De novo transcriptome analysis of rose-scented geranium provides insights into the metabolic specificity of terpene and tartaric acid biosynthesis

Unveiling the Impact of Eco-Friendly Synthesized Nanoparticles on Vegetative Growth and Gene Expression in Pelargonium graveolens and Sinapis alba L

Nanoscale geranium waste (GW) and magnesium nanoparticle/GW nanocomposites (Mg NP/GW) were prepared using green synthesis. The Mg NP/GW samples were subjected to characterization using X-ray diffraction (XRD) and Fourier-transform infrared spectroscopy (FTIR-FT). The surface morphology of the materials was examined using a scanning electron microscope (SEM), and their thermal stability was assessed through thermal gravimetric analysis (TG). The BET-specific surface area, pore volume, and pore size distribution of the prepared materials were determined using the N2 adsorption-desorption method. Additionally, the particle size and zeta potentials of the materials were also measured. The influence of the prepared nanomaterials on seed germination was intensively investigated. The results revealed an increase in seed germination percent at low concentrations of Mg NP/GWs. Upon treatment with Mg NP/GW nanoparticles, a reduction in the mitotic index (MI) was observed, indicating a decrease in cell division. Additionally, an increase in chromosomal abnormalities was detected. The efficacy of GW and Mg NP/GW nanoparticles as new elicitors was evaluated by studying their impact on the expression levels of the farnesyl diphosphate synthase (FPPS1) and geranylgeranyl pyrophosphate (GPPS1) genes. These genes play a crucial role in the terpenoid biosynthesis pathway in Sinapis alba (S. alba) and Pelargonium graveolens (P. graveolens) plants. The expression levels were analyzed using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis. The qRT-PCR analysis of FPPS and GPPS gene expression was performed. The outputs of FPPS1 gene expression demonstrated high levels of mRNA in both S. alba and P. graveolens with fold changes of 25.24 and 21.68, respectively. In contrast, the minimum expression levels were observed for the GPPS1 gene, with fold changes of 11.28 and 6.48 in S. alba and P. graveolens, respectively. Thus, this study offers the employment of medicinal plants as an alternative to fertilizer usage resulting in promoting environmental preservation, optimal waste utilization, reducing water consumption, and cost reduction.

Novel mechanisms for the synthesis of important secondary metabolites in Ginkgo biloba seed revealed by multi-omics data

Although the detailed biosynthetic mechanism is still unclear, the unique secondary metabolites of Ginkgo biloba, including ginkgolic acids (GAs) and terpene trilactones, have attracted increasing attention for their potent medicinal, physiological and biochemical properties. In particular, GAs have shown great potential in the fields of antibacterial and insecticidal activities, making it urgent to elucidate their biosynthetic mechanism. In this study, we systematically revealed the landscape of metabolic-transcriptional regulation across continuous growth stages of G. biloba seeds (GBS) based on multi-omics mining and experimental verification, and successfully identified all major types of GAs and terpene trilactones along with more than a thousand kinds of other metabolites. The phenological changes and the essential gene families associated with these unique metabolites were analyzed in detail, and several potential regulatory factors were successfully identified based on co-expression association analysis. In addition, we unexpectedly found the close relationship between large introns and the biosynthesis of these secondary metabolites. These genes with large introns related to the synthesis of secondary metabolites showed higher gene expression and expression stability in different tissues or growth stages. Our results may provide a new perspective for the study of the regulatory mechanism of these unique secondary metabolites in GBS.

