Search Results (717)

Agronomic practices and interannual climate variability significantly modulate the bioactive composition of agricultural by-products. This study evaluated the effects of farming systems (organic vs. conventional) and geographic locality across two harvest seasons (2022–2023) on the fatty acid (FA) profiles of peel and seeds from the “Mollar de Elche” pomegranate (Punica granatum L.) Protected Designation of Origin (PDO). Gas chromatography (GC-FID) analyses demonstrated that the harvest year, characterized by significantly reduced extreme temperature days in 2023, exerted a dominant, overriding effect on lipid biosynthesis compared to agronomic management. In the seeds, punicic acid was the unequivocal predominant FA, increasing dramatically from an average of ~75,700 mg/kg dry matter (DM) under severe heat stress (2022) to ~150,000 mg/kg DM under milder conditions (2023) (p < 0.001). In the peel, polyunsaturated fatty acid (PUFA) accumulation was strictly dependent on the interaction between localized geographic micro-conditions and climate, rendering the farming system a secondary factor. Crucially, the milder 2023 season significantly enhanced the unsaturated-to-saturated (U/S) ratio in both tissues and markedly improved cardiovascular lipid quality, lowering both the Atherogenic (AI) and Thrombogenic (TI) indices. These findings demonstrate that while organic farming can optimize lipid unsaturation under favorable climatic conditions, severe environmental stress nullifies these agronomic benefits, highlighting the need for climate-resilient strategies to valorize pomegranate by-products. Full article

The Cysteine-rich Polycomb-like Protein (CPP) gene family is a class of transcription factors containing conserved CXC domains that are widely involved in the regulation of plant growth and development, cell division, and stress responses. Based on the ginseng genome and transcriptome database, all members of the PgCPP gene family in Panax ginseng were systematically identified, and comprehensive bioinformatics analyses, including phylogenetic, conserved domain, chromosomal localization and collinearity, cis-acting element, and expression pattern analyses, were conducted. In this study, we identified 44 PgCPP gene family members in ginseng, which were unevenly localized on multiple chromosomes. The phylogenetic tree divided them into three subfamilies, with members in the same subfamily being highly conserved. Conserved domain analysis revealed that all PgCPPs contain typical CXC motifs. Cis-acting elements were abundant in light response, hormone responses (abscisic acid, methyl jasmonate, salicylic acid), and stress response elements. Expression heatmaps demonstrated that different members have specific expression patterns across different ages, tissues, and species. After treatment with MeJA, transcriptional suppression of PgCPP03-4 and PgCPP03-13 was observed, and their expression levels demonstrated significant negative correlations with the contents of six protopanaxadiol-type ginsenosides. These findings suggest that PgCPP03-4 and PgCPP03-13 may act as negative regulators of protopanaxadiol-type ginsenoside biosynthesis within the MeJA signaling pathway. This systematic characterization and identification of the CPP gene family members in P. ginseng establishes a foundational framework for future functional validation and molecular breeding initiatives. Full article

Furanocoumarins and their derivatives are found in various plant species and have attracted considerable attention due to their diverse biological activities. By analyzing the genomes of Apium Graveolens L. and Peucedanum praeruptorum Dunn, we characterized a set of candidate genes encoding key enzymes involved in furanocoumarin biosynthesis, including one prenyltransferase (AgPT1), cyclases (AgCOC1, PpCOC1 and PpCOC2), and methyltransferases (AgOMT1 and AgOMT2). Functional validation in Saccharomyces cerevisiae demonstrated that AgCOC1 and PpCOC2 accept both linear and angular substrates, whereas PpCOC1 accepts only linear substrates. Depending on the reaction conditions, these cyclases can produce compounds with either furan or pyran scaffolds. These findings reveal a previously unappreciated catalytic versatility of cyclases involved in furanocoumarin biosynthesis. Notably, the genes encoding the prenyltransferase and cyclases were found to be co-localized in the genome, which may significantly enhance the efficiency of furanocoumarin biosynthesis. This mechanism may account for the pronounced accumulation of furanocoumarins in Apiaceae plants. Finally, we provide the first evidence that AgOMT1 functions as a multifunctional methyltransferase capable of catalyzing the O-methylation modifications observed in furanocoumarins in A. graveolens. In conclusion, this study fills a research gap in our understanding of furanocoumarin biosynthesis and reveals that genes encoding cyclases and prenyltransferases are clustered in the genome, a pattern that arose during evolution. Full article

