Arabidopsis LOHN1 peptide modulates lateral root spacing under the control of systemic nitrogen-satiety signaling.

Insights into plant receptor signaling are vital in mitigating the impact of climate change and plant disease on agriculture. The role of the BRASSINOSTEROID-INSENSITIVE 1 (BRI1) membrane receptor kinase in promoting growth and development in response to brassinosteroid (BR) hormones is well-established; however, the significance of vascular BRI1-LIKE 1 and 3 (BRL1/3) receptors remains largely overlooked. Here, in Arabidopsis (Arabidopsis thaliana), we reveal that loss of BRL3 causes defects in growth acclimation to elevated temperature. We establish that BRL3 activates the downstream signaling transcription factor BRI1-EMS-SUPPRESSOR 1 (BES1) and regulates the expression of several major growth pathways. We demonstrated via tissue-specific complementation experiments that BRL3 signaling in phloem companion cells is sufficient to regulate thermoresponsive growth. Transcriptome profiling revealed BRL3 regulates growth-related processes, including hormonal homeostasis and the switch to stress responses. Our research uncovers a previously unknown mechanism involving the BRL3 receptor that modulates growth adaptability under elevated temperature conditions, specifically from the phloem companion cells. This discovery challenges the conventional understanding of BR signaling and opens additional possibilities for developing climate-smart crops.

Local trafficking and long-distance transport of small RNAs in plants.

The precise onset of flowering is crucial for successful reproduction. In longer days, the florigen gene FLOWERING LOCUS T (FT) is induced in specific leaf phloem companion cells in Arabidopsis. However, the molecular nature of these cells remains elusive. Here, we utilized bulk nuclei RNA-seq and single nuclei RNA (snRNA)-seq to investigate transcription in FT-expressing cells and other companion cells. Our bulk nuclei RNA-seq demonstrated that FT-expressing cells in cotyledons and true leaves showed differences in FT repressor gene expression. Within true leaves, our snRNA-seq analysis revealed that companion cells with high FT expression form a unique cluster. The cluster expresses other genes encoding small proteins, including the flowering and stem growth inducer FPF1-LIKE PROTEIN 1 (FLP1) and the anti-florigen BROTHER OF FT AND TFL1 (BFT). We also found that the promoters of FT and the genes co-expressed with FT in the cluster were enriched for the binding motif of NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR 1 (NIGT1). Overexpression of NIGT1.2 and NIGT1.4 repressed FT and delayed flowering under nitrogen-rich conditions, implying the roles of NIGT1s as nitrogen-dependent FT repressors. Taken together, our results indicate that unique FT-expressing phloem cells may produce multiple systemic signals to regulate plant growth and development.

We applied dual-organism single-nucleus transcriptomics to study the interaction between grapevine leaves and Erysiphe necator, the causal agent of powdery mildew, at 1 and 5 days postinfection, including controls and three biological replicates. We generated a grapevine leaf atlas encompassing over 100,000 nuclei and a pathogen atlas of more than 3,000 nuclei. We successfully annotated all major grapevine cell types, including mesophyll, epidermis, phloem and xylem parenchyma, companion cells, and guard cells. We identified key E.necator structures, including appressoria, haustoria, and hyphae and provided a list of novel cell type markers for both species. We reveal structure-specific gene expression programs in E.necator, laying a foundation for future studies of fungal development and virulence mechanisms. In the host, we identified spatially distinct expression patterns of defense-related genes. As the infection progressed, we observed the activation of a coordinated immune response involving multiple cell types, mainly epidermal and mesophyll cells. High-dimensional weighted gene co-expression network analysis identified key hubs and networks associated with cell type-specific signaling and defense response. We describe a spatial separation of pattern- and effector-triggered immunity, supporting a model in which pattern-triggered immunity is activated at the site of pathogen contact and effector-triggered immunity is induced in surrounding tissue. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