Aluminum and Fluoride Stresses Altered Organic Acid and Secondary Metabolism in Tea (Camellia sinensis) Plants: Influences on Plant Tolerance, Tea Quality and Safety

Tea plants have adapted to grow in tropical acidic soils containing high concentrations of aluminum (Al) and fluoride (F) (as Al/F hyperaccumulators) and use secret organic acids (OAs) to acidify the rhizosphere for acquiring phosphorous and element nutrients. The self-enhanced rhizosphere acidification under Al/F stress and acid rain also render tea plants prone to accumulate more heavy metals and F, which raises significant food safety and health concerns. However, the mechanism behind this is not fully understood. Here, we report that tea plants responded to Al and F stresses by synthesizing and secreting OAs and altering profiles of amino acids, catechins, and caffeine in their roots. These organic compounds could form tea-plant mechanisms to tolerate lower pH and higher Al and F concentrations. Furthermore, high concentrations of Al and F stresses negatively affected the accumulation of tea secondary metabolites in young leaves, and thereby tea nutrient value. The young leaves of tea seedlings under Al and F stresses also tended to increase Al and F accumulation in young leaves but lower essential tea secondary metabolites, which challenged tea quality and safety. Comparisons of transcriptome data combined with metabolite profiling revealed that the corresponding metabolic gene expression supported and explained the metabolism changes in tea roots and young leaves via stresses from high concentrations of Al and F. The study provides new insight into Al- and F-stressed tea plants with regard to responsive metabolism changes and tolerance strategy establishment in tea plants and the impacts of Al/F stresses on metabolite compositions in young leaves used for making teas, which could influence tea nutritional value and food safety.

Transcriptome Analysis Provides Insights into Potentilla bifurca Adaptation to High Altitude

Potentilla bifurca is widely distributed in Eurasia, including the Tibetan Plateau. It is a valuable medicinal plant in the Tibetan traditional medicine system, especially for the treatment of diabetes. This study investigated the functional gene profile of Potentilla bifurca at different altitudes by RNA-sequencing technology, including de novo assembly of 222,619 unigenes from 405 million clean reads, 57.64% of which were annotated in Nr, GO, KEGG, Pfam, and Swiss-Prot databases. The most significantly differentially expressed top 50 genes in the high-altitude samples were derived from plants that responded to abiotic stress, such as peroxidase, superoxide dismutase protein, and the ubiquitin-conjugating enzyme. Pathway analysis revealed that a large number of DEGs encode key enzymes involved in secondary metabolites, including phenylpropane and flavonoids. In addition, a total of 298 potential genomic SSRs were identified in this study, which provides information on the development of functional molecular markers for genetic diversity assessment. In conclusion, this study provides the first comprehensive assessment of the Potentilla bifurca transcriptome. This provides new insights into coping mechanisms for non-model organisms surviving in harsh environments at high altitudes, as well as molecular evidence for the selection of superior medicinal plants.

Adaptation insights from comparative transcriptome analysis of two Opisthopappus species in the Taihang mountains

Opisthopappus is a major wild source of Asteraceae with resistance to cold and drought. Two species of this genus (Opisthopappus taihangensis and O. longilobus) have been employed as model systems to address the evolutionary history of perennial herb biomes in the Taihang Mountains of China. However, further studies on the adaptive divergence processes of these two species are currently impeded by the lack of genomic resources. To elucidate the molecular mechanisms involved, a comparative analysis of these two species was conducted. Among the identified transcription factors, the bHLH members were most prevalent, which exhibited significantly different expression levels in the terpenoid metabolic pathway. O. longilobus showed higher level of expression than did O. taihangensis in terms of terpenes biosynthesis and metabolism, particularly monoterpenoids and diterpenoids. Analyses of the positive selection genes (PSGs) identified from O. taihangensis and O. longilobus revealed that 1203 genes were related to adaptative divergence, which were under rapid evolution and/or have signs of positive selection. Differential expressions of PSG occurred primarily in the mitochondrial electron transport, starch degradation, secondary metabolism, as well as nucleotide synthesis and S-metabolism pathway processes. Several PSGs were obviously differentially expressed in terpenes biosynthesis that might result in the fragrances divergence between O. longilobus and O. taihangensis, which would provide insights into adaptation of the two species to different environments that characterized by sub-humid warm temperate and temperate continental monsoon climates. The comparative analysis for these two species in Opisthopappus not only revealed how the divergence occurred from molecular perspective, but also provided novel insights into how differential adaptations occurred in Taihang Mountains.

