SEARCH · bioRxiv Science

Results for “plant biology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 91 records · Page 5Linked to original sources

bioRxiv2026

NO VEIN is an ancestral immunity protein involved in plant-virus interaction

The conservation of immune systems from prokaryotes to eukaryotes can guide discovery of immunity genes across the tree of life. Most studies to date have focused on metazoan systems, while the extent of ancestral immunity conservation in plants remains underexplored. Here we show that NO VEIN (NOV), a plant protein previously characterized for its essential developmental roles in Arabidopsis thaliana, shares domain composition and structural similarity with Tiamat, a bacterial antiphage protein. In light of the antiviral function of the bacterial protein, we asked whether NOV is involved in plant-virus interactions. We found that NOV knockdown in the model plant Nicotiana benthamiana resulted in an impaired transcriptional response to tobacco rattle virus, including reduced induction of defense genes, and observed increased potato virus x accumulation in a secondary infection. We also reveal that NOV, previously considered plant-specific, has homologs in animals - pointing to a shared origin. Together, these findings uncover a deeply conserved protein involved in plant-virus interaction, and demonstrate the power of prokaryote-eukaryote homology to reveal new aspects of plant biology.

plant biology↗

bioRxiv2023

Genetic factors explaining anthocyanin pigmentation differences

BackgroundAnthocyanins represent one of the most abundant coloration factors found in plants. Biological functions of anthocyanins range from reproduction to protection against biotic and abiotic stressors. Owing to a clearly visible phenotype of mutants, the anthocyanin biosynthesis and its sophisticated regulation have been studied in numerous plant species. Genes encoding the anthocyanin biosynthesis enzymes are regulated by a transcription factor complex comprising MYB, bHLH and WD40 proteins. ResultsA systematic comparison of anthocyanin-pigmented vs. non-pigmented varieties across flowering plant species was performed. Literature was screened for cases in which genetic factors causing anthocyanin loss were reported. Additionally, transcriptomic data sets from previous studies were reanalyzed to determine the genes most likely to be responsible for color variation based on their expression pattern. The contribution of different structural and regulatory genes to the pigmentation differences was quantified. Gene expression differences concerning transcription factors are by far the most frequent explanation for pigmentation differences observed between two varieties of the same species. Among the transcription factors in the analyzed cases, MYB genes are substantially more likely to explain pigmentation differences than bHLH or WD40 genes. ConclusionsThese findings support previous assumptions about the plasticity of transcriptional regulation and its importance for the evolution of novel coloration phenotypes. Our findings underline the particular significance of MYBs and their apparent dominant role in the specificity of the MBW complex.

plant biology↗

bioRxiv2025

Decoding cellular transcriptional regulatory networks governing wheat inflorescence development

Wheat inflorescence architecture, particularly spikelet and floret development, is critical for grain yield. To decode the cellular transcriptional regulatory network (cTRN) underlying wheat inflorescence development, we integrated multiple single-cell omics technologies to construct a spatiotemporal atlas of transcriptional and chromatin accessibility dynamics. This comprehensive analysis identified 20 cell types, 7,211 cell type-specific genes and 152,333 cell type-specific accessible chromatin regions (csACRs) in the wheat inflorescence. Trajectory analysis identified two sub-clusters of proliferating cells as the origins of spikelet and floret formation, deviating from the traditional developmental model. Key transcription factors and hormone-related genes in the cTRN, along with the csACRs, providing new targets for modulating wheat inflorescence architecture. Our findings provide a high-resolution resource for crop inflorescence research and establish a paradigm for applying spatiotemporal single-cell omics analysis to plant biology.