The precise onset of flowering is crucial to ensure successful plant reproduction. The gene FLOWERING LOCUS T (FT) encodes florigen, a mobile signal produced in leaves that initiates flowering at the shoot apical meristem. In response to seasonal changes, FT is induced in phloem companion cells located in distal leaf regions. Thus far, a detailed molecular characterization of the FT-expressing cells has been lacking. Here, we used bulk nuclei RNA-seq and single nuclei RNA (snRNA)-seq to investigate gene expression in FT-expressing cells and other phloem companion cells. Our bulk nuclei RNA-seq demonstrated that FT-expressing cells in cotyledons and true leaves showed differences especially in FT repressor genes. Within the true leaves, our snRNA-seq analysis revealed that companion cells with high FT expression form a unique cluster in which many genes involved in ATP biosynthesis are highly upregulated. The cluster also expresses other genes encoding small proteins, including the flowering and stem growth inducer FPF1-LIKE PROTEIN 1 (FLP1) and the anti-florigen BROTHER OF FT AND TFL1 (BFT). In addition, we found that the promoters of FT and the genes co-expressed with FT in the cluster were enriched for the consensus binding motifs of NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR 1 (NIGT1). Overexpression of the paralogous NIGT1.2 and NIGT1.4 repressed FT expression and significantly delayed flowering under nitrogen-rich conditions, consistent with NIGT1s acting as nitrogen-dependent FT repressors. Taken together, our results demonstrate that major FT-expressing cells show a distinct expression profile that suggests that these cells may produce multiple systemic signals to regulate plant growth and development.

Tobacco was an important cash crop and model plant, and the senescence (yellowing) of its leaves were essential markers of harvesting and secondary metabolite formation. However, the cellular senescence process and its regulatory mechanisms in tobacco leaves remain unknown. Therefore, we constructed single-cell transcriptome profiles using tobacco leaf tissues at the maturation and senescence stages to clarify the molecular mechanism of the process. We obtained 17,100 high-quality cells and sorted them into 15 clusters. Based on the marker genes of the leaf cells, we sorted the 15 clusters into 10 cell types, including palisade mesophyll, spongy mesophyll, epidermis, xylem, phloem, hydathode, companion, bundle sheath, guard, and trichome cells. Comparison of gene expression patterns in mature and senescent leaf cells revealed that senescence-related cells were mainly associated with palisade mesophyll, spongy mesophyll, epidermis, xylem, and phloem cells. Enrichment analysis indicated that the differentially expressed genes in various cells were mainly related to chlorophyll synthesis and photosynthesis. Interestingly, most genes tended to show downregulated expression during senescence, whereas genes in the sphingolipid metabolism pathway were significantly upregulated in the senescent samples. We hypothesized that genes such as SPT may regulate the senescence process of tobacco leaves through the sphingolipid metabolism pathway. To our knowledge, this is the first study to analyze single-cell transcriptomes in aging tobacco leaves. Our findings offer insights for future molecular and cellular studies on tobacco leaf senescence.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12870-025-07051-2.

In Arabidopsis thaliana, the FLOWERING LOCUS T (FT) gene encodes florigen, a floral stimulus that integrates multiple environmental cues to optimize the timing of flowering, which is crucial for reproductive success. The FT protein is synthesized in the phloem companion cells of leaves but exerts its function in the shoot apical meristem (SAM) to initiate floral morphogenesis. While the environment-dependent regulation of FT transcription in leaves is well studied, the mechanisms underlying FT transport, particularly its cell-to-cell translocation within the SAM, remain poorly understood. In this study, we employed an in vivo bimolecular fluorescence complementation assay to elucidate the molecular mechanisms regulating FT intercellular translocation in the SAM. We demonstrate that low ambient temperature inhibits the cell-to-cell movement of FT in the SAM through abscisic acid signaling pathways, resulting in flowering delay. We further show that the permeability of plasmodesmata (PD) is involved in FT transport; in particular, CALLOSE SYNTHASE (CalS)1 and CalS7 are induced at low temperature, leading to reduced permeability of PD and inhibition of symplastic FT translocation in the SAM. Collectively, our findings provide insights into the molecular mechanisms that regulate the intercellular translocation of FT in the SAM in response to environmental conditions and lead to a framework for the understanding of flowering.

