Search Results (168)

Abiotic stresses—drought, salinity, extreme temperature, flooding, and heavy-metal toxicity—constrain rice (Oryza sativa L.) yield worldwide, and the cellular programmes underlying them are unevenly distributed across cell types that bulk-tissue assays average together. This review examines, from a methodological standpoint, what single-cell and spatial omics technologies can and cannot establish about rice abiotic stress biology. We first define the modality space: single-cell omics measures RNA, chromatin accessibility, DNA methylation, protein, or metabolite features at the resolution of individual cells or nuclei, whereas spatial omics measures such features while retaining tissue coordinates; the two are complementary rather than interchangeable. We then treat each platform class—droplet-based scRNA-seq, combinatorial-indexing approaches including SPLiT-seq, nuclei-based snRNA-seq and multiome, sequencing-based and imaging-based spatial transcriptomics—under a common template covering measurement principle, the questions each can answer, applicability to rice tissues, dominant biases, and the inferences each cannot support. To make evidence strength comparable across a heterogeneous literature, we apply a four-tier scheme throughout: Tier A, direct rice cell-resolved or spatial evidence with functional or field validation; Tier B, robust rice functional and localization evidence without single-cell data; Tier C, cell-resolved evidence without causal validation; and Tier D, cross-species analogy or reasoned proposal. Applying this scheme shows that the genes with genuine breeding traction in rice—SUB1A, OsHKT1;5, OsHMA3, OsNRAMP5, DRO1—rest on Tier B evidence from classical genetics and field testing, whereas the most cell-resolved rice evidence concentrates in root outer layers and barrier formation at Tier C, and heat and cold stress, despite dominating yield loss, lack rice cell-resolved data almost entirely. We extend the discussion beyond transcriptomics to single-cell DNA methylome profiling, spatial proteomics and metabolomics, and three-dimensional analysis of thick plant tissues, in each case distinguishing demonstrated plant capability from mammalian-only capability, and we assess the expanding role of artificial intelligence in annotation, segmentation, batch correction, integration, and perturbation prediction alongside its documented failure modes. Rice, maize, and wheat are compared to identify transferable methodology. Cell-resolved omics has to date improved biological interpretation and candidate prioritization; demonstrating an incremental breeding advantage from it remains an unmet requirement. Full article

Somatic embryogenesis (SE)—the reprogramming of somatic cells to follow an embryogenic pathway—remains inefficient in the tropical monocot areca palm (Areca catechu L.) due to poorly understood constraints on cell fate transition. Using single-factor and orthogonal experiments, we investigated how plant growth regulators (PGRs), nitrogen source, and carbon supply regulate the acquisition of embryogenic competence. The optimal condition (Y3 medium + 6-BA + TDZ + 30 g/L sucrose) yielded a somatic embryo induction rate of 48.62%, more than six-fold higher than that of the unoptimized control. Cytologically, embryogenic callus consisted of small, densely cytoplasmic cells with large, centrally positioned nuclei with decondensed chromatin (i.e., loosely packed, transcriptionally active chromatin) and minimal vacuolation—hallmarks of meristematic, embryogenic-competent cells—whereas non-embryogenic callus contained large, highly vacuolated irregular cells. Histological tracking revealed that areca somatic embryos faithfully recapitulate the zygotic developmental program, including bipolarity establishment and procambium differentiation. Mechanistically, we show that the 6-BA + TDZ combination likely acts by inducing endogenous auxin synthesis; moderate ammonium supply (Y3 medium, NO₃⁻/NH₄⁺ ratio 3.6:1) minimizes browning; and 30 g/L sucrose provides optimal energy supply and osmotic regulation. This optimized SE system establishes a tractable model for studying somatic cell reprogramming in a woody monocot. Full article