Acyl-Acyl Carrier Protein Desaturases and Plant Biotic Interactions

Interactions between land plants and other organisms such as pathogens, pollinators, or symbionts usually involve a variety of specialized effectors participating in complex cross-talks between organisms. Fatty acids and their lipid derivatives play important roles in these biological interactions. While the transcriptional regulation of genes encoding acyl–acyl carrier protein (ACP) desaturases appears to be largely responsive to biotic stress, the different monounsaturated fatty acids produced by these enzymes were shown to take active part in plant biotic interactions and were assigned with specific functions intrinsically linked to the position of the carbon–carbon double bond within their acyl chain. For example, oleic acid, an omega-9 monounsaturated fatty acid produced by Δ⁹-stearoyl–ACP desaturases, participates in signal transduction pathways affecting plant immunity against pathogen infection. Myristoleic acid, an omega-5 monounsaturated fatty acid produced by Δ⁹-myristoyl–ACP desaturases, serves as a precursor for the biosynthesis of omega-5 anacardic acids that are active biocides against pests. Finally, different types of monounsaturated fatty acids synthesized in the labellum of orchids are used for the production of a variety of alkenes participating in the chemistry of sexual deception, hence favoring plant pollination by hymenopterans.

Defining the role of a caffeic acid 3-O-methyltransferase from Azadirachta indica fruits in the biosynthesis of ferulic acid through heterologous over-expression in Ocimum species and Withania somnifera

The recombinant caffeic acid 3-O-methyltransferase gene has been cloned and characterized from Neem. The gene is involved in ferulic acid biosynthesis, a key intermediate component of lignin biosynthesis. Azadirachta indica (Neem) is a highly reputed traditional medicinal plant and is phytochemically well-known for its limonoids. Besides limonoids, phenolics are also distinctively present, which add more medicinal attributes to Neem. Caffeic acid is one of such phenolic compound and it can be converted enzymatically into another bioactive phytomolecule, ferulic acid. This conversion requires transfer of a methyl group from a donor to caffeic acid under the catalytic action of an appropriate methyltransferase. In this study, caffeic acid 3-O-methyltransferase gene from Neem (NCOMT) fruits has been isolated and heterologously expressed in E. coli. The recombinant NCOMT enzyme was purified, which exhibited efficient catalytic conversion of caffeic acid into ferulic acid, a highly potential pharmaceutical compound. The purified recombinant enzyme was physico-kinetically characterized for its catalysis. The analysis of tissue-wide expression of NCOMT gene revealed interesting pattern of transcript abundance reflecting its role in the development of fruit tissues. Further, NCOMT was heterologously overexpressed in Withania somnifera and Ocimum species, to analyze its role in ferulic acid biosynthesis in planta. Thus, the study provides insight for the endogenous role of NCOMT in ferulic acid biosynthesis en route to lignin, an important structural component. To the best of our knowledge, NCOMT pertains to be the first enzyme of the secondary metabolism that has been purified and kinetically characterized from Neem. This study may also have important prospects of applications as the observation on heterologous expression of NCOMT showed its involvement in the maintenance of the in vivo pool of ferulic acid in the plants. Thus, the study involving NCOMT opens up new dimensions of metabolic engineering approaches for the biosynthesis of potential therapeutically important phytomolecules in heterologous systems.

Interaction of Drug Candidates with Various SARS-CoV-2 Receptors: An in Silico Study to Combat COVID-19

The world is currently facing the COVID-19 pandemic caused by the SARS-CoV-2 virus. The pandemic is causing the death of people around the world, and public and social health measures to slow or prevent the spread of COVID-19 are being implemented with the involvement of all members of society. Research institutions are accelerating the discovery of vaccines and therapies for COVID-19. In this work, molecular docking was used to study (in silico) the interaction of 24 ligands, divided into four groups, with four SARS-CoV-2 receptors, Nsp9 replicase, main protease (Mpro), NSP15 endoribonuclease, and spike protein (S-protein) interacting with human ACE2. The results showed that the antimalarial drug Metaquine and anti-HIV antiretroviral Saquinavir interacted with all the studied receptors, indicating that they are potential candidates for multitarget drugs for COVID-19.