The mesophyll of succulent leaves of Aizoaceae plants may have specialized water-storing tissue in perennial species (storage succulents), but not in annual species (all-cell succulents). Storage succulents have peripheral minor veins with either outward-facing xylem (exoscopic), restricted to the basal subfamily Sesuvioideae, or inward-facing xylem (endoscopic) with the phloem adjacent to the chlorenchyma ring, as seen in derived subfamilies such as the hyperdiverse Ruschioideae. Here, we investigate the implications of phloem positioning relative to photosynthesizing cells by comparative transmission electron microscopy, aided by immunolocalization of sucrose transporters (SUT1). Both the exoscopic bundles of Sesuvium portulacastrum (L.) L. (Sesuvioideae) and the endoscopic bundles of Delosperma herbeum (N.E.Br.) N.E.Br. (Ruschioideae) have ordinary companion cells. Given their structural similarity, and considering the proximity of the phloem of exoscopic bundles to the chlorenchyma in other Caryophyllales species, we propose that the widespread occurrence of endoscopic bundles in Ruschioideae reflects the maintenance of an adaptively neutral character state during their adaptive radiation. Contrastingly, the all-cell species Mesembryanthemum crystallinum L. (Mesembryanthemoideae) has companion transfer cells, but SUT1 localizes to sieve elements, leaving the exact function of the transfer cells unclear in the context of the increased export of sugars they are known to provide. Nevertheless, because the reproductive phase of this annual species coincides with the dry season, when mesophyll cells must retain osmoprotective solutes simultaneously with flower development, we suggest that its transfer cells are adaptive by mediating a trade-off between source and sink organs, which does not occur in the two perennial storage succulents.

Florigen-producing cells express FPF1-LIKE PROTEIN 1 to accelerate flowering and stem growth in Arabidopsis.

The vegetative body of Pilostyles (Apodanthaceae) is highly reduced, composed of cell clusters that occupy the bark of the host plant. From these clusters, tracheary elements connect with the host vascular system during the parasite reproductive stages. We analyse the developmental morphology of Pilostyles blanchetii to gain a better understanding of its growth within the host body, in addition to xylem and phloem connections between the two plants, providing new interpretations about the life history of the parasite. Iodine and lead contrast solutions were perfused through samples of parasitized host material before microtomography scanning to facilitate posterior virtual segmentation of parasite structures within host tissues. Samples were then prepared for light, fluorescence and confocal microscopy to analyse xylem and phloem connections between parasite and host plants. We detected the presence of parasitic tissue within the host body before flower meristem differentiation and revealed the interconnectedness of the parasitic endophyte. Parasite-host xylem connections are mediated by highly modified vessel elements differentiated in the parasite sinkers. Within the host bark, the parasite develops small sieve tube elements lacking companion cells. Pilostyles blanchetii develops an extensive tissue network within the bark of its hosts, linking pistillate and staminate flowers, thus suggesting monoecy. Vascular tissue is extremely reduced and includes only vessel elements for the xylem and sieve tube elements for the phloem, which connect directly to the corresponding cells of the host.

Developing high-resolution reference maps of disease-susceptible spatial niches is a critical step to mitigating the profound effects of lung disease. Here, we present an integrated multimodal single-nucleus human lung atlas (snHLA) profiling 746,047 nuclei from 49 mapped lung blocks spanning clinically relevant distal airways, alveoli, and interstitium across 11 healthy adults. Integrating snRNA-seq and SNARE-seq2, which co-assays chromatin accessibility and gene expression from the same nucleus, we resolved 70 molecularly distinct populations and captured 332,846 accessible chromatin regions, nominating new transcriptional regulators of human lung cell diversity. Spatial transcriptomics using MERFISH mapped 25 cell populations across 7 structural neighborhoods and multiplexed immunofluorescence localized cell subtypes and distal airway-defining protein markers, expanding and validating distinct lung structure-specific cell populations. This open access snHLA and companion Cell Type and Marker Gene Dictionary with anatomically aligned nomenclature delivers a foundational resource at an unprecedented resolution to interrogate the origins of lung pathophysiology.