plant biology↗

bioRxiv2023

An Enhancer Trap system to track developmental dynamics in Marchantia polymorpha

A combination of streamlined genetics, experimental tractability and relative morphological simplicity compared to vascular plants makes the liverwort Marchantia polymorpha an ideal model system for studying many aspects of plant biology. Here we describe a transformation vector combining a constitutive fluorescent membrane marker with a nuclear marker that is regulated by nearby enhancer elements, and use this to produce a library of enhancer trap lines for Marchantia. Screening gemmae from these lines allowed for identification and characterization of novel marker lines, including markers for rhizoids and oil cells. The library allowed the identification of a margin tissue running around the thallus edge, highlighted during thallus development. Expression of this marker is correlated with auxin levels. We generated multiple markers for the meristematic apical notch region, which have different spatial expression patterns, reappear at different times during meristem regeneration following apical notch excision and have varying responses to auxin supplementation or inhibition. This reveals that there are proximodistal substructures within the apical notch that could not be observed otherwise. We employed our markers to study Marchantia sporeling development, observing meristem emergence as defining the protonema-to-prothallus stage transition, and subsequent production of margin tissue during the prothallus stage. Exogenous auxin treatment stalls meristem emergence at the protonema stage but does not inhibit cell division, resulting in callus-like sporelings with many rhizoids, whereas pharmacologically inhibiting auxin synthesis and transport does not prevent meristem emergence. This enhancer trap system presents a useful resource for the community and will contribute to future Marchantia research. Significance StatementThe liverwort Marchantia polymorpha is an emerging model species with huge potential for synthetic biology. We generated an enhancer trap library as a resource for Marchantia research and characterized marker lines for several important cell types (rhizoids, thallus margin, apical notch and oil cells). These marker lines can be used to track cellular dynamics in growing plants, exemplified by studying auxin responses and sporeling growth, revealing new insights into thallus development and cell fate specification.

plant biology↗

bioRxiv2022

Plant age-dependent dynamics of annatto pigment (bixin) biosynthesis in Bixa orellana L.

Age affects the production of secondary metabolites, but how developmental cues regulate secondary metabolism remains poorly understood. Annatto (Bixa orellana L.) is a source of bixin, an apocarotenoid used in the worlds food industry worldwide. Understanding how age-dependent mechanisms control bixin biosynthesis is of great interest for plant biology and for pharmaceutical, cosmetic, and textile industries. Here, we used genetic and molecular tools to unravel the role of the annatto age regulated miRNA156 (miR156) targeted SQUAMOSA PROMOTER BINDING PROTEIN LIKE (BoSPL) genes in secondary metabolism. Low expression of several BoSPL genes in miR156 overexpressing annatto plants (OE::156) impacted leaf ontogeny, reducing bixin production and increasing abscisic acid (ABA) levels. Modulation of BoCCD4;4 and BoCCD1 expression, key genes in lycopene cleavage, was associated with diverting the carbon flux from bixin to ABA, whereas upregulation of lycopene {beta} cyclase genes implies the xanthophyll biosynthetic pathway acted as a carbon sink in OE::156 plants. Proteomic analyses revealed low accumulation of most secondary metabolite-related enzymes in OE::156 plants, suggesting that miR156 targeted BoSPLs are required to activate several annatto secondary metabolic pathways. Our findings suggest that carbon flux in B. orellana OE::156 leaves was redirected from bixin to ABA production, indicating an age-dependent leaf dynamics of bixin biosynthesis. Importantly, our study opened a new venue to future annatto breeding programs aiming to improve bixin output.

plant biology↗

bioRxiv2021

Fine-tuning of SUMOylation modulates drought tolerance

SUMOylation is involved in various aspects of plant biology, including drought stress. However, the relationship between SUMOylation and drought stress tolerance is complex; whether SUMOylation has a crosstalk with ubiquitination in response to drought stress remains largely unclear. In this study, we found that both increased and decreased SUMOylation led to increased survival of apple (Malus x domestica) under drought stress: both transgenic MdSUMO2A overexpressing (OE) plants and MdSUMO2 RNAi plants exhibited enhanced drought tolerance. We further confirmed that MdDREB2A is one of the MdSUMO2 targets. Both transgenic MdDREB2A OE and MdDREB2AK192R OE plants (which lacked the key site of SUMOylation by MdSUMO2A) were more drought tolerant than wild-type plants. However, MdDREB2AK192R OE plants had a much higher survival rate than MdDREB2A OE plants. We further showed SUMOylated MdDREB2A was conjugated with ubiquitin by MdRNF4 under drought stress, thereby triggering its protein degradation. In addition, MdRNF4 RNAi plants were more tolerant to drought stress. These results revealed the molecular mechanisms that underlie the relationship of SUMOylation with drought tolerance and provided evidence for the tight control of MdDREB2A accumulation under drought stress mediated by SUMOylation and ubiquitination.

