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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2020

In-cell quantitative structural imaging of phytoplankton using 3D electron microscopy

Phytoplankton is a minor fraction of the global biomass playing a major role in primary production and climate. Despite improved understanding of phytoplankton diversity and genomics, we lack nanoscale subcellular imaging approaches to understand their physiology and cell biology. Here, we present a complete Focused Ion Beam - Scanning Electron Microscopy (FIB-SEM) workflow (from sample preparation to image processing) to generate nanometric 3D phytoplankton models. Tomograms of entire cells, representatives of six ecologically-successful phytoplankton unicellular eukaryotes, were used for quantitative morphometric analysis. Besides lineage-specific cellular architectures, we observed common features related to cellular energy management: i) conserved cell-volume fractions occupied by the different organelles; ii) consistent plastid-mitochondria interactions, iii) constant volumetric ratios in these energy-producing organelles. We revealed detailed subcellular features related to chromatin organization and to biomineralization. Overall, this approach opens new perspectives to study phytoplankton acclimation responses to abiotic and biotic factors at a relevant biological scale.

plant biology↗

bioRxiv2023

A fully sequenced collection of homozygous EMS mutants for forward and reverse genetic screens in Arabidopsis thaliana

Genetic screens are powerful tools for biological research and are one of the reasons for the success of the thale cress Arabidopsis thaliana as a model species. Here, we describe the whole-genome sequencing of 871 Arabidopsis lines from the Homozygous EMS Mutant (HEM) collection as a novel resource for forward and reverse genetics. With an average 576 high-confidence mutations per HEM line, over three independent mutations altering protein sequence are found on average per gene in the collection. Pilot reverse genetics experiments on reproductive, developmental and physiological traits confirmed the efficacy of the tool for identifying both null and knockdown alleles. The possibility of conducting subtle repeated phenotyping of HEM lines and the immediate availability of the mutations will empower forward genetic approaches. The sequence resource is searchable with the ATHEM web interface (https://lipm-browsers.toulouse.inra.fr/pub/ATHEM/), and the biological material is distributed by the Versailles Arabidopsis Stock Center.

plant biology↗

bioRxiv2023

AGAMOUS-like 6 and MYB DOMAIN PROTEIN 80 regulate the development of female and male cones in Pinus densiflora S. et Z.

To shorten the long breeding period of forest trees, it is necessary to explore biological factors and key genes involved in reproduction. We compared the transcriptomes of female and male cones and then identified major biological processes and hub genes associated with the development of female and male cones in Pinus densiflora. The reproductive and vegetative tissues of P. densiflora were sampled from various developmental stages and a reference transcriptome was generated. Functional annotation and Gene Ontology enrichment analysis of differentially expressed genes were performed as well as gene co-expression network analysis for identifying the hub genes involved in the cone development. Lignin biosynthesis and cell wall loosening were activated in the early and late female cones, respectively. Metabolism of pollen wall components was predominant in the early male cones compared with the later stage. In addition, phytohormone-related genes were highly expressed in the early female cones in contrast to the early male cones. Finally, we found that AGAMOUS-like 6 and MYB DOMAIN PROTEIN 80 were hub genes of the female and male cone development, respectively. This study suggests that various biological factors contribute to reproductive developmental processes. Furthermore, these data will provide the new insight into biotechnology and breeding methods for improving cone and seed production of P. densiflora.

plant biology↗

bioRxiv2017

CropQuant: An automated and scalable field phenotyping platform for crop monitoring and trait measurements to facilitate breeding and digital agriculture

Automated phenotyping technologies are capable of providing continuous and precise measurements of traits that are key to todays crop research, breeding and agronomic practices. In additional to monitoring developmental changes, high-frequency and high-precision phenotypic analysis can enable both accurate delineation of the genotype-to-phenotype pathway and the identification of genetic variation influencing environmental adaptation and yield potential. Here, we present an automated and scalable field phenotyping platform called CropQuant, designed for easy and cost-effective deployment in different environments. To manage infield experiments and crop-climate data collection, we have also developed a web-based control system called CropMonitor to provide a unified graphical user interface (GUI) to enable realtime interactions between users and their experiments. Furthermore, we established a high-throughput trait analysis pipeline for phenotypic analyses so that lightweight machine-learning modelling can be executed on CropQuant workstations to study the dynamic interactions between genotypes (G), phenotypes (P), and environmental factors (E). We have used these technologies since 2015 and reported results generated in 2015 and 2016 field experiments, including developmental profiles of five wheat genotypes, performance-related traits analyses, and new biological insights emerged from the application of the CropQuant platform.

