SEARCH · Search bioRxiv

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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.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 73 records · Page 4Linked to original sources

bioRxiv2025

The third alpha helix of plant homeoproteins are generally cell-penetrating to plant cells

Homeoproteins are transcription factors involved in developmental regulation. Animal homeoproteins are generally cell-penetrating to animal cells, capable of crossing membranes through a conserved 3rd alpha helix "penetration" domain. While plants also possess homeoproteins, the cell-penetrating ability of plant homeoproteins has not been investigated. We catalog the 3rd alpha helixes of plant homeoproteins across 851 species and screen a subset for the ability to penetrate walled-plant cells. We identify plant 3rd alpha helixes which are cell-penetrating to plants, the efficiency of which is amino acid sequence dependent, and use these peptides for cytosolic delivery of recombinant protein cargoes. We discover plant homeoproteins are generally cell-penetrating to plants, mirroring the behavior of animal homeoproteins, with applications in plant biotechnology and implications for fundamental plant biology.

plant biology↗

bioRxiv2024

Recognition and localization of maize leaves in RGB images based on Point-Line Net

Plant phenotype detection plays a crucial role in understanding and studying plant biology, agriculture, and ecology. It involves the quantification and analysis of various physical traits and characteristics of plants, such as plant height, leaf shape, angle, number, and growth trajectory. By accurately detecting and measuring these phenotypic traits, researchers can gain insights into plant growth, development, stress tolerance, and the influence of environmental factors. Among these phenotypic information, the number of leaves and growth trajectory of the plant are more accessible. Nonetheless, obtaining these information is labor-intensive and financially demanding. With the rapid development of computer vision technology and artificial intelligence, using maize field images to fully analyze plant-related information such as growth trajectory and number of leaves can greatly eliminate repetitive labor work and enhance the efficiency of plant breeding. However, the application of deep learning methods still faces challenges due to the serious occlusion problem and complex background of field plant images. In this study, we developed a deep learning method called Point-Line Net, which is based on the Mask R-CNN frame-work, to automatically recognize maize field images and determine the number and growth trajectory of leaves and roots. The experimental results demonstrate that the object detection accuracy (mAP) of our Point-Line Net can reach 81.5%. Moreover, to describe the position and growth of leaves and roots, we introduced a new lightweight "keypoint" detection branch that achieved 33.5 using our custom distance verification index. Overall, these findings provide valuable insights for future field plant phenotype detection, particularly for the datasets with dot and line annotations.

plant biology↗

bioRxiv2025

The highly conserved aphid effector pair Mp1-Mp58 associates to form an effector complex that targets host trafficking protein VPS52

Pathogen and pest effectors play a crucial role in manipulating plant biological processes, facilitating infection and infestation. While pathogens and pests secrete repertoires of effectors into their host plants, most effector function studies focus on characterising individual proteins. We previously identified a genetically linked and co-regulated gene pair in the aphid Myzus persicae encoding effectors Mp1 and Mp58. Here, we explored the functional link between these effectors. We used ectopic expression assays in Nicotiana benthamiana followed by co-immunoprecipitation assays and confocal microscopy to explore effector-effector and effector-target interactions and their subcellular localisation. We produced recombinant proteins to validate effector interactions and used computational modelling to predict effector complex 3D structures. We revealed that effectors Mp1 and Mp58 interact in planta and in vitro and likely form an oligomeric complex. Both effectors associate with the host target Vacuolar Protein Sorting associated Protein 52 (VPS52) to form an Mp1-Mp58-VPS52 complex which localises at vesicle-like structures. Our findings point to effector complex formation in plant-insect interactions and highlight a further layer of complexity in the molecular dialogue between plants and insects. Our work also shows the importance of considering the context in which effectors may function within a larger effector repertoire.

plant biology↗

bioRxiv2023

Harnessing deep learning to analyze cryptic morphological variability of Marchantia polymorpha

