Search Results (460)

Lycium barbarum is a traditional medicinal and edible plant species in China, exhibiting notable salt tolerance that enables cultivation in salt-affected soils. However, intensifying soil salinization has rendered severe salt stress a critical limiting factor for its fruit yield and quality. Universal stress proteins (USPs) serve as crucial regulators for plant abiotic stress responses through developmental process modulation. Nevertheless, the characteristics and functional divergence of USP gene family members remain unexplored in L. barbarum. Here, we performed genome-wide identification and characterization of the USP gene family in L. barbarum, revealing 52 members unevenly distributed across all 12 chromosomes. Phylogenetic analysis classified these LbUSP members into four distinct groups, demonstrating the integration of the conserved USP domain and diverse motifs within each group. Collinearity analysis indicated a stronger synteny of LbUSPs with orthologs in Solanum lycopersicum than with other species (Arabidopsis thaliana, Vitis vinifera, and Oryza sativa), demonstrating that gene duplication coupled with functional conservation represented the primary mechanism underlying USP family expansion in L. barbarum. In silico promoter screening detected abundant cis-acting elements associated with abiotic/biotic stress responses (MYB and MYC binding sites), phytohormone regulation (ABRE motif), and growth/development processes (Box-4 and G-box). Transcriptome sequencing and RT-qPCR validation revealed tissue-specific differential expression patterns of LbUSP8, LbUSP11, LbUSP12, LbUSP23, and LbUSP25 in roots and stems under salt stress, identifying them as prime candidates for mediating salt resistance in L. barbarum. Our findings establish a foundation for the functional characterization of LbUSPs and molecular breeding of salt-tolerant L. barbarum cultivars. Full article

Background: Centella asiatica, a medicinally important species that is rich in bioactive compounds, lacks a characterized mitochondrial genome, despite nuclear and chloroplast assemblies. We sequenced and annotated its mitochondrial genome to elucidate its genetic foundations and evolutionary mechanisms. Methods: Assembly using Illumina short-reads and Nanopore long-reads was used to characterize the mitochondrial genome. Analyses included structural characterization, codon usage bias, repetitive sequences, horizontal gene transfer (HGT), collinearity, and phylogeny. The resulting tissue-specific (root, stem, and leaf) long non-coding RNA (lncRNA) profiles identified RNA editing sites. Results: The complete mitochondrial genome (249,777 bp, 45.5% GC) comprises three circular contigs encoding 51 genes (33 protein-coding, 15 tRNA, and 3 rRNA). Comparative genomics revealed synteny with the Apiaceae family of plants and evidence of HGT. Phylogenetic analysis resolved taxonomic relationships within Apiales. We predicted that 547 RNA editing sites would be identified in its protein-coding genes. Tissue profiling identified 725 (root), 711 (stem), and 668 (leaf) editing sites, with >71% concordance to predictions. RNA editing-generated cryptic promoters/terminators occur in mitochondrial core function genes (e.g., ATP synthase, cytochrome c reductase/oxidase, ribosome large subunit, and cytochrome c biogenesis), exhibiting a lower frequency in the leaves compared to the roots and stems. Conclusions: We provide the first complete mitochondrial genome assembly for C. asiatica, delineating its complex structure, tissue-modulated RNA editing, and evolutionary trajectory. This high-quality genomic resource establishes a foundation for molecular evolutionary studies and enhances the genomic toolkit for this pharmacologically significant species. Full article

Gastrodia elata Blume is an important medicinal orchid, yet its large-scale cultivation is increasingly threatened by fungal diseases. The 4-coumarate–CoA ligase (4CL) gene family directs a key step in phenylpropanoid metabolism and plant defence, but its composition and function in G. elata have not been investigated. We mined the G. elata genome for 4CL homologues, mapped their chromosomal locations, and analysed their gene structures, conserved motifs, phylogenetic relationships, promoter cis-elements and codon usage bias. Publicly available transcriptomes were used to examine tissue-specific expression and responses to fungal infection. Subcellular localisation of selected proteins was verified by transient expression in Arabidopsis protoplasts. Fourteen Ge4CL genes were identified and grouped into three clades. Two members, Ge4CL2 and Ge4CL5, were strongly upregulated in tubers challenged with fungal pathogens. Ge4CL2 localised to the nucleus, whereas Ge4CL5 localised to both the nucleus and the cytoplasm. Codon usage analysis suggested that Escherichia coli and Oryza sativa are suitable heterologous hosts for Ge4CL expression. This study provides the first genome-wide catalogue of 4CL genes in G. elata and suggests that Ge4CL2 and Ge4CL5 may participate in antifungal defence, although functional confirmation is still required. The dataset furnishes a foundation for functional characterisation and the molecular breeding of disease-resistant G. elata cultivars. Full article

