accumulated. Conversely, mature PGTs are typically found near the distal end of the mid-vein growth axis and the lateral end of the secondary vein growth axis, where the accumulation rate of isoegomaketone and egomaketone exceeds that of perillaketone in PGTs. We further identified spatial phenotypic parameters, Lsum and d, as independent variables to construct a linear regression model that illustrates the relationship between the spatial phenotypes and metabolite content of PGTs, including perillaketone (R2 = 0.698), egomaketone (R2 = 0.593), isoegomaketone (R2 = 0.662) and the sum of the amount (R2 = 0.773).

CONCLUSIONS

This model proved that the development of PGTs was correlated with the growth of the entire leaf, and the development stage of PGTs can be identifined by spatial phenotypes based on the leaf veins. In conclusion, the findings of this study enhance our understanding of correlation between spatial phenotype and development of glandular trichomes and offer a new approach to explore and study the regulatory mechanism of glandular trichome development.

The revealing of a novel double bond reductase related to perilla ketone biosynthesis in Perilla frutescens

BACKGROUND

Perilla frutescens is widely used as both a medicine and a food worldwide. Its volatile oils are its active ingredients, and, based on the different volatile constituents, P. frutescens can be divided into several chemotypes, with perilla ketone (PK) being the most common. However, the key genes involved in PK biosynthesis have not yet been identified.

RESULTS

In this study, metabolite constituents and transcriptomic data were compared in leaves of different levels. The variation in PK levels was the opposite of that of isoegoma ketone and egoma ketone in leaves at different levels. Based on transcriptome data, eight candidate genes were identified and successfully expressed in a prokaryotic system. Sequence analysis revealed them to be double bond reductases (PfDBRs), which are members of the NADPH-dependent, medium-chain dehydrogenase/reductase (MDR) superfamily. They catalyze the conversion of isoegoma ketone and egoma ketone into PK in in vitro enzymatic assays. PfDBRs also showed activity on pulegone, 3-nonen-2-one, and 4-hydroxybenzalacetone. In addition, several genes and transcription factors were predicted to be associated with monoterpenoid biosynthesis, and their expression profiles were positively correlated with variations in PK abundance, suggesting their potential functions in PK biosynthesis.

CONCLUSIONS

The eight candidate genes encoding a novel double bond reductase related to perilla ketone biosynthesis were identified in P. frutescens, which carries similar sequences and molecular features as the MpPR and NtPR from Nepeta tenuifolia and Mentha piperita, respectively. These findings not only reveal the pivotal roles of PfDBR in exploring and interpreting PK biological pathway but also contribute to facilitating future studies on this DBR protein family.

Formation mechanism of glandular trichomes involved in the synthesis and storage of terpenoids in lavender

BACKGROUND

Lavender (genus Lavandula, family Lamiaceae) is an aromatic plant widely grown as an ornamental plant. The chemical composition of lavender is characterized by monoterpenoids, sesquiterpenoids, and other compounds, which are primarily synthesized and stored in epidermal secretory structures called glandular trichomes (GTs). Volatile organic compounds (VOCs) are responsible for the aroma characteristics of plant oil that drive consumer preference. Aroma is usually regarded as a characteristic trait for the classification of aromatic plants. Interestingly, VOCs are synthesized and stored in GTs. Lamiaceae species such as purple perilla, peppermint, basil, thyme, and oregano usually possess two types of GTs: peltate glandular trichomes (PGTs) and capitate glandular trichomes (CGTs). But the development process of PGTs in lavender has been reported in only a few studies to date.

RESULTS

In this study, we identified and quantified the VOCs in four lavender cultivars by headspace-solid phase micro extraction-gas chromatography mass spectrometry (HS-SPME-GC-MS). A total of 66 VOCs were identified in these four cultivars, the most prominent of which were linalyl acetate and linalool, and flowers were the main site of accumulation of these VOCs. Here, we examined the developmental process of PGTs, including the formation of their base, body, and apex. The apex cells contained secretory cavities, which produced VOCs. Based on the reference genome sequence of the lavender cultivar 'Jingxun 2', several R2R3-MYB subfamily genes related to GT formation were identified. These results will guide the engineering of GTs and molecular breeding of lavender for improving the VOC content.