Characterizing phenotypes is a fundamental aspect of biological sciences, although it can be challenging due to various factors. For instance, the liverwort (Marchantia polymorpha), a model system for plant biology, exhibits morphological variability, making it difficult to identify and quantify distinct phenotypic features using objective measures. To address this issue, we utilized a deep learning-based image classifier that can handle plant images directly without manual extraction of phenotypic features, and analyzed bright-field images of M. polymorpha. This dioicous plant species exhibits morphological differences between male and female wild accessions at an early stage of gemmaling growth, although it remains elusive whether the differences are attributable to sexual dimorphism or autosomal genetic variation. To dissect the genomic factors, we established a male and female set of recombinant inbred lines (RILs) from a set of male and female wild accessions. We then trained deep-learning models to classify the sexes of the RILs and the wild accessions. Our results showed that the trained classifiers accurately classified male and female gemmalings of wild accessions in the first week of growth, confirming the intuition of plant researchers in a reproducible and objective manner. In contrast, the RILs were less distinguishable, indicating that the differences between the parental wild accessions arose from autosomal variations instead of sexual dimorphism. Furthermore, we validated our trained models by an "explainable AI" technique that highlights image regions relevant to the classification. Our findings demonstrate that the classifier-based approach provides a powerful tool for analyzing plant species that lack standardized phenotyping metrics.

plant biology↗

bioRxiv2021

Pontin/Reptin-associated complexes differentially impact plant development and viral pathology

Pontin and Reptin are essential eukaryotic AAA+ ATPases that work together in several multiprotein complexes, contributing to chromatin remodeling and TARGET OF RAPAMCYIN (TOR) kinase complex assembly, among other functions. Null alleles of pontin or reptin are gametophyte lethal in plants, which has hindered studies of their crucial roles in plant biology. Here, we used virus-induced gene silencing (VIGS) to interrogate the functions of Pontin and Reptin in plant growth and physiology, focusing on Nicotiana benthamiana, a model species for the agriculturally significant Solanaceae family. Silencing either Pontin or Reptin caused pleiotropic developmental and physiological reprogramming, including aberrant leaf shape, reduced apical growth, delayed flowering, increased branching, chlorosis, and decreased spread of the RNA viruses Tobacco mosaic virus (TMV) and Potato virus X (PVX). To dissect these pleiotropic phenotypes, we took a comparative approach and silenced expression of key genes that encode subunits of each of the major Pontin/Reptin-associated chromatin remodeling or TOR complexes (INO80, SWR-C/PIE1, TIP60, TOR, and TELO2). We found that many of the pontin/reptin phenotypes could be attributed specifically to disruption of one of these complexes, with tip60 and tor knockdown plants each phenocopying a large subset of pontin/reptin phenotypes. We conclude that Pontin/Reptin complexes are crucial for proper plant development, physiology, and stress responses, highlighting the multifaceted roles these conserved enzymes have evolved in eukaryotic cells.

plant biology↗

bioRxiv2026

The CUTIN SYNTHASE enzyme family was a key driver of cuticle emergence in land plants

The plant cuticle is a key adaptation acquired during the colonization of land. It forms a hydrophobic barrier at the interface with the environment, fulfilling essential protective and developmental functions. Despite its evolutionary significance and central role in land plant biology, the determinants that drove the emergence of the cuticle remain poorly understood. Here, we show that the CUTIN SYNTHASE (CUS) enzyme family, which synthesises the lipidic polyester that forms the structural framework of the cuticle in flowering plants, originated in a common ancestor of land plants, concomitant with terrestrialization. Using the moss Physcomitrium patens, we further demonstrate that CUS function is conserved among land plants. Inactivation of CUS genes disrupts gametophore development, the first tissue forming a cuticle during the moss life cycle, and compromises cuticle integrity. We also show that P. patens CUS enzymes localize to the apoplast, where they mediate the formation of a 10,16-dihydroxyhexadecanoic acid polyester using 2-mono-(10,16-dihydroxyhexadecanoyl)glycerol as substrate. Overall, our results reveal the conservation of CUS catalytic and physiological functions over 500 million years and support a pivotal role for this enzyme family in the emergence of the cuticle in an ancestral land plant during terrestrialization. SIGNIFICANCEThe cuticle is a hallmark of land plants that fulfills essential roles, ranging from protection to development. Elucidating the mechanisms underlying its emergence and formation therefore has the potential to reveal fundamental aspects of land plant evolution and biology. Here, we show that the CUTIN SYNTHASE (CUS) enzyme family, which catalyzes the formation of the cuticle framework in flowering plants, arose in an ancestor of land plants during terrestrialization. Using the moss Physcomitrium patens, we further demonstrate that CUS function has been conserved for 500 million years across bryophytes and tracheophytes. We propose that the emergence of the CUS family was a key event in establishing the plant cuticle during terrestrialization.