Calcineurin B-like (CBL) proteins are plant-specific calcium sensors critical for ion homeostasis and stress tolerance. Here, seven MdCBL genes were genome-wide identified in apple (Malus domestica). We conducted systematic bioinformatic profiling of their physicochemical features, subcellular localization, cis-regulatory elements, phylogeny, secondary structures, phosphorylation sites, and functional annotations and further verified the salt-stress regulatory function of MdCBL5 via transgenic tests. MdCBL proteins contain 210–246 amino acids, with molecular weights of 24,196.73–28,283.39 Da, pI values of 4.63–4.97 and instability indices of 37.12–49.20. Localization prediction placed these proteins in nuclei, cytosol and chloroplasts. Their promoter regions are rich in hormone-responsive (auxin, ABA, salicylic acid) and stress-responsive (cold, drought, salt) cis-elements. Phylogenetic clustering divided MdCBLs into five subgroups (A–E) with high homology to Arabidopsis CBLs. Random coils and α-helices dominate their secondary structures, and serine residues constitute most phosphorylation sites. Functional annotation supports their involvement in calcium signaling, ion transport and diverse stress adaptation. Salt stress experiments have confirmed that MdCBL5 may enhance apple salt resistance by promoting MdSOS gene expression. Meanwhile, transient transformation in apple fruit showed that MdCBL5 can effectively enhance fruit quality traits. Collectively, this study establishes a theoretical foundation for further elucidating the biological functions of the apple MdCBL5 gene and provides valuable insights for genetically improving stress resistance and fruit quality in apple via molecular breeding strategies. Full article

The size of the mitogenome varies greatly in angiosperms from different species, but the causes of expansion remain unclear. Species from the Zingiberaceae family often carry exceptionally large mitogenomes, where this phenomenon can be readily studied. C. kwangsiensis is a medicinal plant that is native to Guangxi, China, and it is traditionally used to treat blood stasis and gynecological conditions. We assembled its complete mitogenome by using the Illumina and Nanopore reads obtained from its analysis. The genome comprises 12 circular contigs with a multi-branched structure, totaling 7.76 Mb. It contains 39 protein-coding genes, 30 tRNAs (transfer RNAs), three rRNAs (ribosomal RNAs), and 652 C-to-U RNA edited sites. Repeated analysis revealed that the dispersed repeats are the major contributors to genome expansion. Comparisons with two other Zingiberaceae mitogenomes suggested that the large genome arose in a common ancestor rather than from a whole-genome duplication, with little contribution from DNA transfers from the chloroplasts and nuclei. Thus, the exceptionally large mitogenome of Curcuma appears to result largely from repeated accumulation in the non-coding regions, such as nuclear genome expansion in angiosperms. This finding also highlights the conservation of core mitochondrial genes. Our work provides new insights into mitogenomic size variations and gene conservation in plant species, including Zingiberaceae. Full article

P. massoniana is an important native economic and ecological tree species in southern China, where seasonal drought has emerged as a critical factor limiting its productivity. The SAUR gene family, recognized as core early auxin-responsive genes, plays a crucial role in balancing plant growth, development, and stress adaptation; however, research related to this family in conifers remains limited. Utilizing the chromosome-level genome of P. massoniana, this study identified 73 SAUR genes (PmSAUR1~73) through bioinformatics methods, systematically analyzing the physicochemical properties of the encoded proteins, chromosomal localization, phylogenetic relationships, gene structures, and cis-acting elements. Combined with transcriptome sequencing and molecular experiments, the drought stress response patterns of these genes were further elucidated. The results indicated that PmSAUR genes predominantly encode alkaline proteins, primarily localized in mitochondria and nuclei, with an uneven distribution across nine chromosomes, where tandem duplication serves as the primary mechanism driving family expansion. Phylogenetic analysis classified these genes into seven subfamilies, which include both conserved clades homologous to angiosperms and branches specific to P. massoniana. All members contain the Auxin_inducible conserved domain, with motif1 identified as the core essential motif. Promoter regions were enriched with MeJA (methyl jasmonate)-responsive (56%), ABA-responsive, and drought stress-related cis-elements. Under drought stress, 38 PmSAUR genes exhibited diverse temporal expression patterns. Four key genes (PmSAUR14, PmSAUR28, PmSAUR54, and PmSAUR73), which are localized in the nucleus and exhibit high expression specifically in male cones or roots, were identified. These genes exhibit an expression pattern consistent with an auxin-negative response (i.e., repressed by IAA and induced by drought) and display a distinctive response pattern characterized by drought-induced upregulation coupled with IAA-mediated downregulation. This mechanism may contribute to the drought adaptation strategies of P. massoniana, involving regulatory processes for aboveground reproduction and adaptation of the underground root system. This study represents the first effort to elucidate the evolutionary characteristics and drought response patterns of the SAUR gene family in P. massoniana, thereby addressing the existing research gap regarding the functions of SAUR genes in coniferous trees. Furthermore, it offers candidate gene resources and theoretical support for the molecular breeding of stress resistance in P. massoniana. In addition, two auxin-induced SAUR genes (PmSAUR22 and PmSAUR37) were identified as contrasting examples, but the main focus of this study is on the four auxin-repressed genes. Full article