SnRK kinases, central regulators of plant stress response, remain uncharacterized in Taxus—an ancient gymnosperm valued for paclitaxel production. This study aimed to identify the Taxus SnRK family and elucidate its functional roles. Specifically, we identified SnRK genes through genomic analysis and assessed tissue-specific expression via transcriptomics, while regulatory networks were deciphered using WGCNA. To overcome experimental constraints, a PEG-mediated protoplast transient expression system was developed using calli, followed by dual-luciferase assays. Consequently, 19 SnRK genes (2 SnRK1, 4 SnRK2, 13 SnRK3) were identified, with tissue-specific expression revealing TaSnRK1.2 upregulation under methyl jasmonate (MeJA) and in stress-resilient tissues (bark/root). Subsequently, WGCNA uncovered a bark/root-specific module containing TaSnRK1.2 with predicted TF interactions (TaGRAS/TaERF). Critically, homologous dual-luciferase assays demonstrated TaSnRK1.2 activates TaGRAS and TaERF promoters (4.34-fold and 3.11-fold induction, respectively). This study establishes the Taxus SnRK family and identifies TaSnRK1.2 as a hub integrating stress signals (e.g., MeJA) to modulate downstream TF networks, while the novel protoplast system enables future functional studies in this medicinal plant. Full article

Uncaria rhynchophylla, a medicinal plant extensively used in traditional Chinese medicine, is an important plant source of terpenoid indole alkaloids (TIAs), but the mechanism of TIA biosynthesis at molecular level remains unclear. Geraniol synthase (GES) serves as a crucial enzyme in catalyzing the formation of geraniol from geranyl pyrophosphate (GPP) in various plants, but the functional characterization of the GES gene in U. rhynchophylla has not been investigated. In this study, a GES was identified and characterized through genome mining and bioinformatic analysis. Functional validation was performed via a protein catalysis experiment, transient expression in Nicotiana benthamiana, and methyl jasmonate (MeJA) induction experiments. The full-length UrGES gene was 1761 bp, encoding a protein product of 586 amino acids with an estimated 67.5 kDa molecular weight. Multiple sequence alignments and phylogenetic analysis placed UrGES within the terpene synthase g (TPS-g) subfamily, showing high similarity to known GESs from other plants. Enzymatic assays confirmed that recombinant UrGES catalyzed GPP conversion to a single product of geraniol. The transient expression of UrGES resulted in geraniol accumulation in N. benthamiana, further confirming its function in vivo. UrGES expression was observed in leaves, stems, and roots, where leaves had the highest transcript levels. Moreover, MeJA treatment significantly upregulated UrGES expression, which positively correlated with an increase in alkaloid content. This study functionally characterizes UrGES as a geraniol synthase in U. rhynchophylla, contributing to the current knowledge of the TIA biosynthetic pathway. These findings may offer insights for future metabolic engineering aiming to enhance TIA yields for pharmaceutical and industrial applications. Full article

The genus Lysionotus belongs to the family Gesneriaceae and includes plants with both ornamental and medicinal value. However, genomic-level data on the genus remains scarce. Previous investigations of Lysionotus have predominantly centered on morphological classification, with only limited exploration of molecular phylogenetics. Comparative analysis of chloroplast genomes within the genus would provide valuable insights into the genetic variations and evolutionary patterns of Lysionotus plants. In this study, we present the analysis of 24 newly sequenced chloroplast genomes from Lysionotus-related members, including widely distributed and locally distributed species. The results showed that the 11 plastome sizes of widely distributed species ranged from 152,928 to 153,987 bp, with GC content of 37.43–37.49%; the 13 plastome sizes of locally distributed species ranged from 153,436 to 153,916 bp, with GC content of 37.43–37.48%. A total of 24 chloroplast genomes owned typical quadripartite structures, and the number of tRNA (36 tRNAs) and rRNA (4 rRNAs) were observed for all 24 genomes. However, the number of their protein-coding sequences (CDs) varied at individual levels. No contraction and expansion of IR borders, gene rearrangements, or inversions were detected. mVISTA and Pi showed inverted repeats (IR) region was more conserved than the single copy region, coding region was more conserved than the non-coding region. Additionally, the repeat sequences and codon usage bias of Lysionotus plastomes were also conserved. Our results offer a comprehensive understanding of the genetic differences among these species and shed light on their phylogenetic systematics. Full article