plant biology↗

bioRxiv2019

Metabolic labeling of RNAs uncovers hidden features and dynamics of the Arabidopsis thaliana transcriptome

Transcriptome analysis by RNA sequencing (RNA-seq) has become an indispensable core research tool in modern plant biology. Virtually all RNA-seq studies provide a snapshot of the steady-state transcriptome, which contains valuable information about RNA populations at a given time, but lacks information about the dynamics of RNA synthesis and degradation. Only a few specialized sequencing techniques, such as global run-on sequencing (GRO-seq), have been applied in plants and provide information about RNA synthesis rates. Here, we demonstrate that RNA labeling with a modified, non-toxic uridine analog, 5-ethynyl uridine (5-EU), in Arabidopsis thaliana seedlings provides insight into the dynamic nature of a plant transcriptome. Pulse-labeling with 5-EU allowed the detection and analysis of nascent and unstable RNAs, of RNA processing intermediates generated by splicing, and of chloroplast RNAs. We also conducted pulse-chase experiments with 5-EU, which allowed us to determine RNA stabilities without the need for chemical inhibition of transcription using compounds such as actinomycin and cordycepin. Genome-wide analysis of RNA stabilities by 5-EU pulse-chase experiments revealed that this inhibitor-free RNA stability measurement results in RNA half-lives much shorter than those reported after chemical inhibition of transcription. In summary, our results show that the Arabidopsis nascent transcriptome contains unstable RNAs and RNA processing intermediates, and suggest that half-lives of plant RNAs are largely overestimated. Our results lay the ground for an easy and affordable nascent transcriptome analysis and inhibitor-free analysis of RNA stabilities in plants.

plant biology↗

bioRxiv2022

CURLYLEAF is a key modulator of apoplast water status in Arabidopsis leaf

The apoplast of plant leaf, the intercellular space between mesophyll cells, is normally largely filled with air with a minimal amount of water in it, which is essential for key physiological processes such as gas exchange to occur. Interestingly, phytopathogens exploit virulence factors to induce a water-rich environment, known as "water soaking", in the apoplast of the infected leaf tissue to promote disease. We propose that plants evolved a "water soaking" pathway, which normally keeps a "minimized and balanced" water level in the leaf apoplast for plant growth but is disturbed by microbial pathogens to facilitate infection. Investigation of the "water soaking" pathway and leaf water control mechanisms is a fundamental, yet previously-overlooked, aspect of plant physiology. To identify key components in the "water soaking" pathway, we performed a genetic screen to isolate Arabidopsis severe water soaking (sws) mutants that show leaf water over-accumulation under high air humidity, a condition required for visible water soaking. Here we report the sws1 mutant, which displays rapid water soaking upon high humidity treatment due to a loss-of-function mutation in CURLY LEAF (CLF), encoding a histone methyl-transferase in the POLYCOMB REPRESSIVE COMPLEX 2 (PRC2). We found that the sws1 (clf) mutant exhibits an enhanced abscisic acid (ABA) level and stomatal closure, which are indispensable for its water soaking phenotype and mediated by CLFs direct regulation of a group of ABA-associated NAC transcription factors, NAC019/055/072. Interestingly, the clf mutant showed a weakened immunity, which likely also contributes to the water soaking phenotype. In addition, the clf plant supports a significantly higher level of Pseudomonas syringae pathogen-induced water soaking and bacterial multiplication, in an ABA pathway and NAC019/055/072-dependent manner. Collectively, our study probes into a fundamental question in plant biology and demonstrates CLF as a key modulator of leaf water status via epigenetic regulation of ABA pathway and stomatal movement.

plant biology↗

bioRxiv2024

Heterogenous transcriptomes of Nicotiana tabacum BY-2 suspension cell lines adapted to various osmoticum