The Cytochrome P450 (CYP) superfamily plays an important role in the regulation of plant growth and development. However, the composition, evolutionary characteristics, and potential functions of CYPs in celery remain largely unexplored. Therefore, the objective of this study was to perform a genome-wide characterization of the Apium graveolens Cytochrome P450 (AgCYP) gene family and investigate its potential roles in seed development. In this study, a total of 227 AgCYPs were identified, and phylogenetic analysis classified them into six clades. Conserved motif and domain evaluations indicated that most AgCYP proteins possess conserved P450 domains. Chromosomal localization revealed an unequal distribution of AgCYPs across the 11 celery chromosomes. Duplicated AgCYP gene pairs were identified by synteny and Ka/Ks analyses, indicating that the duplicated AgCYPs have undergone strong purifying selection. Inter-genomic synteny analysis further reflects the closer relationship within Apiaceae. Analysis of cis-acting elements in the promoter regions identified an abundance of elements associated with light, hormone, and environmental stress. Moreover, AgCYPs showed stage-specific expression patterns and were correlated with monoterpene and phthalide accumulation during celery seed development, suggesting their potential functions in secondary metabolism in seed development. Treatment with exogenous auxin and its transport and biosynthesis inhibitors differentially induced distinct expression responses among AgCYPs, indicating their possible participation in auxin-related regulatory pathways. Moreover, candidate genes were selected. They exhibited diverse tissue-specific expression patterns and were potentially localized to the endoplasmic reticulum and interacted with some auxin-related proteins. In conclusion, this study provides the first comprehensive framework for understanding the functional diversification of AgCYPs in celery seeds, providing new insights into the evolutionary features and biological functions of the AgCYP gene family and establishing a foundation for future functional studies and molecular breeding applications. Full article

Strictosidine synthases (STRs) are catalytic enzymes involved in terpenoid indole alkaloid biosynthesis, whereas STR-like (STRL) genes in cereal crops remain poorly understood. Previous studies of the maize STR-like (STRL) gene family have mainly provided genome-wide identification, phylogenetic classification, structural annotation and expression profiling, but the evolutionary constraints and molecular mechanisms underlying STRL diversification remain insufficiently resolved. In this study, we investigated the maize STRL gene family from an evolutionary and structural perspective by integrating sequence divergence, codon usage bias, selection pressure, protein structural modelling, Gene Ontology (GO) enrichment and tissue-specific expression analysis. A total of 21 ZmSTRL genes were analyzed and their comparative and phylogenetic analyses revealed conserved lineages together with maize-associated expansion patterns. Codon usage and neutrality analyses indicated heterogeneous evolutionary constraints among ZmSTRL genes, suggesting that mutational pressure alone does not explain their sequence divergence. Protein conservation and three-dimensional structural modelling showed a generally conserved STR-related catalytic framework, while member-specific variation in terminal and loop regions suggested localized structural divergence. GO enrichment supported conserved catalytic and metabolic signatures, but these associations were interpreted as putative functional evidence rather than direct functional confirmation. Tissue-specific qRT-PCR analysis revealed divergent expression patterns among selected ZmSTRL genes in root, stem, leaf, and anther tissues, indicating possible regulatory specialization. Overall, this study provides an evolutionary-constraint-based framework for understanding STRL diversification in maize and identifies candidate genes and structural features for future functional validation. Full article

