Genome-Wide Comparative Profiles of Triterpenoid Biosynthesis Genes in Ginseng and Pseudo Ginseng Medicinal Plants
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PROVIDER: S-EPMC10672587 | biostudies-literature | 2023 Nov
REPOSITORIES: biostudies-literature
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Project description:Herb genomics and comparative genomics provide a global platform to explore the genetics and biology of herbs at the genome level. Panax ginseng C.A. Meyer is an important medicinal plant for a variety of bioactive chemical compounds of which the biosynthesis may involve transport of a wide range of substrates mediated by oligopeptide transporters (OPT). However, information about the OPT family in the plant kingdom is still limited. Only 17 and 18 OPT genes have been characterized for Oryza sativa and Arabidopsisthaliana, respectively. Additionally, few comprehensive studies incorporating the phylogeny, gene structure, paralogs evolution, expression profiling, and co-expression network between transcription factors and OPT genes have been reported for ginseng and other species. In the present study, we performed those analyses comprehensively with both online tools and standalone tools. As a result, we identified a total of 268 non-redundant OPT genes from 12 flowering plants of which 37 were from ginseng. These OPT genes were clustered into two distinct clades in which clade-specific motif compositions were considerably conservative. The distribution of OPT paralogs was indicative of segmental duplication and subsequent structural variation. Expression patterns based on two sources of RNA-Sequence datasets suggested that some OPT genes were expressed in both an organ-specific and tissue-specific manner and might be involved in the functional development of plants. Further co-expression analysis of OPT genes and transcription factors indicated 141 positive and 11 negative links, which shows potent regulators for OPT genes. Overall, the data obtained from our study contribute to a better understanding of the complexity of the OPT gene family in ginseng and other flowering plants. This genetic resource will help improve the interpretation on mechanisms of metabolism transportation and signal transduction during plant development for Panax ginseng.
| S-EPMC6337337 | biostudies-literature
Project description:Panax ginseng is an important medicinal plant, and ginsenosides are the main bioactive molecules of ginseng. The TCP (TBI, CYC, PCF) family is a group of transcription factors (TFs) that play an important role in plant growth and development, hormone signalling and synthesis of secondary metabolites. In our study, 78 PgTCP transcripts were identified from the established ginseng transcriptome database. A phylogenetic tree analysis showed that the 67 PgTCP transcripts with complete open reading frames were classified into three subfamilies, including CIN, PCF, and CYC/TB1. Protein structure analysis showed that PgTCP genes had bHLH structures. Chromosomal localization analysis showed that 63 PgTCP genes were localized on 17 of the 24 chromosomes of the Chinese ginseng genome. Expression pattern analysis showed that PgTCP genes differed among different lineages and were spatiotemporally specific. Coexpression network analysis indicated that PgTCP genes were coexpressed and involved in plant activities or metabolic regulation in ginseng. The expression levels of PgTCP genes from class I (PCF) were significantly downregulated, while the expression levels of PgTCP genes from class II (CIN and CYC/TB1) were upregulated, suggesting that TCP genes may be involved in the regulation of secondary metabolism in ginseng. As the PgTCP26-02 gene was found to be related to ginsenoside synthesis, its predicted protein structure and expression pattern were further analysed. Our results provide new insights into the origin, differentiation, evolution and function of the PgTCP gene family in ginseng, as well as the regulation of plant secondary metabolism.
| S-EPMC10787463 | biostudies-literature
Project description:The available phytochemical characteristics of the medicinal plants and derived herbal material often lack data concerning the content of steroids (including phytosterols) and triterpenoids, that can be responsible for various beneficial properties and therapeutic effects, either directly, or as a result of synergistic action with other bioactive constituents. The aim of the present work was the analysis of the content of these compounds in herbal material (leaves, aerial parts) derived from selected medicinal plants (Cistus ladanifer, Cistus monspeliensis, Erica arborea, Globularia alypum, Pistacia lentiscus, Rhamnus alaternus), widely used in folk medicine in the Mediterranean region. Results obtained by gas chromatography-mass spectrometry (GC-MS)-targeted profiling revealed the diversity in the profiles and contents of steroids and triterpenoids in the analyzed plant material, ranging from 5.7% d.w. in E. arborea to 0.1% in G. alypum. The obtained results supplement the existing phytochemical data of the investigated medicinal plants, pointing to the E. arborea aerial parts and P. lentiscus leaves as valuable resources of phytosterols and bioactive triterpenoids.