Leaf vasculature not only acts as a channel for nutrients and signaling information but also influences leaf morphology. It consists of several distinct cell types with specialized functions. Cell type-specific characterizations based on single-cell RNA sequencing technology could aid in understanding the identities of vascular tissues and their roles in leaf morphogenesis in Brassica rapa. Here, we generated a single-cell transcriptome landscape of the Chinese cabbage leaf vasculature. A total of 12 cell clusters covering seven known cell types were identified. Different vascular cell types were characterized by distinct identities. The xylem parenchyma and companion cells exhibited an active expression pattern of amino acid metabolism genes. Tracheary elements and sieve elements were enriched in many genes related to cell wall biosynthesis, and the phloem parenchyma was enriched in many sugar transporter-encoding genes. Pseudo-time analyses revealed the developmental trajectories of the xylem and phloem and the potential roles of auxin and ethylene in xylem development. Furthermore, we identified key candidate regulators along the differentiation trajectory of the sieve elements and companion cells. Most of the homoeologous genes in the syntenic triads from the three subgenomes showed asymmetric gene expression patterns in different vascular cell types. Collectively, our study revealed that Chinese cabbage leaf vasculature cells had highly heterogeneous transcriptomes, providing new insights into the complex processes of leaf vasculature development in B. rapa leafy vegetables and other Brassica crops.

ABSTRACTMineral deficiency is a major problem in agriculture. Plant adaption to low mineral environments involves signaling between shoots and roots, via the food transport cells, the sieve elements. However, due to the sequestered position of the sieve elements in the vascular bundles, identifying shoot‐to‐root mobile signals is challenging. In herbaceous species, sieve elements and companion cells (CCs) are isolated from other leaf tissues. We hypothesize that phloem CCs play an essential role by synthesizing shoot‐to‐root signals in response to mineral deficiency. To test this hypothesis, we analyzed gene expression responses in Arabidopsis CCs under phosphorus deficiency using TRAP‐Seq. Phosphorus was chosen for its importance in plant growth and the known role of shoot‐to‐root signaling in regulating root phosphate transporters during deficiency. Our findings revealed that CCs exhibit more dramatic molecular responses than other leaf cells. We also found that many genes altered in CCs have potential functions in regulating root growth. This is unexpected because it has been widely believed that shoot‐to‐root signaling is not involved in root growth regulation under P deficiency. The importance of CCs in regulating mineral deficiency may extend beyond phosphorus because shoot‐to‐root signaling is a common response to the deficiency of various minerals.

RNA interference (RNAi) is a promising technology for controlling insect pests of agriculture. This technology is mediated through the application of double-stranded RNAs (dsRNAs), which are processed within the insect cells into small interfering RNAs (siRNAs). These molecules then target and reduce the expression of the insect-specific genes that can kill or reduce the performance of the pest. The application of these RNA biopesticides generally falls under two methods: foliar sprays and expression of RNAi constructs within transgenic plants. Here, we provide evidence supporting feasibility of using transgenic plants to deliver RNAi-based biopesticides against their aphid pests. Our findings suggest that, under the Cucumis melo galactinol synthase 1 promoter, the companion cells of transformed Arabidopsis thaliana plants express dsRNAs but not siRNAs at detectable levels. Further, oral application of either siRNAs or dsRNAs is equally effective in reducing the expression of transcripts of the integral membrane protein aquaporin 1 in Acyrthosiphon pisum pea aphids. We did not find any dsRNAs or siRNAs remaining in the insects or honeydew 48 h post-exposure, suggesting a low risk of contamination of these molecules beyond the target phloem-piercing insect pests.