An evaluation of plant ploidy is an important task in breeding and biotechnology. Current methods of ploidy assessment (flow cytofluorometry and microscopy) are time-consuming and costly, and not applicable to real-world agricultural conditions. We developed an automated method for ploidy assessment based on fluorescence microscopy, which aims to accelerate and reduce the cost of plant ploidy analysis. The method is based on the automated selection of plant nuclei in fluorescence micrographs, followed by analysis of nuclear area, fluorescence intensity of the Hoechst DNA-binding probe, and nuclear geometry (circularity, roundness, solidity). The study was conducted on monocotyledonous and dicotyledonous plants with known genome sizes. Triticum aestivum Wt (6n, hexaploid) and Temp (4n, tetraploid) are monocotyledonous, and Capsella bursa-pastoris (4n, tetraploid) and Capsella rubella (2n, dT/iploid) are dicotyledonous. A simple fluorescent staining protocol combined with automated analysis using our ImageJ macro enables reliable separation of both monocotyledonous and dicotyledonous plants by genome size with an accuracy close (for dicots) or comparable (for monocots) to flow cytofluorometry. For ploidy separation in monocots, the most sensitive parameters are fluorescence intensity, nucleus area, and circularity. For ploidy separation in dicots, the most sensitive parameters are nucleus area, fluorescence intensity, and circularity. Full article

Drought frequently threatens the yield and quality of Carya cathayensis Sarg. cultivated in mountainous regions. To search for effective drought-resistant regulators is of great significance for alleviating short-term seasonal drought in C. cathayensis during dry seasons, thereby stabilizing its yield and quality. Silicon dioxide nanoparticles (SiO₂ NPs) mitigate abiotic stress in plants. To give insight into the regulatory role of SiO₂ NPs in mitigating drought stress, polyethylene glycol 6000 (PEG-6000) was used to simulate varying degrees of drought conditions, and the growth phenotype, photosynthetic physiological characteristics, antioxidant defense system, and cellular ultrastructure of C. cathayensis leaves were analyzed to evaluate the impacts of foliar-applied exogenous SiO₂ NPs. The results indicated that, compared with severe drought, 200 mg/L SiO₂ NP application to plants under severe drought treatment significantly increased superoxide dismutase and peroxidase activities and chlorophyll and nitrogen contents, while malondialdehyde levels decreased. Furthermore, SiO₂ NP application notably enhanced the net photosynthetic rate, stomatal conductance, and electron transport efficiency. This effectively alleviated both stomatal and non-stomatal limitations, thereby mitigating drought-induced photosynthetic inhibition. Additionally, Transmission electron microscopy revealed that SiO₂ NPs effectively preserved the structural integrity of chloroplasts, mitochondria, and nuclei, reducing drought-induced ultrastructural damage. In conclusion, exogenous SiO₂ NPs enhance drought tolerance in C. cathayensis by synergistically modulating photosynthesis, antioxidant defense, and cellular structural stability. Full article