plant biology↗

bioRxiv2023

The cuticular wax compositions and crystal coverage of leaves and petals differ in a consistent manner between plant species

1Both leaves and petals are covered in a cuticle, which itself contains and is covered by, cuticular waxes. The waxes perform various roles in plants lives, and the cuticular composition of leaves has received much attention. To date, the cuticular composition of petals has been largely ignored. Being the outermost boundary between the plant and the environment, the cuticle is the first point of contact between a flower and a pollinator, yet we know little about how plant-pollinator interactions shape its chemical composition. Here, we investigate the general structure and composition of floral cuticular waxes by analysing the cuticular composition of leaves and petals of 49 plant species, representing 19 orders and 27 families. We show that the flowers of plants from across the phylogenetic range are nearly devoid of wax crystals, and that the total wax load of leaves in 90% of the species is higher than that of petals. The proportion of alkanes is higher, and the chain-lengths of the aliphatic compounds are shorter in petals than in leaves. We argue these differences are a result of the adaptation to the different roles leaves and petals play in plant biology.

plant biology↗

bioRxiv2018

Functional phenomics: An emerging field integrating high-throughput phenotyping, physiology, and bioinformatics

HighlightFunctional phenomics is an emerging field in plant biology that relies on high-throughput phenotyping, big data analytics, controlled manipulative experiments, and simulation modelling to increase understanding of plant physiology.\n\nAbstractThe emergence of functional phenomics signifies the rebirth of physiology as a 21st century science through the use of advanced sensing technologies and big data analytics. Functional phenomics highlights the importance of phenotyping beyond only identifying genetic regions because a significant knowledge gap remains in understanding which plant properties will influence ecosystem services beneficial to human welfare. Here, a general approach for the theory and practice of functional phenomics is outlined including exploring the phene concept as a unit of phenotype. The functional phenomics pipeline is proposed as a general method for conceptualizing, measuring, and validating utility of plant phenes. The functional phenomics pipeline begins with ideotype development. Second, a phenotyping platform is developed to maximize the throughput of phene measurements. A mapping population is screened measuring target phenes and indicators of plant performance such as yield and nutrient composition. Traditional forward genetics allows genetic mapping, while functional phenomics links phenes to plant performance. Based on these data, genotypes with contrasting phenotypes can be selected for smaller yet more intensive experiments to understand phene-environment interactions in depth. Simulation modeling can be used to understand the phenotypes and all stages of the pipeline feed back to ideotype and phenotyping platform development.

plant biology↗

bioRxiv2021

Generation of guard cell RNA-seq transcriptomes during progressive drought and recovery using an adapted INTACT protocol for Arabidopsis thaliana shoot tissue