The HAIRY MERISTEM (HAM) gene family encodes Type I and II GRAS domain transcriptional regulators in plants. Type II HAMs, predominantly expressed in meristems and regulated by microRNA171, are essential for maintaining undifferentiated meristems, a role conserved across various species. Conversely, the functions of Type I HAMs have been less characterized. In this study, we investigated the role of SlHAM4, a Type I HAM in tomato. CRISPR-induced SlHAM4 loss-of-function mutations (slham4 CR ) resulted in shoot and fruit abnormalities, which were fully reversed by reintroducing SlHAM4, driven by its native promoter, into the mutant background. Mutant abnormalities included simpler leaves and increased anthocyanin pigmentation in the leaf and sepal primordia, reminiscent of phenotypes observed in certain Arabidopsis mutants with compromised phloem. In addition, slham4 CR plants produced significantly smaller fruits with a subset developing catface-like scars, attributed to tears that occurred in the pericarp of setting fruits. Using a GUS reporter gene driven by the native SlHAM4 promoter, we found that SlHAM4 is predominantly expressed in phloem tissues. Consistent with this, transcriptome analysis of mutant anthesis ovaries revealed specific downregulation of genes implicated in phloem development and function, particularly those expressed in companion cells. However, histological analysis showed no obvious abnormalities in phloem vasculature. Taken together, our data suggest that SlHAM4 plays a role in shoot and fruit development likely by regulating genes essential for phloem function.

Micromorphological and phytochemical studies play a major role in quality control and standardization of traditional or herbal medications. In the present research, micromorphological assessment of Heliotropium rarifloum stocks was performed through light and scanning electron microscopies (LM & SEM). The anatomy of leaves, stem and root showed salient histological features. Both surfaces of the leaves had setose glandular trichomes measuring 20-38 × 6-15 µm. The lower epidermis had comparatively a maximum anomocytic stomata (16-35) and stomatal index (12-33). The mature pollen grains were small (74 µm) and spheroidal shaped, with psilate exine (2 μm) sculpturing. Vein termination and vein islet number of the upper epidermis were 5-20 and 5-15, respectively. The palisade ratio of the leaf lamina for the upper and lower epidermis was 2-10 and 2-8. LM and SEM of the powdered samples displayed crystals, phloem fibers, xylem, vessels, sieve tube elements, companion cells, and tracheids. Extractive values determination, fluorescence, and phytochemical analysis were employed for quality control according to the World Health Organization (WHO) guidelines. Phytochemical screening revealed various secondary metabolites. It is suggested that H. rariflorum might be a reliable source of nutrients and secondary metabolites and might be more medically effective. The current findings confirm its standardization and validation.

In Chinese cabbage development the interplay between shoot apex activity and vernalization is pivotal for flowering timing. The intricate relationship between various cell types in the shoot apex meristem and their roles in regulating flowering gene expression in Chinese cabbage is not yet fully understood. A thorough analysis of single-cell types in the Chinese cabbage shoot apex and their influence on flowering genes and vernalization is essential for deeper insight. Our study first established a single-cell transcriptomic atlas of Chinese cabbage after 25 days of non-vernalization. Analyzing 19 602 single cells, we differentiated them into 15 distinct cell clusters using established marker genes. We found that key genes in shoot apex development and flowering were primarily present in shoot meristematic cells (SMCs), companion cells (CCs), and mesophyll cells (MCs). MADS-box protein FLOWERING LOCUS C 2 (BrFLC2), a gene suppressing flowering, was observed in CCs, mirroring patterns found in Arabidopsis. By mapping developmental trajectories of SMCs, CCs, and MCs, we elucidated the evolutionary pathways of crucial genes in shoot apex development and flowering. The creation of a single-cell transcriptional atlas of the Chinese cabbage shoot apex under vernalization revealed distinct alterations in the expression of known flowering genes, such as VERNALIZATION INSENSITIVE 3 (VIN3), VERNALIZATION 1 (VRN1), VERNALIZATION 2 (VRN2), BrFLC, and FLOWERING LOCUS T (FT), which varied by cell type. Our study underscores the transformative impact of single-cell RNA sequencing (scRNA-seq) for unraveling the complex differentiation and vernalization processes in the Chinese cabbage shoot apex. These insights are pivotal for enhancing breeding strategies and cultivation management of this vital vegetable.