| S-EPMC9866667 | biostudies-literature
Project description:BackgroundBacopa monnieri commonly known as Brahmi is utilized in Ayurveda to improve memory and many other human health benefits. Bacosides enriched standardized extract of Bacopa monnieri is being marketed as a memory enhancing agent. In spite of its well known pharmacological properties it is not much studied in terms of transcripts involved in biosynthetic pathway and its regulation that controls the secondary metabolic pathway in this plant. The aim of this study was to identify the potential transcripts and provide a framework of identified transcripts involved in bacosides production through transcriptome assembly.ResultsWe performed comparative transcriptome analysis of shoot and root tissue of Bacopa monnieri in two independent biological replicate and obtained 22.48 million and 22.0 million high quality processed reads in shoot and root respectively. After de novo assembly and quantitative assessment total 26,412 genes got annotated in root and 18,500 genes annotated in shoot sample. Quality of raw reads was determined by using SeqQC-V2.2. Assembled sequences were annotated using BLASTX against public database such as NR or UniProt. Searching against the KEGG pathway database indicated that 37,918 unigenes from root and 35,130 unigenes from shoot were mapped to 133 KEGG pathways. Based on the DGE data we found that most of the transcript related to CYP450s and UDP-glucosyltransferases were specifically upregulated in shoot tissue as compared to root tissue. Finally, we have selected 43 transcripts related to secondary metabolism including transcription factor families which are differentially expressed in shoot and root tissues were validated by qRT-PCR and their expression level were monitored after MeJA treatment and wounding for 1, 3 and 5 h.ConclusionsThis study not only represents the first de novo transcriptome analysis of Bacopa monnieri but also provides information about the identification, expression and differential tissues specific distribution of transcripts related to triterpenoid sapogenin which is one of the most important pharmacologically active secondary metabolite present in Bacopa monnieri. The identified transcripts in this study will establish a foundation for future studies related to carrying out the metabolic engineering for increasing the bacosides biosynthesis and its regulation for human health benefits.
| S-EPMC5490213 | biostudies-literature
Project description:BackgroundEntada phaseoloides (L.) Merr. is an important traditional medicinal plant. The stem of Entada phaseoloides is popularly used as traditional medicine because of its significance in dispelling wind and dampness and remarkable anti-inflammatory activities. Triterpenoid saponins are the major bioactive compounds of Entada phaseoloides. However, genomic or transcriptomic technologies have not been used to study the triterpenoid saponin biosynthetic pathway in this plant.ResultsWe performed comparative transcriptome analysis of the root, stem, and leaf tissues of Entada phaseoloides with three independent biological replicates and obtained a total of 53.26 Gb clean data and 116,910 unigenes, with an average N50 length of 1218 bp. Putative functions could be annotated to 42,191 unigenes (36.1%) based on BLASTx searches against the Non-redundant, Uniprot, KEGG, Pfam, GO, KEGG and COG databases. Most of the unigenes related to triterpenoid saponin backbone biosynthesis were specifically upregulated in the stem. A total of 26 cytochrome P450 and 17 uridine diphosphate glycosyltransferase candidate genes related to triterpenoid saponin biosynthesis were identified. The differential expressions of selected genes were further verified by qPT-PCR.ConclusionsThe dataset reported here will facilitate the research about the functional genomics of triterpenoid saponin biosynthesis and genetic engineering of Entada phaseoloides.
| S-EPMC7493163 | biostudies-literature
Project description:Vietnamese ginseng (Panax vietnamensis Ha et Grushv.), also known as Ngoc Linh ginseng, is a high-value herb in Vietnam. Vietnamese ginseng has been proven to be effective in enhancing the immune system, human memory, anti-stress, anti-inflammatory, anti-cancer, and prevent aging. The present study reports the first draft whole-genome of Vietnamese ginseng and the identification of potential genes involved in the triterpenoid metabolic pathway. De novo whole-genome assembly was performed successfully from a data of approximately 139 Gbps of 394,802,120 high quality reads to generate 9815 scaffolds with an N50 value of 572,722 bp from the leaf of Vietnamese ginseng. The assembled genome of Vietnamese ginseng is 3,001,967,204 bp long containing 79,374 gene models. Among them, there are 55,012 genes (69.30%) were annotated by various public molecular biology databases. The potential genes involved in triterpenoid saponin biosynthesis in Vietnamese ginseng and their metabolic pathway were also predicted." Three genes encoding squalene monooxygenase isozymes in Vietnamese ginseng were cloned, sequenced and characterized. Moreover, expression levels of several key genes involved in terpenoid biosynthesis in different parts of Vietnamese ginseng were also analyzed. The SSR markers were detected by various programs from both of assembly full dataset of Vietnamese ginseng genome and predicted genes. The present work provided important data of the draft whole-genome of Vietnamese ginseng for further studies to understand the role of genes involved in ginsenoside biosynthesis and their metabolic pathway at the molecular level of this rare medicinal species.Supplementary informationThe online version contains supplementary material available at 10.1007/s12298-021-01076-1.