Plants abiotic stress response and adaptation belong to the most important subjects in plants biology. Here, we present Nicotiana tabacum suspension cell lines adapted during long term cultures to high concentrations of NaCl, KCl, mannitol and sorbitol. Obtained lines differ in osmotic stress agents and final media osmolarities. RNA-seq analysis revealed similarities, as well as differences in adapted lines transcriptomes. Presented here BY-2 cells lines form a good model to reveal molecular mechanisms of plants adaptations to salt and osmotic stress on cellular level.

plant biology↗

bioRxiv2025

The Q-Warg Pipeline: A Robust and Versatile Workflow for Quantitative Analysis of Protoplast Culture Conditions

Single cells offer a simplified model for investigating complex mechanisms such as cell-cell adhesion. Protoplasts, plant cells without cell walls (CWs), have been instrumental in plant research, industrial applications, and breeding. However, due to the absence of a CW, protoplasts are not considered "true" plant cells and making them less relevant for biophysical studies. Current protocols for CW recovery in protoplasts vary widely among laboratories and starting materials, requiring lab-specific optimizations that often depend on expert knowledge and qualitative assessments. To address this, we have developed a user-friendly streamlined workflow, the Q-Warg pipeline, which enables quantitative comparison of various conditions for CW recovery post-protoplasting. This pipeline employs fluorescence imaging and tailored processing to measure parameters such as morphometry, cell viability, and CW staining intensity. Using this approach, we optimized culture conditions to obtain single plant cells (SPCs) with recovered CWs. Additionally, we demonstrated the robustness and versatility of the workflow by quantifying different fluorescent signals in protoplast suspensions. Overall, the Q-Warg pipeline provides a widely available and user-friendly solution for robust and unbiased characterization of protoplasts culture. The quantitative data generated by the pipeline may be useful in the future to decipher the mechanisms regulating protoplast viability and regeneration. Significance statementSeveral fields of plant biology, ranging from biotechnology to biomechanics, have recently regained a strong interest in using and studying protoplasts and single cells. Here, we developed a widely accessible quantitative workflow to characterize cell culture recovery after protoplasting along with the demonstration of its usefulness and versatility in various cases. We hope this tool can help other research groups to streamline the procedure needed to establish single plant cell approaches in their lab.

plant biology↗

bioRxiv2026

BioIMA: a one-click desktop tool for standardized extraction of phenotypic traits from biological images

Standardized extraction of quantitative phenotypes from images is increasingly important across plant biology, from ecological and evolutionary studies to genetics, breeding, and functional genomics. However, as large image datasets are increasingly used for trait analysis, many biologically relevant traits, including size, shape, color, and spatial patterning, are still measured manually or using fragmented semi-automated workflows. These limitations reduce throughput, reproducibility, and accessibility, especially for researchers without computational expertise. Here, we present BioIMA, an open-source desktop tool for rapid and standardized phenotyping from biological images. BioIMA integrates foundation model-based segmentation with automated trait computation, allowing users to extract quantitative measurements from images through an intuitive graphical interface and without model training. To validate its performance, we quantified a set of knot morphological traits in two Populus species, as these measurements are typically time-consuming to perform manually. Automatic measurements showed strong agreement with manual ImageJ-based measurements (R2 > 0.95), while reducing per-image processing time by approximately 75% (from ~15 s to ~4 s). BioIMA was further applied to diverse plant datasets, including Helianthus and Rhododendron images with varying morphologies and background conditions. Although developed for plant phenotyping, BioIMA may also be extended to other biological samples where region-based size, shape, or color traits are of interest. By combining accessibility and standardization in a lightweight local application, BioIMA provides a practical community resource for image-based phenotyping in ecological and evolutionary studies.

bioinformatics↗

bioRxiv2023

Green Index: a widely accessible method to quantify greenness of photosynthetic organisms