Laccases (EC 1.10.3.2, LAC) are copper-containing glycoproteins involved in lignin biosynthesis, and as such, they play important roles in plant development and stress responses. In this study, a genome-wide analysis of the LAC gene family was performed in Pinus massoniana (Chinese red pine), identifying 78 PmaLAC genes, all predicted to encode cell membrane-localized proteins. These genes were unevenly distributed across eight chromosomes, with notable clusters on chromosomes 7 and 8, indicating gene duplication-driven expansion in P. massoniana. Phylogenetic analysis revealed that PmaLAC genes are classified into five subfamilies, reflecting the lineage-specific expansion and evolutionary divergence of gymnosperm LAC genes. Conserved motif and gene structure analyses showed high conservation among PmaLAC proteins. Promoter analysis identified numerous cis-acting elements related to hormone signaling, stress, and light responses. RNA-seq analysis revealed distinct tissue-specific expression patterns for PmaLAC gene family members. Moreover, degradome analysis combined with dual-luciferase assays supported the interaction between miR397c-9 and PmaLAC31, suggesting that miR397c-9 negatively regulates PmaLAC31 and indicating a potentially conserved miRNA-mediated regulatory mechanism. Overall, this study provides a systematic overview of the composition, evolution, and potential regulation mechanisms of the PmaLAC gene family in P. massoniana, providing a useful resource for future functional characterization of PmaLAC genes. Full article

Sea cucumber Apostichopus japonicus is one of the few animals capable of synthesizing saponins, which are critical components of its nutritional quality and health-beneficial properties. However, the specific mechanism underlying saponin biosynthesis in sea cucumbers remains unclear despite previous investigations. This study aimed to characterize the molecular pathway and regulatory mechanism of saponin biosynthesis in A. japonicus. Thirteen candidate genes involved in de novo saponin skeleton synthesis were identified from the A. japonicus genome, and their full-length cDNAs were obtained via PCR-RACE. Sequence analysis predicted the intracellular localization of these genes. Combined in situ hybridization and quantitative real-time PCR analyses revealed their high expression in coelomocytes, indicating coelomocytes as the primary saponin synthesis sites. Knockdown of mevalonate kinase (AjMVK) and two oxidosqualene cyclases (AjPS and AjLS) caused a more obvious decrease in saponin levels, identifying them as key biosynthetic enzymes. Yeast two-hybrid assays revealed that AjPS and AjLS interact with ficolins, complement component 3-2, O-linked β-N-acetylglucosamine transferase, and α-L-fucosidase, whose regulatory effects were further validated by RNA interference and saponin content measurements. These results suggest that saponin biosynthesis in A. japonicus is regulated by the complement lectin pathway and modulated by glycosylation enzymes, providing a molecular foundation for enhancing bioactive saponin production for pharmaceutical and nutraceutical applications. Full article

The soybean aphid (Aphis glycines) and soybean cyst nematode (Heterodera glycines) are major aboveground and belowground pests of soybean (Glycine max) in the U.S. Midwest, but the molecular basis of their combined effects on soybean defense remains poorly understood. This study examines how soybean genotypes influence demographic and root-transcriptomic responses to single and combined pest infestation. Soybean cyst nematode reproduction increased under combined infestation in the susceptible cultivar but remained unchanged in the resistant cultivar, whereas soybean aphid populations declined when plants were also infested with nematodes. Root RNA-seq revealed strong time-dependent transcriptional responses, with substantially more differentially expressed genes at 30 days post-infestation than at 5 days post-infestation. Co-expression and enrichment analyses showed that early responses were associated with defense signaling, plant–pathogen interaction, and cutin, suberin, and wax biosynthesis, whereas later responses involved redox processes, isoflavonoid biosynthesis, phenylpropanoid metabolism, and one-carbon metabolism. Several differentially expressed soybean genes co-localized with known soybean cyst nematode resistance quantitative trait loci, including genes near the rhg1 region. Together, these results suggest that soybean genotypes strongly influence soybean aphid–soybean cyst nematode interactions and identify candidate genes and pathways that may contribute to durable resistance against interacting aboveground and belowground pests. Full article