| S-EPMC8526660 | biostudies-literature
Project description:To elucidate the medicinal nature of black ginseng (BG) by comparison of the effects of four Chinese herbs with different medicinal natures on the deficiency-heat syndrome rat model which was established by intragastric administration of traditional Chinese drugs with hot nature, the appearance indexes, biochemical indexes, and pathological sections of thyroid and stomach were examined. In addition, the seven short-chain fatty acids (SCFAs) in rat feces were also determined by headspace gas chromatography-mass spectrometry to reveal the action mechanism of the drugs with different natures. Results indicated that all the 4 drugs could exhibit similar actions in regulating the biochemical indexes of triiodothyronine (T3), thyroxine (T4), thyrotropin-releasing hormone (TRH), thyroid-stimulating hormone (TSH), and corticosterone (CORT) representing the hypothalamus-pituitary-thyroid (HPT) and hypothalamus-pituitary-adrenal (HPA) axes of the animal. However, cold-natured cortex phellodendri (HB) and ginseng leaves (GLs) showed stronger downregulation of the AChE activity of the nervous system. Red ginseng (RG) and BG tested exhibited stronger upregulation of the liver Na+-K+-ATPase activity. Principal component analysis (PCA) showed that GLs are similar to those of HB which belongs to the cold-nature drug, whereas BG showed closer to RG which attributes to a warm-nature drug. Thus, BG could be ascribed to a warm-nature drug. Further research disclosed that RG and BG mainly regulated the acetic acid and GL and HB primarily modulated the isovaleric acid and hexanoic acid in rat feces, which could be the features of drugs with warm or cold nature on the regulation of SCFAs in rats. It is for the first time that the medicinal nature of BG and its effect on the SCFAs were examined.
| S-EPMC9056217 | biostudies-literature
Project description:Ragweed pollen is primarily responsible for the hay fever allergies of sufferers throughout the world. A proteome study of three ragweed plants (Ambrosia artemisiifolia, Ambrosia trifida, and Ambrosia psilostachya) was undertaken to document and compare their protein profiles. Proteins extracted from the pollen of the three plants were subjected to one dimensional electrophoresis followed by tandem liquid chromatography-mass spectroscopy. Peptide sequence mapping permitted discovery of proteins not previously reported for all three plants and 45% of the identified proteins were shared by all three of them. Application of stringent criteria revealed not only a majority of known allergens for short ragweed but also allergens not previously reported for the other two plants. Additionally, potentially allergy inducing enolases are reported for the three plants. These results suggest that all three ragweed plants could contribute to the allergy malady.
| S-EPMC5491094 | biostudies-literature
Project description:Psidium guajava L., a fruit crop belonging to the Myrtaceae family, is highly valued for its nutritional and medicinal properties. The family exhibits a diverse chemical profile of essential oils and serves as a valuable resource due to its ecological interactions, adaptability, and dispersal capacity. The Myrtaceae family has been extensively studied for its terpenoids. Genetic studies have focused on foliar terpene yield in species from the Eucalypteae and Melaleucaceae tribes. To understand the evolutionary trends in guava breeding, this study predicted terpene synthase genes (TPS) from different cultivars. Through this analysis, 43 full-length TPS genes were identified, and approximately 77% of them exhibited relative expression in at least one of the five investigated plant tissues (root, leaf, bud, flower, and fruit) of two guava cultivars. We identified intra-species variation in the terpene profile and single nucleotide polymorphisms (SNPs) in twelve TPS genes, resulting in the clustering of 62 genotypes according to their essential oil chemotypes. The high concentration of sesquiterpenes is supported by the higher number of TPS-a genes and their expression. The expansion for TPS sub-families in P. guajava occurred after the expansion of other rosids species. Providing insight into the origin of structural diversification and expansion in each clade of the TPS gene family within Myrtaceae. This study can provide insights into the diversity of genes for specialized metabolites such as terpenes, and their regulation, which can lead to a diverse chemotype of essential oil in different tissues and genotypes. This suggests a mode of enzymatic evolution that could lead to high sesquiterpene production, act as a chemical defense and contribute to the adaptive capacity of this species to different habitats.
| S-EPMC10770072 | biostudies-literature
Project description:Thymol, as a dietary monoterpene, is a phenol derivative of cymene, which is the major component of the essential oil of Trachyspermum ammi (L.). It shows multiple biological activities: antifungal, antibacterial, antivirus and anti-inflammatory. T. ammi, commonly known as ajowan, belongs to Apiaceae and is an important medicinal seed spice. To identify the putative genes involved in thymol and other monoterpene biosynthesis, we provided transcriptomes of four inflorescence tissues of two ajowan ecotypes, containing different thymol yield. This study has detected the genes encoding enzymes for the go-between stages of the terpenoid biosynthesis pathways. A large number of unigenes, differentially expressed between four inflorescence tissues of two ajowan ecotypes, was revealed by a transcriptome analysis. Furthermore, differentially expressed unigenes encoding dehydrogenases, transcription factors, and cytochrome P450s, which might be associated with terpenoid diversity in T. ammi, were identified. The sequencing data obtained in this study formed a valuable repository of genetic information for an understanding of the formation of the main constituents of ajowan essential oil and functional analysis of thymol-specific genes. Comparative transcriptome analysis led to the development of new resources for a functional breeding of ajowan.
| S-EPMC6128898 | biostudies-literature