Plant phenotyping involves the quantitative determination of complex plant traits using image analysis. One important parameter is how green plant tissues appear to the observer, which is indicative of their health and developmental stage. Various formulas have been developed to quantify this by calculating leaf greenness scores. We have developed a revised formula called "Green Index" (GI) devised out of the need to quantitatively assess how the apparent greenness of seedlings changes during de-etiolation. The GI calculation is simple, uses widely available RGB values of pixels in images as input, and does not require commercial software platforms or advanced computational skills. In this study we describe the conception of the GI formula, compare it with other widely used greenness formulas, and test its wider application in plant phenotyping using the open source free software platform RawTherapee. We demonstrate the utility of the GI in addressing common issues encountered in assessing plant biology experiments, underscoring its potential as a reliable and accessible tool. Finally, we explore the correlation between GI and chlorophyll content, assess its reliance on different types of photography, and summarizes the key steps for its effective utilization.

plant biology↗

bioRxiv2022

Chloroplast protein import determines plant proteostasis and retrograde signaling

Proteins containing polyglutamine (polyQ) repeats are prone to aggregation and can lead to distinct human pathologies. For instance, Huntingtons disease is caused by an abnormal expansion of the polyQ stretch (> Q35) of Huntingtin (HTT) protein. However, plants express hundreds of proteins containing polyQ regions, but no pathologies arising from these factors have been reported to date. Here, we ask how plants maintain the proteostasis of polyQ-containing proteins, which are intrinsically enriched in the plant proteomes. To this end, we overexpressed an aggregation-prone fragment of human HTT (Q69) in plant cells. In contrast to invertebrate and mammalian transgenic models, we find that Arabidopsis thaliana plants suppress Q69 aggregation. This elevated proteostasis ability is mediated through the import and degradation of Q69 in chloroplasts. Conversely, inhibition of chloroplast protein import either genetically or pharmacologically reduces the capacity of plant cells to prevent Q69 aggregation. We find that Q69 interacts with the chloroplast stromal processing peptidase (SPP). Notably, expression of synthetic Arabidopsis SPP is sufficient to suppress aggregation of polyQ-expanded HTT in human cells. Beyond ectopically expressed Q69-HTT, endogenous polyQ-containing proteins also aggregate in Arabidopsis upon inhibition of chloroplast import. Among them, the plastid casein kinase 2 (pCK2), which contains a polyQ region next to the chloroplast targeting sequence motif, can also be localized into the nucleus. Upon inhibition of chloroplast import, pCK2 accumulates at higher levels in the nucleus and forms diamond-shaped amyloid-like fibrils surrounding the chloroplasts. These results indicate that the differential conformation and redistribution of pCK2 to the nucleus depends on chloroplast import efficiency, providing a role of polyQ repeats in chloroplast to nucleus communication (i.e. retrograde signaling). Together, our findings establish chloroplast protein import and proteases as determinants of polyQ proteostasis, with important implications for plant biology that can also lead to therapeutic approaches for human diseases that involve protein aggregation.

plant biology↗

bioRxiv2023

Plant Expression Omnibus - a comparative transcriptomic database for 103 Archaeplastida

The Plant Expression Omnibus (PEO) is a web application that provides biologists with access to gene expression insights across over 100 plant species, [~]60,000 manually annotated RNA-seq samples, and more than four million genes. The tool allows users to explore the expression patterns of genes across different organs, identify organ-specific genes, and discover top co-expressed genes for any gene of interest. PEO also provides functional annotations for each gene, allowing for the identification of genetic modules and pathways. PEO is designed to facilitate comparative kingdom-wide gene expression analysis and provide a valuable resource for plant biology research. We provide two case studies to demonstrate the utility of PEO in identifying candidate genes in pollen coat biosynthesis and investigating the biosynthetic pathway components of capsaicin in Capsicum annuum. The database is freely available at https://expression.plant.tools/.

plant biology↗

bioRxiv2026

A broad-host-range Rhizobium rhizogenes strain enables transient expression across diverse crops and establishes functional assays in faba bean