CONCLUSIONS

In this study, we identified the VOCs in four lavender cultivars. We analyzed the formation of GTs, and compared the number and diameter size of PGTs among four lavender cultivars. Additionally, we identified four candidate genes belonging to the R2R3-MYB family.

A high-resolution study of PM2.5 accumulation inside leaves in leaf stomata compared with non-stomatal areas using three-dimensional X-ray microscopy

Plant leaves retain atmospheric particulate matter (PM) on their surfaces, helping PM removal and risk reduction of respiratory tract infection. Several processes (deposition, resuspension, rainfall removal) can influence the PM accumulation on leaves and different leaf microstructures (e.g., trichomes, epicuticular waxes) can also be involved in retaining PM. However, the accumulation and distribution of PM on leaves, particularly at the stomata, are unclear, and the lack of characterization methods limits our understanding of this process. Thus, in this study, we aimed to explore the pathway through which PM_2.5 (aerodynamic diameter ≤ 2.5 μm) enters plant leaves, and the penetration depth of PM_2.5 along the entry route. Here, an indoor experiment using diamond powder as a tracer to simulate PM_2.5 deposition on leaves was carried out. Then, the treated and non-treated leaves were scanned by using three-dimensional (3D) X-ray microscopy. Next, the grayscale value of the scanned images was used to compare PM_2.5 accumulation in stomatal and non-stomatal areas of the treated and non-treated leaves, respectively. Finally, a total PM_2.5 volume from the abaxial epidermis was calculated. The results showed that, first, a large amount of PM_2.5 accumulates within leaf stomata, whereas PM_2.5 does not accumulate at non-stomatal areas. Then, the penetration depth of PM_2.5 in stomata of most tree species was 5-14 μm from the abaxial epidermis. For the first time, 3D X-ray microscope scanning was used to confirm that a pathway by which PM_2.5 enters the leaves is through the stomata, which is fundamental for further research on how PM_2.5 translocates and interacts with tissues and cells in leaves.

The Current Developments in Medicinal Plant Genomics Enabled the Diversification of Secondary Metabolites' Biosynthesis

Medicinal plants produce important substrates for their adaptation and defenses against environmental factors and, at the same time, are used for traditional medicine and industrial additives. Plants have relatively little in the way of secondary metabolites via biosynthesis. Recently, the whole-genome sequencing of medicinal plants and the identification of secondary metabolite production were revolutionized by the rapid development and cheap cost of sequencing technology. Advances in functional genomics, such as transcriptomics, proteomics, and metabolomics, pave the way for discoveries in secondary metabolites and related key genes. The multi-omics approaches can offer tremendous insight into the variety, distribution, and development of biosynthetic gene clusters (BGCs). Although many reviews have reported on the plant and medicinal plant genome, chemistry, and pharmacology, there is no review giving a comprehensive report about the medicinal plant genome and multi-omics approaches to study the biosynthesis pathway of secondary metabolites. Here, we introduce the medicinal plant genome and the application of multi-omics tools for identifying genes related to the biosynthesis pathway of secondary metabolites. Moreover, we explore comparative genomics and polyploidy for gene family analysis in medicinal plants. This study promotes medicinal plant genomics, which contributes to the biosynthesis and screening of plant substrates and plant-based drugs and prompts the research efficiency of traditional medicine.

Metabolomic profiling of developing perilla leaves reveals the best harvest time

Ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS) and gas chromatography-mass spectrometry (GC-MS) were applied to analyze metabolites in perilla leaves (PLs) during its developmental process. In total, 118 metabolites were identified, including volatile and non-volatile compounds, such as terpenoids, sugars, amino acids, organic acids, fatty acids, phenolic acids, flavonoids, and others. Principal component analysis (PCA) indicated great variations of metabolites during PLs development. Clustering analysis (CA) clarified the dynamic patterns of the metabolites. The heatmap of CA showed that most of the detected metabolites were significantly accumulated at stage 4 which is the pre anthesis period, and declined afterwards. The results of the present study provide a comprehensive overview of the metabolic dynamics of developing PLs which suggested that pre anthesis period is the best harvest time for PLs.