Prunus mume (mei), a traditional ornamental plant in China, is renowned for its fragrant flowers, primarily emitted by its petals. However, the cell types of mei petals and where floral volatile synthesis occurs are rarely reported. The study used single-cell RNA sequencing to characterize the gene expression landscape in petals of P. mume 'Fenhong Zhusha' at budding stage (BS) and full-blooming stage (FS). Six major cell types of petals were identified: epidermal cells (ECs), parenchyma cells (PCs), xylem parenchyma cells, phloem parenchyma cells, xylem vessels and fibers, and sieve elements and companion cells complex. Cell-specific marker genes in each cell type were provided. Floral volatiles from mei petals were measured at four flowering development stages, and their emissions increased from BS to FS, and decreased at the withering stage. Fifty-eight differentially expressed genes (DEGs) in benzenoid/phenylpropanoid pathway were screened using bulk RNA-seq data. Twenty-eight DEGs expression increased from BS to FS, indicating that they might play roles in floral volatile synthesis in P. mume, among which PmBAHD3 would participate in benzyl acetate synthesis. ScRNA-seq data showed that 27 DEGs mentioned above were expressed variously in different cell types. In situ hybridization confirmed that PmPAL2, PmCAD1, PmBAHD3,5, and PmEGS1 involved in floral volatile synthesis in mei petals are mainly expressed in EC, PC, and most vascular tissues, consistent with scRNA-seq data. The result indicates that benzyl acetate and eugenol, the characteristic volatiles in mei, are mostly synthesized in these cell types. The first petal single-cell atlas was constructed, offering new insights into the molecular mechanism of floral volatile synthesis.

Detailed anatomical features of bark are used and interpreted in plant taxonomy, phylogenetics, and other areas of plant science. However, the delicate nature of bark cells, combined with the difficulty of obtaining high-quality sections and reliable data, limits the potential for utilizing and processing bark. In this study, the anatomical structure of the bark of 10 Quercus species growing in Yunnan Province, China, was characterized in detail. The results indicate that the anatomical features of the barks of 10 Quercus spp. show a certain degree of consistency. Specifically, sieve tubes are distributed in solitary elements or in small groups, mostly as compound sieve plates containing 2-8 sieve areas, suggesting that Quercus spp. may occupy a conservative evolutionary position. Additionally, for the first time, this study reports the presence of simple sieve plates in the sieve tube elements of Quercus phloem. Each sieve tube element has a companion cell on one side. The companion cell strands contain 2-7 cells. Axial parenchyma is diffuse, with parenchyma strands typically consisting of 4-7 cells; druses are present within chambered crystalliferous cells. Phloem rays are of two distinct sizes and often exhibit dilatation and sclerification, and the ray composition consists of procumbent cells. Sclerenchyma is composed of fibers and sclereids, both of which contain prismatic crystals. Most of the fibers are gelatinous fibers, which are distributed in discontinuous tangential bands of about five cells in width. Sclereids appear in clusters. The presence of sclerenchyma provides mechanical support to the bark, reducing the collapse of the phloem. Periderm usually consists of around 10-30 layers of phellem, and Quercus acutissima and Q. variabilis can reach dozens or hundreds layers. The phelloderm typically consists of from two to five layers, with Q. variabilis having up to ten or more layers. The filling tissue of lenticels in all Quercus species is nonstratified (homogeneous) and largely nonsuberized. Overall, this study enriches our comprehension of Quercus bark anatomy, elucidating evolutionary patterns, functional adaptations, and ecological ramifications within this significant botanical genus.