Nitrogen (N) is an essential macronutrient for plant growth. NIN–like protein (NLP) transcription factors play important roles in nitrate signaling and response in plants. However, a comprehensive analysis of the NLP gene family in sorghum is still lacking. In this study, we identified five NLP genes in sorghum, and a high collinearity of NLP was detected in sorghum, rice and maize. N deficiency decreased SbNLP3 and SbNLP4 expression levels in roots, and the expression of SbNLP1 and SbNLP2 declined in roots during nitrate resupply. Subcellular localization analysis revealed that SbNLP1 was mostly detected in nuclei and cytoplasm. Compared with wild–type rice ZH11 plants, SbNLP1 overexpression plants showed improved low nitrogen (LN) tolerance, with longer roots and shoots under LN conditions. Transcriptome analysis between overexpression lines OE1–5 and ZH11 showed that 773 and 967 differentially expressed genes (DEGs) were identified in roots and shoots under LN conditions, respectively. In contrast, 674 and 1283 DEGs were identified in roots and shoots under normal nitrogen (NN) conditions, respectively. Thirty–seven N–related DEGs were identified in roots through GO enrichment under LN conditions, and terms of plant hormone signal transduction, biosynthesis of secondary metabolites and plant–pathogen interaction were identified through KEGG enrichment. WGCNA analysis also revealed plant hormone signal transduction pathways and plant pathogen interaction pathways in OE1–5 under LN conditions. These results provide a basis for N use efficiency (NUE) improvement in sorghum and functional analysis of SbNLPs. Full article

Background: Malva sylvestris (the common mallow) is an herbaceous species widely used in ethnobotanical practices to treat gastrointestinal, hepatic and urinary inflammation. Objectives: Despite these beneficial effects on human health, the antineoplastic potential of this plant has not yet been fully explored. Thus, in the present study, two human colon cancer cell lines (i.e., HCT-116 and Caco-2) were treated with an extract obtained from M. sylvestris flowers (MFE), whose composition in terms of phytochemicals and microRNAs has been recently published by our research group, to explore its potential bioactivity. Methods/Results: MTT and Trypan blue assays demonstrated that MFE reduced tumour cell growth without causing significant cytotoxicity or apoptosis. Following the diphenylboric acid 2-aminoethyl ester-induced fluorescence of some plant metabolites, microscopy analysis proved that MFE components crossed the cell membranes, accumulating into nuclei. Wound assay and transwell tests documented that MFE was also able to reduce cell motility and invasiveness. In both cell lines qPCR experiments demonstrated that MFE caused the over-expression of factors, like VIMENTIN and E-CADHERIN, which negatively influence epithelial–mesenchymal transition in colon cancers. However, the effects of MFE appeared to be time-, dose- and cell type-dependent. In fact, the treatment induced senescence in P53-null Caco-2 cells (i.e., ROS, β-galactosidase and P21^WAF1/Cip1) and a premise of differentiation (i.e., P27^Kip1) in P53-wild-type HCT-116 cells, also via the CDK2/c-MYC/AKT axis, justifying its antiproliferative property. In parallel, the transfection of tumour cells with pure synthetic miR160b-5p—a microRNA identified in M. sylvestris flowers and predicted to target the human CDK2 transcript—resulted in gene silencing, thereby suggesting its central role in mediating the cross-kingdom effects of MFE on the investigated cancer models. Conclusions: Overall, these findings open new perspectives on the common mallow as a source of potential antimetastatic compounds and on the possible use of its plant microRNAs in the development of gene therapies. Full article