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.

Transcriptome profiling of spike provides expression features of genes related to terpene biosynthesis in lavender

Lavender (Lavandula angustifolia) is an important economic plant because of the value of its essential oil (EO). The Yili Valley in Xinjiang has become the largest lavender planting base in China. However, there is a lack of research on the gene expression regulation of EO biosynthesis and metabolism in local varieties. Here, de novo transcriptome analysis of inflorescence of three development stages from initial flower bud to flowering stage 50% from two lavender cultivars with contrasting EO production revealed the dynamics of 100,177 differentially expressed transcripts (DETs) in various stages of spike development within and across the cultivars. The lavender transcriptome contained 77 DETs with annotations related to terpenoid biosynthesis. The expression profiles of the 27 genes involved in the methylerythritol phosphate (MEP) pathway, 22 genes in the mevalonate (MVA) pathway, 28 genes related to monoterpene and sesquiterpene biosynthesis during inflorescence development were comprehensively characterized, and possible links between the expression changes of genes and contents of EO constituents were explored. The upregulated genes were mainly concentrated in the MEP pathway, while most genes in the MVA pathway were downregulated during flower development, and cultivars with a higher EO content presented higher expression of genes in the MEP pathway, indicating that EOs were chiefly produced through the MEP pathway. Additionally, MYB transcription factors constituted the largest number of transcripts in all samples, suggesting their potential roles in regulating EO biosynthesis. The sequences and transcriptional patterns of the transcripts will be helpful for understanding the molecular basis of lavender terpene biosynthesis.

Bioengineering tools for the production of pharmaceuticals: current perspective and future outlook

The bioengineering tools have significant advantages through less time-consuming and utilized as a promising stage for the production of pharmaceutical bioproducts under the single platform. This review highlighted the advantages and current improvement in the plant, animal and microbial bioengineering tools and outlines feasible approaches by biological and process's bioengineering levels for advancing the economic feasibility of pharmaceutical's production. The critical analysis results revealed that system biology and synthetic biology along with advanced bioengineering tools like transcriptome, proteome, metabolome and nano bioengineering tools have shown a promising impact on the development of pharmaceutical's bioproducts. Tools to overcome and resolve the accompanying encounters of pharmaceutical's production that include nano bioengineering tools are also discussed. As a summary and prospect, it also gives new insight into the challenges and possible breakthrough of the development of pharmaceutical's bioproducts through bioengineering tools.

Long noncoding RNAs and miRNAs regulating terpene and tartaric acid biosynthesis in rose-scented geranium

This study aimed to explore the noncoding RNAs, which have emerged as key regulatory molecules in biological processes, in rose-scented geranium. We analyzed RNA-seq data revealing 26 784 long noncoding RNAs (lncRNAs) and 871 miRNAs in rose-scented geranium. A total of 466 lncRNAs were annotated using different plant lncRNA public databases. Furthermore, 372 lncRNAs and 99 miRNAs were detected that target terpene and tartarate biosynthetic pathways. An interactome, comprising of lncRNAs, miRNAs, and mRNAs, was constructed that represents a noncoding RNA regulatory network of the target mRNAs. Real-time quantitative PCR expression validation was done for selected lncRNAs involved in the regulation of terpene and tartaric acid pathways. This study provides the first insights into the regulatory functioning of noncoding RNAs in rose-scented geranium.