Drought is an important environmental stress that limits crop production. Guard cells (GC) act to control the rate of water loss. To better understand how GCs change their gene expression during a progressive drought we generated guard cell-specific RNA-seq transcriptomes during mild, moderate, and severe drought stress. We additionally sampled re-watered plants that had experienced severe drought stress. These transcriptomes were generated using the INTACT system to capture the RNA from GC nuclei. We optimized the INTACT protocol for Arabidopsis thaliana leaf tissue, incorporating fixation to preserve RNA during nuclear isolation. To be able to identify gene expression changes unique to GCs, we additionally generated transcriptomes from all cell types, using a 35S viral promoter to capture the nuclei of all cell types in leaves. These data sets highlight shared and unique gene expression changes between GCs and the bulk leaf tissue. The timing of gene expression changes is different between GCs and other cell types: we found that only GCs had detectable gene expression changes at the earliest drought time point. The drought responsive GC and leaf RNA-seq transcriptomes are available in the Arabidopsis ePlant at the Bio-Analytic Resource for Plant Biology website.

plant biology↗

bioRxiv2018

Rootstock effects on scion phenotypes in a ‘Chambourcin’ experimental vineyard

Understanding how root systems modulate shoot system phenotypes is a fundamental question in plant biology and will be useful in developing resilient agricultural crops. Grafting is a common horticultural practice that joins the roots (rootstock) of one plant to the shoot (scion) of another, providing an excellent method for investigating how these two organ systems affect each other. In this study, we use the French-American hybrid grapevine Chambourcin (Vitis L.) as a model to explore the rootstock-scion relationship. We examined leaf shape, ion concentrations, and gene expression in Chambourcin grown own-rooted as well as grafted to three different rootstocks ( SO4, 1103P and 3309C) across two years and three different irrigation treatments. Results described here demonstrate that 1) the largest source of variation in leaf shape stems from the interaction of rootstock by irrigation; 2) leaf position, but also rootstock and rootstock by irrigation interaction, are the primary sources of variation in leaf ion concentrations; and 3) gene expression in scion leaves exhibited significantly different patterns of gene expression from ungrafted vines, and these expression patterns were rootstock-specific. Our work provides an initial description of the subtle and complex effect of grafting on Chambourcin leaf morphology, ionomics and gene expression in grapevine scions. Further work across multiple years, environments and additional phenotypes is required in order to determine how the relationship between the rootstock and the scion can best be leveraged for adapting grapevines to a changing climate.

plant biology↗

bioRxiv2024

Development of a Versatile System to Facilitate Targeted Knockout/Elimination Using CRISPR/Cas9 for Highly Duplicated Gene Families in Arabidopsis Sexual Reproduction

CRISPR/Cas9-based targeted gene editing is a fundamental technique for studying gene functions in various organisms. In plants, the introduction of a T-DNA construct harboring Cas9 nuclease and single guide RNA (sgRNA) sequences induces sequence-specific DNA double-strand breaks, inducing the loss of gene function. Arabidopsis thaliana is a model for CRISPR/Cas9 system development and gene function studies; the introduction of Cas9 under the egg or zygote promoter and multiple sgRNA modules generates heritable or non-mosaic mutants for multiple targets in the T1 generation of A. thaliana. Recent reports reflect use of several CRISPR/Cas9 vectors in generating single- and higher-order mutants; however, the development of a reliable, cost-effective, and high-throughput CRISPR/Cas9 platform is necessary for targeting highly duplicated gene families. In this study, we have developed a simple and user-friendly construction system for the CRISPR/Cas9 vector series with improved gene editing efficiency by simply inserting a single intron into Cas9, and effectively demonstrated the simultaneous knockout of multiple genes involved in A. thaliana sexual reproduction. An unbiased PCR-mediated mutant identification in the T1 generation revealed that our CRISPR/Cas9 system can support a > 70 kb deletion of > 30 tandemly duplicated synergid-specific genes and simultaneous knockout of five redundant genes essential for double fertilization. We performed a one-shot knockout of seven homologous pollen tube receptor-like kinase genes and identified their specific and overlapping roles in pollen tube growth and guidance. Our system can potentially facilitate further research in experimental plant biology to search for genetically unidentified components using reverse genetic candidate approaches.