For over 3000 years, the perennial herb mugwort (Artemisia argyi) has served as a cornerstone of traditional Asian medicine. Its clinical efficacy is driven by a diverse array of specialized metabolites, most notably flavonoids and volatile oils. While B-box (BBX) transcription factors are known to dictate photomorphogenic development and secondary metabolic pathways in plants, this specific gene family has not yet been systematically analyzed in A. argyi. Leveraging a chromosome-level genomic assembly, we comprehensively identified and analyzed the complete repertoire of AarBBX genes, profiling their structural organization, physicochemical attributes, conserved motifs, promoter architecture, and spatial expression dynamics. The AarBBX family segregates into five distinct evolutionary clades and comprises 114 members, exceeding the gene counts in the diploid relatives Artemisia annua (27) and Arabidopsis thaliana (32), a numerical increase potentially attributable to the tetraploid genome architecture of A. argyi. Promoter scanning revealed a high density of cis-acting elements linked to light perception and environmental stress responses. Integrating RNA-seq transcriptomics with tissue-specific expression profiling, we identified prominent candidate light-responsive AarBBX genes that are highly active in green, photosynthetic tissues and acutely responsive to shifts in light conditions, providing a foundation for future exploration of their potential relationship with secondary metabolic pathways, including flavonoid and terpenoid biosynthesis. Furthermore, we validated the potential operational compartments and structural interactions of these proteins utilizing green fluorescent protein (GFP) subcellular localization and yeast two-hybrid (Y2H) screenings. Collectively, these findings provide new insights into the evolutionary trajectory and regulatory potential of the B-box (BBX) proteins in A. argyi, offering a prioritized candidate gene set for subsequent investigations into their potential roles in light-regulated secondary metabolism, including flavonoid and terpenoid pathways. Full article

Relict yew plants (Taxus L.) are not only ornamental plants with valuable wood but also have the ability to synthesize the unique compound taxol, which is successfully used in the treatment of cancer due to its powerful cytotoxic effect. Due to the presence of taxol, all parts of yew plants are extremely poisonous, but there have been cases where animals have eaten yew cones without fatal consequences. The biosynthesis of taxol is carried out due to the interaction of the isoprenoid and phenolic pathways of the secondary metabolism of plants. Despite the close attention of researchers to the peculiarities of taxol metabolism, there is very little data on the tissue and intracellular localization of both taxols and phenolic compounds in yew plants. Polyphenols are known to be physiologically active mediators involved in respiration, photosynthesis, plant growth and development, as well as in the process of in vitro dedifferentiation. Since Taxus is a relict species and has a limited and hard-to-reach range in nature, technologies that allow yew plants to be restored without removing plant material from the natural environment are of great practical importance: overcoming deep physiological dormancy of seeds, microclonal reproduction and initiation of plant growth. In vitro cultures are possible sources of biologically active and medicinal products. The aims and objectives of this study are to determine the characteristics of the formation and localization of phenolic compounds with high biological activity in various organs of plants of the genus Taxus and to determine the biological activity of ethanolic extracts from this plant. The objects of this study were the generative organs of Taxus canadensis, collected during the entire growing season (April–October) from plants growing in the Moscow region. The localization of various classes of polyphenols was determined by histochemical methods using light microscopy. Histochemical studies have shown the abundant presence of polyphenols in yew megastrobiles, microstrobiles, cones, seeds and aril. Ethanolic plant extracts were used to determine the biological activity. Flavans were dominant in the aril at various stages of vegetation, which was confirmed by our biochemical and histochemical studies. Extractive substances of T. canadensis show high antibacterial activity, especially in its shoot extracts. Ethanolic extracts from plant shoots showed greater biological activity than seed extracts. Aril extracts had the lowest cytotoxicity. Full article