Agrobacterium-mediated transient expression has revolutionized plant research, enabling numerous landmark discoveries across diverse areas of plant biology. Yet this powerful approach remains largely confined to solanaceous species, leaving most economically important crop families without a comparable rapid assay platform. Here, we show that an engineered Rhizobium rhizogenes strain, AS109, mediates efficient transient expression across diverse dicot species spanning multiple taxonomic families, consistently outperforming commonly used laboratory agrobacterial strains. Leveraging the broad host range of AS109, we establish a suite of functional assays in faba bean (Vicia faba), including protein localisation, RNA interference-mediated gene silencing, cell-surface elicitor recognition screens, nucleotide-binding leucine-rich repeat receptor (NLR) activation, and infection cell biology at the host-pathogen interface. We further demonstrate that both singleton NLRs and sensor-helper NLR pairs from Solanaceae retain effector recognition and cell death activity when transferred into faba bean, establishing a rapid platform for evaluating cross-family transferability of disease-resistance genes. AS109 thus provides an accessible and versatile chassis for functional genomics in non-model crops, bridging the widening gap between hypothesis generation and experimental validation across diverse plant species.

plant biology↗

bioRxiv2019

Optimization of a Modular Steroid-Inducible Gene Expression System for Use in Rice

Chemically inducible systems that provide both spatial and temporal control of gene expression are essential tools, with many applications in plant biology. Using Golden Gate modular cloning, we have created a monocot-optimized dexamethasone (DEX)-inducible pOp6/LhGR system and tested its efficacy in rice using the reporter enzyme {beta}-glucuronidase (GUS). The system is tightly regulated and highly sensitive to DEX application, with six hours of induction sufficient to induce high levels of GUS activity in transgenic callus. In seedlings, GUS activity was detectable in the root after in vitro application of just 0.01M DEX. However, transgenic plants manifested severe developmental perturbations when grown on higher concentrations of DEX. The direct cause of these growth defects is not known, but the rice genome contains sequences with high similarity to the LhGR target sequence lacO, suggesting non-specific activation of endogenous genes by DEX induction. These off-target effects can be minimized by quenching with isopropyl {beta}-D-1-thiogalactopyranoside (IPTG). The system is thus suitable for general use in rice, when the method of DEX application and relevant controls are tailored appropriately for each specific application.

plant biology↗

bioRxiv2021

MoBiFC: development of a modular bimolecular fluorescence complementation toolkit for the analysis of chloroplast protein-protein interactions.

The bimolecular fluorescence complementation (BiFC) assay has emerged as one of the most popular methods for analysing protein-protein interactions (PPIs) in plant biology. This includes its increasing use as a tool for dissecting the molecular mechanisms of chloroplast function. However, the construction of chloroplast fusion proteins for BiFC can be difficult, and the availability and selection of appropriate controls is not trivial. Furthermore, the challenges of performing BiFC in restricted cellular compartments has not been specifically addressed. Here we describe the development of a flexible modular cloning-based toolkit (MoBiFC) for chloroplast BiFC and proximity labelling using synthetic biology principles. The approach facilitates the cloning process for chloroplast-targeted proteins, allows robust ratiometric quantification, and the toolkit comes with model positive and negative controls. Our study also highlights many potential pitfalls including the choice of fluorescent protein (FP) split, negative controls, cell type, and reference FP. Finally, we provide an example of how users can enrich the toolset by providing functional proximity labelling modules, and we discuss how MoBiFC could be further improved and extended to other compartments of the plant cell.

plant biology↗

bioRxiv2026

Inherited proliferation states organize plant transcriptomes

A central question in plant biology is whether natural transcriptome variation primarily reflects environmental adaptation or intrinsic genetic programs. Using transcriptomes from 665 natural Arabidopsis thaliana accessions, we show that inherited population structure, not environmental gradients, is the primary organizer of global transcriptome architecture. Genomic population structure uniquely explains 30.0% of transcriptome-wide variation, while environmental variables account for only 2.5%. This architecture is dominated by a single co-expression program (proliferation Module Eigengene: prolifME), enriched for cell cycle regulation and ribosome biogenesis, regulated by a bipartite transcription factor architecture, and genetically encoded at discrete loci with broad trans-regulatory effects. This proliferation program is associated with reduced plant size, biomass, growth rate and water-use efficiency, and these relationships persist under common-garden conditions. Gene contributions to this proliferation program are non-randomly conserved in rice and maize across 150-200 million years of divergence. These findings identify an intrinsic transcriptional proliferation program as a primary state of plant population transcriptomes, conserved across plant species.

plant biology↗