plant biology↗

bioRxiv2024

Lactuca super-pangenome reduces bias towards reference genes in lettuce research

Breeding of lettuce (Lactuca sativa L.), the most important leafy vegetable worldwide, for enhanced disease resistance and resilience relies on multiple wild relatives to provide the necessary genetic diversity. In this study, we constructed a super-pangenome based on four Lactuca species (representing the primary, secondary and tertiary gene pools) and comprising 474 accessions. We include 68 newly sequenced accessions to improve cultivar coverage and add important foundational breeding lines. With the super-pangenome we find substantial presence/absence variation (PAV) and copy-number variation (CNV). Functional enrichment analyses of core and variable genes show that transcriptional regulators are conserved whereas disease resistance genes are variable. PAV-genome-wide association studies (GWAS) and CNV-GWAS are largely congruent with single-nucleotide polymorphism (SNP)-GWAS. Importantly, they also identify several major novel quantitative trait loci (QTL) for resistance against Bremia lactucae in variable regions not present in the reference lettuce genome. The usability of the super-pangenome is demonstrated by identifying the likely origin of non-reference resistance loci from the wild relatives Lactuca serriola, Lactuca saligna and Lactuca virosa. The provided methodology and data provide a strong basis for research into PAVs, CNVs and other variation underlying important biological traits of lettuce and other crops.

plant biology↗

bioRxiv2025

In situ GCIB Cryo-Sectioning Enables Subcellular Cryo-ToF-SIMS Imaging of Arabidopsis Seeds

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) enables label-free molecular imaging at submicrometric resolution, but its application to biological samples remains limited due to sample preparation challenges. Conventional fixation or dehydration alters morphology and induces analyte relocation, while cryo-transfer systems are costly and technically demanding. We present an in situ cryo-etching approach using a gas cluster ion beam (GCIB) and a new sample holder with a flat titanium ridge mask, enabling the sectioning of frozen specimens directly inside the ToF-SIMS instrument. Using Arabidopsis thaliana seeds as a model, this method produced flat, artefact-free surfaces suitable for subcellular imaging without chemical treatment or cryo-transfer. Mass spectra showed intact molecular profiles up to 1000 Da, and ToF-SIMS ion maps revealed preserved tissue architecture and distinct subcellular compartments at a resolution of [~]1 {micro}m. Compared to air-dried cryosections, cryo-etching eliminated structural collapse and analyte delocalization. This workflow provides a practical and accessible route for cryo-ToF-SIMS analysis of hydrated biological materials, combining structural fidelity with molecular integrity. It offers a simple alternative to conventional cryo-transfer methods for high-resolution chemical imaging.

plant biology↗

bioRxiv2023

Assessing the activity of different plant-derived molecules and potential biological nitrification inhibitors on a range of soil ammonia- and nitrite- oxidizing strains

Nitrification is associated with significant losses of fertilizer-derived ammonium from agroecosystems. The use of biological nitrification inhibitors (BNIs), in place of synthetic nitrification inhibitors (SNIs), holds a great potential to effectively reduce N losses and conforms with the current move towards ecological-intensified agriculture. Knowledge of the activity of BNIs to soil nitrifiers is limited and is mostly based on bioassays with a single Nitrosomonas europaea strain. We determined the in vitro activity of multiple plant-derived compounds as BNIs like (i) root-derived compounds (sakuranetin, MHPP, and zeanone); (ii) other phytochemicals (caffeic acid, quinic acid, chlorogenic acid and shikimic acid), and (iii) analogues of statins (simvastatin), triazoles (1-butyl-4-propyl-triazole, 1,4-dibutyltriazole) and zeanone (2-methoxy-1,4-naphthoquinone), on ecophysiologically and phylogenetically distinct soil-derived ammonia-oxidizing bacteria (AOB) (Nitrosospira multiformis and N. europaea), ammonia-oxidizing archaea (AOA) (Candidatus Nitrosotalea sinensis and Candidatus Nitrosocosmicus franklandianus), and a nitrite-oxidizing bacterium (NOB) (Nitrobacter sp. NHB1). AOA were more sensitive than AOB to BNIs. Sensitivity within AOA group was BNI-dependent, unlike AOB for which N. multiformis was consistently more sensitive than N. europaea. Interestingly, several compounds were inhibitory to Nitrobacter sp. with MHPP and caffeic acid being more potent to the NOB compared to the AOB and AOA strains, an observation with potentially serious implications for soil quality and agricultural production. Overall, zeanone, MHPP and caffeic acid were the most potent BNIs towards AOB, zeanone and 2-methoxy-1,4-naphthoquinone were the most effective compounds against AOA, while caffeic acid was the most potent BNI on Nitrobacter sp. We provide pioneering evidence for the activity range of multiple BNIs on soil nitrifiers, stress the need for revisiting the biological screening systems currently used for BNI determination and we sought for a more thorough monitoring of the impact of BNI candidates on a range of both target and non-target microorganisms.