The Phytochemical Composition, Biological Effects and Biotechnological Approaches to the Production of High-Value Essential Oil from Geranium

Geraniaceae family plants are highly reputed aromatic and medicinal perennial branched herbs. The high economic value of these plants is due to their secondary metabolites, especially essential oil of foliage, which is a complex mixture of volatile phytochemicals, such as terpenes, esters, aldehydes, alcohols, ketones and phenols. The main phytoconstituents of the essential oil belong to the terpenoid group of metabolites, such as monoterpenes, sesquiterpenes, diterpenes and their esters. Of these, geraniol, linalool, citronellol and their esters (50–70%) generally constitute a major portion of essential oil, responsible for its fragrance. Essential oil is biosynthesized in specialized tissues known as glandular trichomes present in leaves, green branches and fresh flowers. Geraniaceae family plants have been highly useful in the perfumery, cosmetics, aromatherapy, pharmaceuticals and food industries. Several pharmacological properties such as antifungal, anti-inflammatory, anti-cancerous, anti-depressant, antibacterial, antioxidant, antiseptic, anti-dysentery, and antidiabetic properties are attributed to the presence of geranium oil. Further, it improves blood circulation, treats congestion, cleans the lymphatic system, strengthens the immune system, and is effective in combating nervousness, constipation, insomnia, anxiety and high blood pressure. The chapter discusses the phytochemical composition, pharmacological properties, genomics of essential oil biosynthetic pathway, enhancement of essential oil yield, and several biotechnological approaches to enhance the quantity as well as quality of essential oil in geranium.

Functional Analysis of Four Terpene Synthases in Rose-Scented Pelargonium Cultivars (Pelargonium × hybridum) and Evolution of Scent in the Pelargonium Genus

Pelargonium genus contains about 280 species among which at least 30 species are odorant. Aromas produced by scented species are remarkably diverse such as rose, mint, lemon, nutmeg, ginger and many others scents. Amongst odorant species, rose-scented pelargoniums, also named pelargonium rosat, are the most famous hybrids for their production of essential oil (EO), widely used by perfume and cosmetic industries. Although EO composition has been extensively studied, the underlying biosynthetic pathways and their regulation, most notably of terpenes, are largely unknown. To gain a better understanding of the terpene metabolic pathways in pelargonium rosat, we generated a transcriptome dataset of pelargonium leaf and used a candidate gene approach to functionally characterise four terpene synthases (TPSs), including a geraniol synthase, a key enzyme responsible for the biosynthesis of the main rose-scented terpenes. We also report for the first time the characterisation of a novel sesquiterpene synthase catalysing the biosynthesis of 10-epi-γ-eudesmol. We found a strong correlation between expression of the four genes encoding the respective TPSs and accumulation of the corresponding products in several pelargonium cultivars and species. Finally, using publically available RNA-Seq data and de novo transcriptome assemblies, we inferred a maximum likelihood phylogeny from 270 pelargonium TPSs, including the four newly discovered enzymes, providing clues about TPS evolution in the Pelargonium genus. Notably, we show that, by contrast to other TPSs, geraniol synthases from the TPS-g subfamily conserved their molecular function throughout evolution.

Identification of Glutathione Peroxidase (GPX) Gene Family in Rhodiola crenulata and Gene Expression Analysis under Stress Conditions

Glutathione peroxidases (GPXs) are important enzymes in the glutathione-ascorbate cycle for catalyzing the reduction of H₂O₂ or organic hydroperoxides to water. GPXs play an essential role in plant growth and development by participating in photosynthesis, respiration, and stress tolerance. Rhodiola crenulata is a popular traditional Chinese medicinal plant which displays an extreme energy of tolerance to harsh alpine climate. The GPXs gene family might provide R. crenulata for extensively tolerance to environment stimulus. In this study, five GPX genes were isolated from R. crenulata. The protein amino acid sequences were analyzed by bioinformation softwares with the results that RcGPXs gene sequences contained three conserve cysteine residues, and the subcellular location predication were in the chloroplast, endoplasmic reticulum, or cytoplasm. Five RcGPXs members presented spatial and temporal specific expression with higher levels in young and green organs. And the expression patterns of RcGPXs in response to stresses or plant hormones were investigated by quantitative real-time PCR. In addition, the putative interaction proteins of RcGPXs were obtained by yeast two-hybrid with the results that RcGPXs could physically interact with specific proteins of multiple pathways like transcription factor, calmodulin, thioredoxin, and abscisic acid signal pathway. These results showed the regulation mechanism of RcGPXs were complicated and they were necessary for R. crenulata to adapt to the treacherous weather in highland.