Strigolactones (SLs), as a class of novel plant hormones, play important roles in the regulation of plant branching. However, their function in branch development of wintersweet remains unclear. In this study, a gene involved in SLs biosynthesis, CpD27, was identified and isolated from wintersweet. The sequence characteristics, expression patterns, subcellular localization, and functional analysis through heterologous expression in Arabidopsis thaliana were investigated. Multiple sequence alignment showed that CpD27 contains the conserved D27 protein domain DUF4033. Quantitative real-time PCR analysis revealed that CpD27 is expressed in various vegetative organs of wintersweet, with the highest expression in leaves, followed by axillary buds. It is also expressed in all floral organs, with the highest expression level in the outer petals. CpD27 expression is induced by hormones (ABA and ACC) and low temperature (4 °C). Subcellular localization analysis indicated that CpD27 is localized in the chloroplasts of Arabidopsis. Heterologous expression of CpD27 in Arabidopsis delayed bolting. The number of both rosette branches and cauline branches in transgenic plants was reduced compared with wild-type plants. In addition, the expression of AtBRC1 was significantly upregulated in transgenic lines, suggesting that CpD27 has a function similar to that of its homolog in Arabidopsis. Overall, these results indicate that CpD27 plays a conserved role in the SLs-mediated branching pathway, which regulates branch development in wintersweet. This study provides a molecular and theoretical basis for further understanding branch development in wintersweet. Full article

1-Deoxy-D-xylulose-5-phosphate synthase (DXS) serves as the initial rate-limiting enzyme in the methylerythritol phosphate (MEP) pathway, governing the biosynthesis of precursors for photosynthetic pigments and terpenoids. In this study, the LaDXS2-2 gene was cloned and functionally characterized in lavender (Lavandula angustifolia). The full-length coding sequence (CDS) of LaDXS2-2 spans 2178 base pairs, encoding a protein of 725 amino acids. Phylogenetic analysis revealed that LaDXS2-2 is most closely related to the DXS from Salvia miltiorrhiza. Expression profiling demonstrated that LaDXS2-2 was highly expressed in flower buds, and its transcript levels were significantly upregulated (p < 0.05) in response to ethephon, high light intensity, and low temperature, while exhibiting tissue-specific responses to gibberellin application. Subcellular localization assays confirmed LaDXS2-2 is targeted to the chloroplast. Heterologous overexpression of LaDXS2-2 in tobacco resulted in a marked increase in photosynthetic pigment content, enhanced the actual photochemical efficiency of photosystem II [Y(II)], and reduced non-photochemical quenching (NPQ). Integrated transcriptomic and metabolomic analyses further revealed that LaDXS2-2 overexpression activated the diterpenoid biosynthesis pathway and upregulated amino acid metabolism as well as the TCA cycle, while competitively suppressing phenylpropanoid and flavonoid biosynthesis pathways. These findings indicate that LaDXS2-2 not only enhances photosynthetic efficiency by promoting the synthesis of photosynthetic pigments but also suggests a potential role in influencing primary carbon and nitrogen metabolism, as inferred from transcriptomic and metabolomic data. This functionality may ultimately influence plant growth and metabolic homeostasis. Overall, this study provides a theoretical foundation for the synergistic improvement of photosynthetic efficiency and secondary metabolism in crops. Full article