plant biology↗

bioRxiv2025

Maternal Light and Temperature Modulate Seed Longevity in Arabidopsis

Seed longevity is defined as the length of time a seed can preserve its germination capacity, and it is a relevant trait for disciplines from agriculture to ecology. Seed longevity is a polygenic trait influenced by genetic and environmental factors. Despite the recognized impact of climate change on many reproductive aspects of plant biology, studies focused on how these new conditions affect this trait are scarce. In this work, we describe how environmental conditions to which the plants are exposed during seed development, termed the maternal environment effect, modulate longevity of the new developed seeds. Eight Arabidopsis thaliana natural accessions were grown on a combination of four different environmental scenarios: 22{degrees}C or 27{degrees}C at both low-light or high-light intensity. The combined effect of both 27{degrees}C and high light conditions generated seeds with higher longevity, although the effect is accession dependent. Similarly, an anticorrelation was found between seed dormancy and seed longevity when seeds were developed at 22{degrees}C under HL conditions, highlighting the importance of the environment in determining final seed properties. Transcriptome analysis of the Bor-4 accession, whose seeds presented the highest difference in longevity between conditions, revealed a very dynamic composition of stored mRNAs modulated by the four different environmental conditions during seed development. Nearly 80% of the differentially expressed genes exhibited a combined effect when both temperature and light-intensity were altered. Results suggest that seeds subjected to higher temperature and light intensity are primed with antioxidant defences and have a higher potential to deploy raffinose family oligosaccharides, which would be critical to safeguard cellular components during the ageing process.

plant biology↗

bioRxiv2026

City life: airborne DNA metagenomic biodiversity monitoring reveals dynamic changes across time and space

Airborne environmental DNA can capture biodiversity across the tree of life, but low sample biomass makes rapid, untargeted detection technically challenging. We combined 45-min air collection, nanopore sequencing and real-time taxonomic analysis in a shotgun metagenomic workflow capable of producing results within 3 hours. Across 77 samples from 13 London sites, including a year of weekly sampling at the Natural History Museum Wildlife Garden, we detected 1,916 species spanning bacteria, fungi, plants and animals. Communities varied spatially and seasonally, shifting from plant dominance in spring to ascomycete dominance in summer and basidiomycete dominance in late autumn and winter. Plant read abundance increased with upwind vegetation, linking airborne signals to surrounding habitat. Detection of catalogued garden plants depended on reference availability, dispersal biology, plant size and proximity to the collector. Together, these findings establish airborne shotgun metagenomics as a platform for rapid, repeated and scalable biodiversity assessment across space and time.

ecology↗

bioRxiv2026

Prime-Editing in Marchantia paleacea: Expanding the Genome-Editing Toolbox in Bryophytes

Since the development of CRISPR-based genome editing tools, a number of novel technologies have emerged. This includes Prime-Editing that acts as a search and replace genome editing tool. Prime-Editing has been deployed across multiple clades, including in a few flowering plants. Here, we report on the development of an efficient Prime Editor (PE) for the model bryophyte Marchantia. Initial tests were conducted on Acetolactate Synthase as a target and revealed an average efficiency above 40%. The system has been developed in the GoldenGate cloning system, facilitating construct design. The development of PE in Marchantia expands the Genome-Editing tools available for this emerging model in plant biology.

plant biology↗

bioRxiv2023

MINI-EX version 2: cell-type-specific gene regulatory network inference using an integrative single-cell transcriptomics approach

Understanding and predicting cell-type-specific gene regulatory networks (GRNs) is essential for unraveling the complex interactions between transcription factors (TFs) that modulate the expression of target genes and control diverse biological processes in multicellular organisms. MINI-EX (Motif-Informed Network Inference based on single-cell EXpression data) is an integrative tool tailored for identifying cell-type-specific GRNs in plants. Leveraging single-cell transcriptomics data, MINI-EX constructs expression-based networks and integrates TF motif information to produce GRNs with increased accuracy. Furthermore, it assigns regulatory modules to distinct cell types and prioritizes candidate regulators by employing a strategy that encompasses network centrality measures, functional annotations, and expression specificity. Taken together, MINI-EX offers a powerful approach to identify cell-type-specific transcriptional cascades and enhance our understanding of TF functions in plant biology. Here, we discuss recent advancements in the tools latest version and explain how single-cell GRNs can be identified for non-model species lacking TF motif information. Additionally, we provide a comprehensive guide to use MINI-EX, covering the entire pipeline from preparing input files starting from a single-cell experiment, over configuring parameters, to interpreting output data.