Pepper (Capsicum annuum), a widely cultivated vegetable of significant economic importance globally, is frequently subjected to attacks from pathogens such as Ralstonia solanacearum, as well as high-temperature stress. However, the mechanisms by which pepper combats these stresses remain poorly understood. Herein, we reported that the expression of the leucine-rich repeat protein CaLRR13, which lacks a nucleotide-binding site (NBS), kinase domains, and a transmembrane region, was transcriptionally activated by both R. solanacearum inoculation and high-temperature stress. Through transient overexpression in the epidermal cells of Nicotiana benthamiana leaves, we found that CaLRR13 localized in both the cytoplasm and the nuclei. Reducing the expression of CaLRR13 via virus-induced gene silencing (VIGS) increased the sensitivity of pepper to R. solanacearum infection and high-temperature exposure, accompanied by reduced expression of immunity- and thermotolerance-related genes, including CaWRKY40, CaPR1, CaNPR1, CaDEF1, and CaHSP24. In contrast, transient overexpression of CaLRR13 in pepper leaves induced a like-hypersensitive response (HR) and enhanced the expression of the aforementioned immunity- and thermotolerance-related genes. Thus, we conclude that CaLRR13 plays a positive role in pepper immunity against R. solanacearum and thermotolerance, providing a new perspective on the crosstalk and management of plant responses to these two stresses. Full article

Background/Objectives: Recent studies have revealed that plants produce lipid-derived microvesicles with potent anti-inflammatory properties. In turmeric (Curcuma longa L.), such microvesicles have been identified in rhizome juice and shown to exert beneficial effects in murine models of colitis. In this study, we investigated whether turmeric extracts commonly used in phytotherapy (30% ethanolic or aqueous extracts, and freeze-dried or spray-dried preparations) contain Curcuma-derived microvesicles (CuMVs), and we evaluated the influence of extraction processes on their aggregation and morphology. Methods: All extracts were processed using a standardized protocol involving differential centrifugation, filtration, and ultracentrifugation. CuMVs with sizes from 50 to 200 nm were detected in all pellets, but CuMVs from dehydrated extracts were markedly aggregated compared to those from liquid preparations. Results: The 30% ethanolic extract yielded the most polydisperse CuMVs and was therefore selected for functional immunomodulatory analyses on macrophages. Protein quantification indicated that 600 mL of 30% ethanolic extract contained approximately 60 µg of CuMVs which contained curcumin and its derivatives demethoxycurcumin (DMC), and bisdemethoxycurcumin (BDMC) identified by high-performance thin-layer chromatography (HPTLC). Green fluorescence in the form of small dots close to the nuclei was detected in recipient THP-1 macrophages, indicating the incorporation of CuMVs and therefore the transfer of the naturally fluorescent curcumin. CuMV treatment reduced ROS production, downregulated CD86, and upregulated CD163 expression. Furthermore, CuMVs increased the expression of IL-10 and TGF-β, as well as antibacterial cytokines (IL-1β, IL-6, and TNF-α), and enhanced RAW macrophage migration. Depletion of CuMVs from turmeric extracts markedly reduced their immunomodulatory effects. Conclusions: Collectively, these findings emphasize the importance of preserving CuMVs during the industrial processing of turmeric, as they play a crucial role in curcuminoid delivery and in mediating the immunomodulatory properties of turmeric extracts. Full article

As reported in earlier work, when a pea apyrase, psNTP9 (PS), and a modified version of it, psNTP9-DM (DM), are expressed in Saccharomyces cerevisiae, they localize to nuclei, binding to largely non-overlapping promoter regions of chromatin. PS- and DM-expressing yeast also exhibit different expression profiles for potentially regulated target genes, consistent with observed phenotypes. In the present study, we use ChIP-seq assays to show that PS and DM also associate with largely different promoter regions of Arabidopsis genes, with similar non-overlapping expression profiles for potential target genes. Functional studies, using electrophoretic mobility shift assays (EMSA), verified PS-specific binding to yeast or plant promoter binding sites. DM binding to both heterologous dsDNA and to PS-specific binding site sequences was minimal. AlphaFold3 modeling of PS protein binding to a yeast PHM6 promoter sequence identified potential DNA-binding residues and a potential binding site motif (5′-(G/T)GG(G/T)A-3′) that is also present in two Arabidopsis promoter binding sites. These novel findings extend the previously known functions of PS and other plant apyrases in the Golgi or extracellular matrix, and support their potential function as DNA-binding proteins that can regulate gene expression in both yeast and Arabidopsis. Full article