The genus Datura L. has pharmacological activities due to its source of bioactive compounds. The effects of bioactive compounds can vary depending on species, geographical location, and environmental conditions. The purpose of this review is to summarize the most recent progress and to provide a comprehensive overview of studies concerning genetic alteration and bioactive compounds in the genus Datura, based on Scopus publications between 2015 and 2025. Throughout history, the genus Datura (Solanaceae) contains nine species of medicinal plants. A key component of elucidating the diversification process of congeneric species is identifying the factors that encourage species variation. A comparative gene family analysis provides an understanding of the evolutionary history of species by identifying common genetic/genomic mechanisms that are responsible for species responses to biotic and abiotic environments. The diverse range of bioactive compounds it contains contributes to its unique bioactivity. Datura contains tropane alkaloids (such as hyoscyamine and scopolamine), datumetine, withametelin, daturaolone, and atropine. Several compounds have been isolated and refined for use in treating various conditions as a result of recent progress in therapeutic development. Daturaolone, for example, is used to treat certain neurological disorders. In addition to providing renewed opportunities for the discovery of new compounds, these advancements also provide insights into the genetic basis for their biosynthesis. Our discussion also includes pitfalls as well as relevant publications regarding natural products and their pharmacological properties. The pace of discovery of bioactive compounds is set to accelerate dramatically shortly, owing to both careful perspectives and new developments. Full article

This review highlights the critical role of chemotaxonomy in the identification, authentication, and discovery of bioactive compounds in medicinal plants. By analyzing secondary metabolites using techniques like UV spectroscopy, FTIR, HPLC, GC-MS, NMR, LC-MS-Qtof, and MALDI-TOF MS, chemotaxonomy ensures accurate plant identification, supporting the safe and effective use of plants in herbal medicine. Key secondary metabolites used in chemotaxonomic identification include alkaloids, flavonoids, terpenoids, phenolics, tannins, and plant peptides. Chemotaxonomy also facilitates the discovery of novel compounds with therapeutic potential, contributing to drug development. The integration of chemotaxonomy with genomics and proteomics allows a deeper understanding of plant biosynthesis and the mechanisms behind bioactive compound production. However, challenges due to variability in metabolite profiles and the lack of standardized methods remain, and future research should focus on developing global databases, improving standardization, and incorporating artificial intelligence and machine learning to enhance plant identification and bioactive compound discovery. The integration of chemotaxonomy with personalized medicine offers the potential to tailor plant-based therapies to individual genetic profiles, advancing targeted treatments. This review underscores chemotaxonomy’s importance in bridging traditional knowledge and modern science, offering sustainable solutions for medicinal plant use and drug development. Full article

Humulus lupulus L. (hop) is a multipurpose crop valued for its essential role in beer production and for its bioactive compounds with recognized medicinal properties. Otherwise, climate change represents a major challenge to agriculture, particularly impacting the cultivation of crops with stenoecious characteristics, such as hop. This highlights the urgent need to enhance crop resilience to adverse environmental conditions. The phytohormone abscisic acid (ABA) is a key regulator of plant responses to abiotic stress, yet the ABA signaling pathway remains poorly characterized in hop. Harnessing the publicly available hop genomics resources, we identified eight members of the PYRABACTIN RESISTANCE 1 LIKE ABA receptor family (HlPYLs). Phylogenetic and gene structure analyses classified these HlPYLs into the three canonical ABA receptor subfamilies. Furthermore, all eight HlPYLs are likely functional, as suggested by the protein sequence visual analysis. Expression profiling indicates that ABA perception in hop is primarily mediated by the HlPYL1-like and HlPYL8-like subfamilies, while the HlPYL4-like group appears to play a more limited role. Structure modeling and topology predictions of HlPYL1b and HlPYL2 provided insights into their potential functional mechanisms. To assess the physiological relevance of ABA signaling in hop, we evaluated the impact of exogenous ABA application during the ex vitro acclimatization phase. ABA-treated plants exhibited more robust growth, reduced stress symptoms, and improved acclimatization success. These effects were associated with reduced leaf transpiration and enhanced stomatal closure, consistent with ABA-mediated drought tolerance mechanisms. Altogether, this study provides the first comprehensive characterization of ABA receptor components in hop and demonstrates the practical utility of ABA in improving plant performance under ex vitro conditions. These findings lay the groundwork for further functional studies and highlight ABA signaling as a promising target for enhancing stress resilience in hop, with broader implications for sustainable agriculture in the face of climate change. Full article