Integrated metabolomic and transcriptomic analyses reveal molecular response of anthocyanins biosynthesis in perilla to light intensity

The perilla anthocyanins have important medicinal and ornamental value, and their contents are significantly affected by light intensity. In view of their molecular mechanisms were not well understood, we integrated the metabolomic and transcriptomic analyses of the light-sensitive perilla variety under different light intensity. The perilla leave color were obviously affected under different treatments. Totally 140 flavonoid metabolites and 2461 genes showed steady change, among which 60 flavonoid metabolites were increased accumulation and 983 genes were upregulated expression under elevated light intensity treatment. Light treatment prominently affected the expression of genes involved in the main anthocyanin metabolites accumulation in perilla leaves. Using WGCNA analysis, we identified 4 key genes in anthocyanin biosynthesis pathway (CHI, DFR, and ANS) and 147 transcription factors (MYB, bHLH, bZIP, ERF, and NAC) involved in malonylshisonin biosynthesis. Among them, 6 MYBs and 4 bZIPs were predicted to play important roles in light regulation of malonylshisonin biosynthesis based on phylogenetic construction, correlation analysis, cis-acting element identification and qPCR verification. The identified key genes and regulatory factors will help us to understand the potential mechanism of photo-regulated anthocyanin accumulation in perilla.

Identification and characterization of a novel gene involved in glandular trichome development in Nepeta tenuifolia

Nepeta tenuifolia is a medicinal plant rich in terpenoids and flavonoids with antiviral, immunoregulatory, and anti-inflammatory activities. The peltate glandular trichome (PGT) is a multicellular structure considered to be the primary storage organ for monoterpenes; it may serve as an ideal model for studying cell differentiation and the development of glandular trichomes (GTs). The genes that regulate the development of GTs have not yet been well studied. In this study, we identified NtMIXTA1, a GT development-associated gene from the R2R3 MYB SBG9 family. NtMIXTA1 overexpression in tobacco resulted in the production of longer and denser GTs. Virus-induced gene silencing of NtMIXTA1 resulted in lower PGT density, a significant reduction in monoterpene concentration, and the decreased expression of genes related to monoterpene biosynthesis. Comparative transcriptome and widely targeted metabolic analyses revealed that silencing NtMIXTA1 significantly influenced the expression of genes, and the production of metabolites involved in the biosynthesis of terpenoids, flavonoids, and lipids. This study provides a solid foundation describing a mechanism underlying the regulation of GT development. In addition, this study further deepens our understanding of the regulatory networks involved in GT development and GT development-associated metabolite flux, as well as provides valuable reference data for studying plants with a high medicinal value without genetic transformation.

Morphogenesis, ultrastructure, and chemical profiling of trichomes in Artemisia argyi H. Lév. & Vaniot (Asteraceae)

Glandular trichomes of Artemisia argyi H. Lév. & Vaniot are the key tissues for the production of flavonoid and terpenoid metabolites. Artemisia argyi H. Lév. & Vaniot is an herbaceous perennial plant that has been widely used in traditional medicine for thousands of years. Glandular trichomes (GTs) and nonglandular trichomes (NGTs) have been reported on the leaf surface of A. argyi. The aim of this study was to elucidate the morphogenetic process and to analyze the metabolites of trichomes in A. argyi. The morphogenesis of GTs and NGTs was characterized using light, scanning, and transmission electron microscopy. The constituents of GTs were analyzed using laser microdissection combined with gas and liquid chromatography-mass spectrometry. Five developmental stages of two types of GTs and four developmental stages of one type of NGTs were observed. Two types of mature GT and one type of NGT were composed of 10, 5, and 4-6 cells, respectively. A large storage cavity was detected between the cuticle and cell walls in the first type of mature GT. Large nuclei, nucleoli, and mitochondria were observed in the basal and intermediate cells of the second type of GT. In addition, large vacuoles were observed in the basal and apical cells, and large nuclei were observed in the middle cells of NGTs. One monoterpene and seven flavonoids were identified in GTs of A. argyi. We suggest that GTs are the key tissues for the production of bioactive metabolites in A. argyi. This study provides an important theoretical basis and technical approach for clarifying the regulatory mechanisms for trichome development and bioactive metabolite biosynthesis in A. argyi.