Background: Uridine diphosphate glucose (UDP-Glc) is one of the key substrates for the biosynthesis of gallotannins in plants. UDP-glucose dehydrogenase (UGD) catalyzes the irreversible oxidation of UDP-Glc to UDP-glucuronic acid (UDP-GlcA), thus affecting the biosynthesis and accumulation of gallotannins in the Chinese gallnut. Methods and Results: In this study, we identified three members of the RcUGD family from the Rhus chinensis genome. Protein sequence alignment revealed that all three RcUGDs possess the conserved NAD⁺ coenzyme binding motif GAGYVGG and the catalytic motif GFGGSCFQKDIL. qRT-PCR analysis revealed that the expression levels of RcUGD3 in stem and root tissues were respectively 10-fold and 13-fold greater than that in the leaves, in which gallotannin accumulation was higher. RcUGD3 expression level declined by 63% during early (24 d) gallnut development, suggesting an inverse relationship between RcUGD3 expression level and gallotannin biosynthesis. In addition, subcellular localization analysis using the tobacco transient transformation system showed that RcUGD proteins are broadly distributed throughout the cell. Moreover, an in vitro enzyme activity assay indicated that the recombinant RcUGD3 protein catalyzed UDP-Glc to produce UDP-GlcA as shown by HPLC. Taken together, our results suggested that RcUGD3 protein is responsible for UDP-Glc degradation and probably plays a regulatory role in gallotannin biosynthesis in the Chinese gallnut. Conclusions: This study lays a foundation for further elucidating the function and expression regulation mechanism of the RcUGD gene family and provides new insights for the super-accumulation mechanisms of gallotannins in Chinese gallnuts. Full article

Background: Anthocyanin biosynthesis is tightly controlled by MYB transcription factors, yet the role of repressors, particularly those in the DIVARICATA-like (DIV) subfamily, remains poorly characterized. Methods: A genome-wide identification of MYB family members was performed in the mulberry (Morus atropurpurea) genome using a hidden Markov model and BLAST-based searches. Putative MYB genes were phylogenetically classified, and their expression profiles were analyzed across three fruit developmental stages. A DIV-like R2R3-MYB candidate, MaDIV, was functionally characterized via subcellular localization, quantitative real-time PCR, and heterologous overexpression in tobacco. Results: A total of 145 MaMYB genes were identified and classified into 31 distinct subfamilies. MaDIV expression showed a progressive decline during fruit ripening, which significantly correlated with increasing anthocyanin accumulation. Heterologous overexpression of MaDIV in tobacco led to a 42% reduction in floral anthocyanin content compared with wild-type plants. Concomitantly, the expression of the key anthocyanin biosynthetic gene NtDFR was strongly suppressed, whereas the flavonol synthase gene NtFLS1 was significantly upregulated. Conclusions: These findings point to a possible involvement of MaDIV in the regulation of anthocyanin biosynthesis and provide preliminary evidence for the functional diversification of the DIV-like MYB subfamily in plants. The results contribute to a better understanding of the transcriptional control of fruit pigmentation in mulberry and related species. Full article

Cellulose is the strongest cell wall polymer defining plant cell shape and growth, and the most abundant biopolymer on the Earth. Its synthesis by the plasma membrane (PM)-localized cellulose synthase complexes (CSCs) depends on surrounding lipids that establish the membrane microenvironment in which CSCs work and form vesicles delivering and removing CSCs to and from the PM by exo- and endocytosis. The role of exact lipid molecular species in these processes is poorly understood. In the present work we used hypocotyls of etiolated wild-type Col-0 and mutant ixr1-1 Arabidopsis thaliana seedlings grown with or without isoxaben, a specific cellulose synthesis inhibitor, as a model to reveal lipid molecular species associated with cellulose biosynthesis. Different lipid classes were separated by thin-layer chromatography (TLC) and their molecular species were analyzed by liquid chromatography–triple quadrupole tandem mass spectrometry (LC-QqQ-MS/MS). A total of 250 lipid molecular species were identified. Col-0 plants maintained stable levels of membrane glycerophospholipids but displayed significant remodeling of their acyl chains. In the presence of isoxaben, they accumulated three times more phosphatidic acids, a hallmark of a stress response. The isoxaben-resistant mutant ixr1-1 was characterized by a higher relative content of phosphatidylethanolamines, potentially rendering membranes more labile, as well as plastid galactolipids, which accumulated under isoxaben treatment. The multifaceted effects of isoxaben, including its impact on endomembrane lipids, suggest that it has additional binding sites beyond CSC. Full article