Amomum villosum Lour., a perennial medicinal plant in the Zingiber genus, usually requires approximately 3–4 years of vegetative growth from seed germination to first fruiting, resulting in high initial investment costs and a prolonged revenue cycle, which pose significant challenges to the industry’s sustainable development. Our research team observed a distinct premature fruiting phenomenon in A. villosum. We investigated the regulatory mechanisms underlying premature fruiting in A. villosum by identifying the key differentially expressed genes (DEGs) and metabolic pathways governing the premature fruiting (Precocious) and typical plants (CK) of the ‘Yunsha No.8’ cultivar. Transcriptomic sequencing (RNA-seq) and bioinformatic analyses were performed using the DNBSEQ^TM platform. The sequencing generated 29.0 gigabases (Gb) of clean data, and 115,965 unigenes were identified, with an average length of 1368 bp. Based on the sequencing results, 1545 DEGs were identified. Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were annotated for these DEGs. This study identifies phytohormone signaling, carbohydrate and lipid metabolism, and polysaccharide degradation as critical pathways controlling premature fruiting in A. villosum. Six randomly selected DEGs were validated using real-time fluorescence quantitative polymerase chain reaction (RT-qPCR), and the results corroborated the transcriptome data, confirming their reliability. This study lays the foundation for the elucidation of the molecular mechanisms and metabolic pathways driving premature fruiting in A. villosum. Full article

Plant mitochondrial genomes exhibit extensive size variability and structural complexity. Here, we report the complete mitochondrial genome of Trichopus zeylanicus, an endemic medicinal plant from the Western Ghats. The mitochondrial genome was assembled using a combination of Illumina short-read and PacBio long-read sequencing technologies, followed by extensive annotation and comparative analysis. The circular mitogenome spans 709,127 bp with a GC content of 46%, encoding 32 protein-coding genes, 17 tRNAs, and three rRNAs. Comparative analysis with other monocot mitochondrial genomes revealed conserved gene clusters but also significant lineage-specific rearrangements. Despite genome size similarities, T. zeylanicus displayed marked divergence in gene order, suggesting that genome size does not necessarily correlate with structural conservation. The genome contains 6.7% chloroplast-derived sequences and 324 predicted RNA-editing sites, predominantly in the first and second codon positions. Phylogenetic analysis based on mitochondrial genes placed T. zeylanicus as a distinct lineage within Dioscoreales, supporting its evolutionary uniqueness. This work provides the first mitogenomic resource for Dioscoreales and advances our understanding of mitochondrial diversity and evolution in monocots. Full article

Paeonia ludlowii, a critically endangered species endemic to Tibet, China, possesses significant ornamental, culinary, and medicinal value. However, its mitochondrial genome remains understudied, limiting insights into its evolutionary mechanisms and constraining conservation genetics applications and molecular breeding programs. We present the first complete assembly and comprehensive analysis of the P. ludlowii mitochondrial genome. Most remarkably, we discovered that the P. ludlowii mitogenome exhibits an atypical dual-circular structure, representing the first documented occurrence of this architectural feature within the genus Paeonia. The assembled genome spans 314,371 bp and encodes 42 tRNA genes, 3 rRNA genes, and 31 protein-coding genes, with a pronounced adenine–thymine bias. This multipartite genome structure is characterized by abundant repetitive elements (112 functionally annotated SSRs, 33 tandem repeats, and 945 dispersed repeats), which potentially drive genome rearrangements and facilitate adaptive evolution. Analyses of codon usage bias and nucleotide diversity revealed highly conserved gene expression regulation with limited variability. Phylogenetic reconstruction confirms that P. ludlowii, P. suffruticosa, and P. lactiflora form a monophyletic clade, reflecting close evolutionary relationships, while extensive syntenic collinearity with other Paeonia species underscores mitochondrial genome conservation at the genus level. Extensive inter-organellar gene transfer events, particularly from chloroplast to mitochondrion, suggest that such DNA exchanges enhance genetic diversity and promote environmental adaptation. The discovery of the dual-circular architecture provides novel insights into plant mitochondrial genome evolution and structural plasticity. This study elucidates the unique structural characteristics of the P. ludlowii mitochondrial genome and establishes a crucial genetic foundation for developing targeted conservation strategies and facilitating molecular-assisted breeding programs for this endangered species. Full article