plant biology↗

bioRxiv2025

Triphenylphosphonium is an effective targeting moiety for plants mitochondria

Small signaling molecule regulates key physiological processes in plants, often in a spatially distinct manner. However, current methods for applying small-molecules, endogenous or synthetic, in plants research lack spatial precision, limiting the ability to study and utilize their localized effects. Here, we validate triphenylphosphonium (TPP) as a mitochondrial targeting motif in plants. Using fluorescently labeled TPP conjugates in Arabidopsis thaliana, we demonstrate mitochondria-specific accumulation, even in the presence of plastids. This precise localization enables detailed imaging of mitochondria and mitochondrial DNA in living plants. We further exploit this targeting ability by developing a TPP-ciprofloxacin conjugate to selectively inhibit mitochondrial DNA gyrase, an enzyme involved in organellar DNA replication. Unlike free ciprofloxacin, which disrupts both mitochondrial and chloroplast DNA gyrase activity, the TPP-conjugate specifically targets mitochondrial gyrase, leading to slower plant growth without affecting chloroplast function. This targeted inhibition triggers a mitochondrial retrograde response, characterized by increased reactive oxygen species levels and the upregulation of stress-response genes in the nucleus. Our findings establish TPP as a reliable tool for mitochondrial targeting in plants and open avenues for both fundamental research and agricultural applications. By enabling organelle-specific manipulation in species not amenable to genetic engineering, TPP-based strategies have potential for advancing plant biology and precision agriculture.

plant biology↗

bioRxiv2025

Cross-species optimization of nuclei isolation in plants

Single-cell technologies are transforming plant biology, yet broadly transferable nuclei isolation remains a key bottleneck for snRNA-seq. We developed a reproducible, Percoll-based workflow that is applicable to multiple maize tissues and eight additional plant species. In maize, nuclei from root, stem, leaf, and embryo consistently concentrated at the 80% Percoll interface and exhibited high integrity, with typical recoveries > 50,000 nuclei per sample. For other species, gradient compositions were tuned according to genome size to achieve efficient enrichment and clean suspensions, and yields ranged from 20,000 to 50,000 nuclei per sample. Downstream validation showed that nuclei from special interest maize and Tripsacum generated high-quality 10x Genomics snRNA-seq libraries, as supported by cDNA quality profiles. These results demonstrate the versatility and robustness of the method across species and tissues.

plant biology↗

bioRxiv2025

Uncoupling hypersensitive cell death response and disease resistance activated by effector-triggered immunity

Effector-triggered immunity (ETI) is a major defence strategy in plants and is frequently associated with the hypersensitive response (HR), a localized form of programmed cell death long assumed to be essential for pathogen resistance. However, the causal relationship between HR and effective immunity remains unresolved. We show that the Arabidopsis cbp60g sard1 double mutant exhibits exaggerated ETI-associated HR but only partial resistance to bacterial and oomycete pathogens, thereby genetically uncoupling cell death from disease resistance without pleiotropic defects. Genome-wide transcriptome profiling reveals that the absence of CBP60g and SARD1 disrupts the balance between immune activators and suppressors, including reduced induction of the Nudix hydrolase NUDT7. Overexpression of NUDT7 diminishes but does not abolish the heightened HR phenotype in cbp60g sard1 mutant, indicating that multiple negative regulators act redundantly to restrain immune-associated cell death. These findings demonstrate that HR is not an obligatory determinant of effective resistance and provide mechanistic insight into how plants coordinate transcriptional networks to balance pathogen defence with the containment of host cell death. By refining the relationship between HR and immunity, this work challenges a long-standing paradigm in plant biology and advances our understanding of immune regulation.

plant biology↗