Transcriptome Analysis of Stephania tetrandra and Characterization of Norcoclaurine-6-O-Methyltransferase Involved in Benzylisoquinoline Alkaloid Biosynthesis

Stephania tetrandra (S. Moore) is a source of traditional Chinese medicine that is widely used to treat rheumatism, rheumatoid arthritis, edema, and hypertension. Benzylisoquinoline alkaloids (BIAs) are the main bioactive compounds. However, the current understanding of the biosynthesis of BIAs in S. tetrandra is poor. Metabolite and transcriptomic analyses of the stem, leaf, xylem, and epidermis of S. tetrandra were performed to identify candidate genes associated with BIAs biosynthesis. According to the metabolite analysis, the majority of the BIAs accumulated in the root, especially in the epidermis. Transcriptome sequencing revealed a total of 113,338 unigenes that were generated by de novo assembly. Among them, 79,638 unigenes were successfully annotated, and 42 candidate structural genes associated with 15 steps of BIA biosynthesis identified. Additionally, a new (S)-norcoclaurine-6-O-methyltransferase (6OMT) gene was identified in S. tetrandra, named St6OMT2. Recombinant St6OMT2 catalyzed (S)-norcoclaurine methylation to form (S)-coclaurine in vitro. Maximum activity of St6OMT2 was determined at 30°C and pH 6.0 in NaAc-HAc buffer. Its half-life at 50°C was 22 min with the K_m and k_cat of 28.2 μM and 1.5 s^-1, respectively. Our results provide crucial transcriptome information for S. tetrandra, shedding light on the understanding of BIAs biosynthesis and further gene functional characterization.

Combined transcriptomic and metabolomic analysis reveals the potential mechanism of seed germination and young seedling growth in Tamarix hispida

Background

Seed germination is a series of ordered physiological and morphogenetic processes and a critical stage in plant life cycle. Tamarix hispida is one of the most salt-tolerant plant species; however, its seed germination has not been analysed using combined transcriptomics and metabolomics.

Results

Transcriptomic sequencing and widely targeted metabolomics were used to detect the transcriptional metabolic profiles of T. hispida at different stages of seed germination and young seedling growth. Transcriptomics showed that 46,538 genes were significantly altered throughout the studied development period. Enrichment study revealed that plant hormones, such as auxin, ABA, JA and SA played differential roles at varying stages of seed germination and post-germination. Metabolomics detected 1022 metabolites, with flavonoids accounting for the highest proportion of differential metabolites. Combined analysis indicated that flavonoid biosynthesis in young seedling growth, such as rhoifolin and quercetin, may improve the plant’s adaptative ability to extreme desert environments.

Conclusions

The differential regulation of plant hormones and the accumulation of flavonoids may be important for the seed germination survival of T. hispida in response to salt or arid deserts. This study enhanced the understanding of the overall mechanism in seed germination and post-germination. The results provide guidance for the ecological value and young seedling growth of T. hispida.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08341-x.