Hippophae rhamnoides subsp. sinensis is extensively found in China, where the annual precipitation ranges from 400 to 800 mm. It is the most dominant species in natural sea buckthorn forests and the primary cultivar for artificial ecological plantations. Additionally, it exhibits significant nutritional and medicinal value, making it a renowned eco-economic tree species. Despite extensive research into its ecological functions and health benefits, the mitochondrial genome of this widespread species has not yet been published, and knowledge of the mitochondrial genome is crucial for understanding plant environmental adaptation, evolution, and maternal inheritance. Therefore, the complete mitochondrial genome was successfully assembled by aligning third-generation sequencing data to the reference genome sequence using the Illumina NovaSeq 6000 platform and Nanopore Prometh ION technologies. Additionally, the gene structure, composition, repeat sequences, codon usage bias, homologous fragments, and phylogeny-related indicators were also analyzed. The results showed that the length of the mitochondrial genome is 454,489 bp, containing 30 tRNA genes, three rRNA genes, 40 PCGs, and two pseudogenes. A total of 411 C-to-U RNA editing sites were identified in 33 protein-coding genes (PCGs), with higher frequencies observed in ccmFn, ccmB, nad5, ccmC, nad2, and nad7 genes. Moreover, 31 chloroplast-derived fragments were detected, accounting for 11.86% of the mitochondrial genome length. The ccmB, nad4L, and nad7 genes related to energy metabolism exhibited positive selection pressure. The mitochondrial genome sequence similarity between H. rhamnoides subsp. sinensis and H. tibetana or H. salicifolia was 99.34% and 99.40%, respectively. Fifteen shared gene clusters were identified between H. rhamnoides subsp. sinensis and H. tibetana. Phylogenetically, the Rosales order showed close relationships with Fagales, Fabales, Malpighiales, and Celastrales. These findings provide fundamental data for exploring the widespread distribution of H. rhamnoides subsp. sinensis and offer theoretical support for understanding the evolutionary mechanisms within the Hippophae genus and the selection of molecular breeding targets. Full article

Plant triterpenoids are structurally diverse specialized metabolites with significant ecological, medicinal, and agricultural importance. Oxidosqualene cyclases (OSCs) catalyze the crucial cyclization step in triterpenoid biosynthesis, generating the fundamental carbon skeletons that determine their structural diversity and biological functions. Genome-wide identification of OSC genes was performed using bioinformatics tools, including HMMER and BLASTP, followed by phylogenetic analysis, gene structure analysis, conserved domain and motifs identification, cis-regulatory element prediction, protein–protein interaction analysis, and expression profiling using publicly available transcriptome data from UV-B treated A. annua six-week-old seedlings. We identified 24 AaOSC genes, classified into CAS, LAS, LUS, and unknown subfamilies. Phylogenetic analysis revealed evolutionary relationships with OSCs from other plant species. Gene structure analysis showed variations in exon–intron organization. Promoter analysis identified cis-regulatory elements related to light responsiveness, plant growth and development, hormone signaling, and stress response. Expression profiling revealed differential expression patterns of AaOSC genes under UV-B irradiation. This genome-wide characterization provides insights into the evolution and functional diversification of the OSC gene family in A. annua. The identified AaOSC genes and their regulatory elements lay the foundation for future studies aimed at manipulating triterpenoid biosynthesis for medicinal and biotechnological applications, particularly focusing on enhancing stress tolerance and artemisinin production. Full article

Berberine, a bioactive isoquinoline alkaloid derived from medicinal plants such as Berberis and Coptis species, shows significant promise for managing obesity and associated metabolic disorders. This review synthesizes evidence on its modulation of AMP-activated protein kinase (AMPK) signaling, gut microbiota composition, lipid metabolism, and adipokine networks, elucidating how these actions converge to suppress adipogenesis and improve insulin sensitivity. Metabolomic profiling reveals critical shifts in bile acid metabolism, short-chain fatty acid production, and mitochondrial function. Recent studies also highlight berberine’s anti-inflammatory effects and regulatory influence on glucose homeostasis. Despite its promise, challenges in oral bioavailability and drug interactions necessitate the development of advanced delivery strategies. We further discuss nanoformulations and multi-omics approaches, which integrate data from genomics, transcriptomics, proteomics, and metabolomics, provide new insights into berberine’s mechanisms, and may guide personalized therapeutic applications. While promising, further studies are needed to validate these findings in humans and translate them into effective clinical strategies. Full article