Background/Objectives: Cerebral ischemia and reperfusion injury, induced by bilateral common carotid artery occlusion and reperfusion (BCCAO/R), cause extensive neuronal damage and cognitive impairment. Bouvardia ternifolia (BtD), a plant known for its anti-inflammatory and neuroprotective effects, may offer therapeutic benefits against ischemic injury. This study aimed to evaluate the neuroprotective effects of BtD root extract on neuronal integrity, oxidative stress, and p53 protein expression following global cerebral ischemia in rats. Methods: Adult male Sprague Dawley rats were subjected to the BCCAO/R procedure for 60 min, followed by six days of reperfusion. Experimental groups included BCCAO/R+BtD, BCCAO/R+silymarin (reference control), BCCAO/R+vehicle, and sham controls. Neuronal morphology in the cortex, striatum, hippocampus, and cerebellum was assessed histologically. Oxidative stress markers, including reactive oxygen species (ROS), lipid peroxidation (LPO), reduced glutathione (GSH), and superoxide dismutase (SOD), were measured, along with the expression of p53 protein. Results: Treatment with BtD significantly decreased oxidative stress markers—LPO (82.2%), ROS (88.2%), GSH (66.5%), and SOD (54%)—and reduced p53 expression levels by 75%. Histological evaluation revealed that neurons in the BCCAO/R+BtD and BCCAO/R+silymarin groups maintained normal morphology, characterized by elongated cells and well-defined nuclei. In contrast, the BCCAO/R+vehicle group exhibited marked neuronal damage, including pyknosis, nuclear fragmentation, and interstitial edema, particularly in the hippocampal CA1 and cortical regions. BtD treatment significantly preserved neuronal structure and enhanced antioxidant defenses. Conclusions:Bouvardia ternifolia extract demonstrates neuroprotective potential in cerebral ischemia by maintaining neuronal architecture, reducing oxidative stress, and modulating p53 expression, supporting its therapeutic relevance in ischemia–reperfusion injury. Full article

A recent study challenges a fundamental principle of eukaryotic biology that each nucleus houses a complete genome. Two plant pathogenic fungi, Sclerotinia sclerotiorum and Botrytis cinerea, exhibit a segregated pattern of haploid chromosome distribution across two or more nuclei within each cell. The unequal distribution of the genome between nuclei suggests a coordinated system of internuclear recognition and regulation of cellular functions, a phenomenon previously associated with communication between nuclei of opposite mating type in both ascomycetes and basidiomycetes. Thus, the new study not only shatters expectations about genome biology but also opens new research avenues for understanding fungal adaptation and nuclear behavior. Full article

Daffodils are among the most popular bulbous plants for cut flowers, especially Trumpet cultivars. The aim of this study was to evaluate changes in cut daffodil flowers and to determine the response of perianth senescence in cut daffodil flowers in a different way than the corona does and to determine whether the senescence of cut daffodil flowers is correlated with PCD symptoms. During the senescence of cut daffodil flowers, there was an increase in free proline, malondialdehyde and hydrogen peroxide contents and increased catalase activity. Typically, senescence processes occurred faster in the perianth than in the corona, excluding carbohydrates, which had a higher content in the perianth than in the corona. One of the symptoms of daffodil flower senescence was the degradation of cell nuclei. In addition, chromatin fragmentation could also be observed in the corona. The nuclei in the perianth began to change their spherical shape and decay. In the corona, the nuclear envelope retained its continuity much longer and started to disintegrate later than in the perianth. This is possibly because the corona has a longer vase life than the perianth. Full article