De novo sequencing, assembly and characterisation of Aloe vera transcriptome and analysis of expression profiles of genes related to saponin and anthraquinone metabolism

BACKGROUND

Aloe vera is a perennial, succulent, drought-resistant plant that exhibits many pharmacological characteristics such as wound healing ability against skin burns, anti-ulcer, anti-inflammatory, anti-tumor, anti-viral, anti-hypercholesterolemic, anti-hyperglycemic, anti-asthmatic and much more. Despite great medicinal worth, little genomic information is available on Aloe vera. This study is an initiative to explore the full-scale functional genomics of Aloe vera by generating whole transcriptome sequence database, using Illumina HiSeq technology and its progressive annotation specifically with respect to the metabolic specificity of the plant.

RESULTS

Transcriptome sequencing of root and leaf tissue of Aloe vera was performed using Illumina paired-end sequencing technology. De novo assembly of high quality paired-end reads, resulted into 1,61,733 and 2,21,792 transcripts with mean length of 709 and 714 nucleotides for root and leaf respectively. The non-redundant transcripts were clustered using CD-HIT-EST, yielding a total of 1,13,063 and 1,41,310 unigenes for root and leaf respectively. A total of 6114 and 6527 CDS for root and leaf tissue were enriched into 24 different biological pathway categories using KEGG pathway database. DGE profile prepared by calculating FPKM values was analyzed for differential expression of specific gene encoding enzymes involved in secondary metabolite biosynthesis. Sixteen putative genes related to saponin, lignin, anthraquinone, and carotenoid biosynthesis were selected for quantitative expression by real-time PCR. DGE as well as qRT PCR expression analysis represented up-regulation of secondary metabolic genes in root as compared to leaf. Furthermore maximum number of genes was found to be up-regulated after the induction of methyl jasmonate, which stipulates the association of secondary metabolite synthesis with the plant's defense mechanism during stress. Various transcription factors including bHLH, NAC, MYB were identified by searching predicted CDS against PlantTFdb.

CONCLUSIONS

This is the first transcriptome database of Aloe vera and can be potentially utilized to characterize the genes involved in the biosynthesis of important secondary metabolites, metabolic regulation, signal transduction mechanism, understanding function of a particular gene in the biology and physiology of plant of this species as well as other species of Aloe genus.

RNA-seq-based genome annotation and identification of long-noncoding RNAs in the grapevine cultivar 'Riesling'

BACKGROUND

The technological advances of RNA-seq and de novo transcriptome assembly have enabled genome annotation and transcriptome profiling in highly heterozygous species such as grapevine (Vitis vinifera L.). This work is an attempt to utilize a de novo-assembled transcriptome of the V. vinifera cultivar 'Riesling' to improve annotation of the grapevine reference genome sequence.

RESULTS

Here we show that the transcriptome assembly of a single V. vinifera cultivar is insufficient for a complete genome annotation of the grapevine reference genome constructed from V. vinifera PN40024. Further, we provide evidence that the gene models we identified cannot be completely anchored to the previously published V. vinifera PN40024 gene models. In addition to these findings, we present a computational pipeline for the de novo identification of lncRNAs. Our results demonstrate that, in grapevine, lncRNAs are significantly different from protein coding transcripts in such metrics as length, GC-content, minimum free energy, and length-corrected minimum free energy.

CONCLUSIONS

In grapevine, high-level heterozygosity necessitates that transcriptome characterization be based on cultivar-specific reference genome sequences. Our results strengthen the hypothesis that lncRNAs have thermodynamically different properties than protein-coding RNAs. The analyses of both coding and non-coding RNAs will be instrumental in uncovering inter-cultivar variation in wild and cultivated grapevine species.