Biological investigations on macro-morphological characteristics, polyphenolic acids, antioxidant activity of Perilla frutescens (L) Britt. grown under open field

Perilla frutescens, perilla is a functional food, spice and medicinal herb and ornamental plant in the family of Lamiaceae. Thus, macro-morphological characteristics, phenolic acids, antioxidants of twelve accessions of P. frutescens grown under open field were studied. High polymorphism was found among the perilla accessions and macroscopic features of perilla genotypes showed variable results. Perilla can be classified into two clearly phenotypes green and purple, within these two other colours were appeared. A good level of biomass production was recorded for JTD3, 203P, PS2, 203P respectively. Principal component analysis was performed to cluster phenolic acids. GB phenotype exhibited the major content of polyphenols, followed by JTD3 then J1. Regarding antioxidant capacity, JTD3 showed the highest value followed by 203P and GB respectively. The HPLC analysis showed that the most abundant phenolic acids were ellagic acid which is accumulated in a higher percentage in NP606, 588P and JTD3 cultivars respectively, followed by salicylic acid and gallic acid. This is the first report of cultivation of various Perilla varieties under open field environmental conditions, not only to increase productivity but also to improve the quality. Therefore, the present study results confirm the importance of the Perilla species for human consumption, therapeutic and ornamental purposes.

Comparison of Pulegone and Estragole Chemotypes Provides New Insight Into Volatile Oil Biosynthesis of Agastache rugosa

The aerial parts of Agastache rugosa are rich in essential oils containing monoterpenoids, phenylpropanoids, and aromatic compounds. These are used as herbs, perfume plants, and ornamental plants. Based on the difference in the constituents of the essential oil, A. rugosa is divided into pulegone and estragole chemotypes, but the mechanism of key metabolite biosynthesis in these two A. rugosa chemotypes remains unclear. In this study, we compared the morphological differences, metabolite constituents, and transcriptomic data between the two chemotypes of A. rugosa. Monoterpenoid was the main compound in the pulegone chemotype, and phenylpropanoid was the main compound in the estragole chemotype; however, limonene was detected in both chemotypes. Furthermore, 46 genes related to pulegone and estragole biosynthesis were identified. Limonene synthase, limonene-3-hydroxylase, and isopiperitenol dehydrogenase were upregulated in the pulegone chemotype, while phenylalanine ammonia-lyase, 4-coumarate: CoA ligase, CYP73A, coumaroyl-aldehyde dehydrogenase, and eugenol synthase were downregulated in the pulegone chemotype. We identified chavicol methyl transferase and limonene-3-hydroxylase in A. rugosa. This work not only provides the difference in morphology and metabolites in pulegone and estragole chemotypes, but also offers a molecular mechanism of volatile oil biosynthesis, which could be a basis for specialized metabolites in specialized chemotypes.

Functional Characterization and Structural Insights Into Stereoselectivity of Pulegone Reductase in Menthol Biosynthesis

Monoterpenoids are the main components of plant essential oils and the active components of some traditional Chinese medicinal herbs like Mentha haplocalyx Briq., Nepeta tenuifolia Briq., Perilla frutescens (L.) Britt and Pogostemin cablin (Blanco) Benth. Pulegone reductase is the key enzyme in the biosynthesis of menthol and is required for the stereoselective reduction of the Δ2,8 double bond of pulegone to produce the major intermediate menthone, thus determining the stereochemistry of menthol. However, the structural basis and mechanism underlying the stereoselectivity of pulegone reductase remain poorly understood. In this study, we characterized a novel (-)-pulegone reductase from Nepeta tenuifolia (NtPR), which can catalyze (-)-pulegone to (+)-menthone and (-)-isomenthone through our RNA-seq, bioinformatic analysis in combination with in vitro enzyme activity assay, and determined the structure of (+)-pulegone reductase from M. piperita (MpPR) by using X-ray crystallography, molecular modeling and docking, site-directed mutagenesis, molecular dynamics simulations, and biochemical analysis. We identified and validated the critical residues in the crystal structure of MpPR involved in the binding of the substrate pulegone. We also further identified that residues Leu56, Val282, and Val284 determine the stereoselectivity of the substrate pulegone, and mainly contributes to the product stereoselectivity. This work not only provides a starting point for the understanding of stereoselectivity of pulegone reductases, but also offers a basis for the engineering of menthone/menthol biosynthetic enzymes to achieve high-titer, industrial-scale production of enantiomerically pure products.