microbiology↗

bioRxiv2023

The Arabidopsis Information Resource in 2024

Since 1999, The Arabidopsis Information Resource (www.arabidopsis.org) has been curating data about the Arabidopsis thaliana genome. Its primary focus is integrating experimental gene function information from the peer-reviewed literature and codifying it as controlled vocabulary annotations. Our goal is to produce a gold standard functional annotation set that reflects the current state of knowledge about the Arabidopsis genome. At the same time, the resource serves as a nexus for community-based collaborations aimed at improving data quality, access and reuse. For the past decade, our work has been made possible by subscriptions from our global user base. This update covers our ongoing biocuration work, some of our modernization efforts that contribute to the first major infrastructure overhaul since 2011, the introduction of JBrowse2, and the resources role in community activities such as organizing the structural reannotation of the genome. For gene function assessment, we used Gene Ontology annotations as a metric to evaluate: (1) what is currently known about Arabidopsis gene function, and (2) the set of unknown genes. Currently, 74% of the proteome has been annotated to at least one Gene Ontology term. Of those loci, half have experimental support for at least one of the following aspects: molecular function, biological process, or cellular component. Our work sheds light on the genes for which we have not yet identified any published experimental data and have no functional annotation. Drawing attention to these unknown genes highlights knowledge gaps and potential sources of novel discoveries. Article SummaryThe Arabidopsis Information Resource (TAIR, www.arabidopsis.org) is a comprehensive website about Arabidopsis thaliana, a small plant thats very easy to grow and analyze in the laboratory and is used to understand how many other plants function. We share our progress in data collection and organization, website and tool improvement, and our involvement in community projects.

plant biology↗

bioRxiv2020

Genome-Wide Association Mapping of Sugarcane Yellow Leaf Virus Resistance

A major disease affecting sugarcane, a leading sugar and energy crop, is sugarcane yellow leaf (SCYL), caused by the sugarcane yellow leaf virus (SCYLV). Despite damages caused by SCYLV, the genetic basis of resistance to this virus remains largely unknown. Several methodologies have arisen to identify molecular markers associated with SCYLV resistance, which are crucial for marker-assisted selection and understanding response mechanisms to this virus. We investigated the genetic basis of SCYLV resistance using dominant and codominant markers and genotypes of interest for breeding. A sugarcane panel inoculated with SCYLV was analyzed for SCYL symptoms, and viral titer was estimated by RT-qPCR. This panel was genotyped with 662 dominant markers and 70,888 SNPs and indels with allele proportion information. We used polyploid-adapted genome-wide association analyses and machine-learning algorithms coupled with feature selection methods to establish marker-trait associations. While each approach identified unique marker sets associated with phenotypes, convergences were observed between them, demonstrating their complementarity. Lastly, we annotated these markers, identifying genes encoding emblematic participants in virus resistance mechanisms and previously unreported candidates involved in viral responses. Our approach could accelerate sugarcane breeding targeting SCYLV resistance and facilitate studies on biological processes leading to this trait.

plant biology↗

bioRxiv2019

LYS3 encodes a prolamin-box-binding transcription factor that controls embryo growth in barley and wheat

Mutations at the LYS3 locus in barley have multiple effects on grain development, including an increase in embryo size and a decrease in endosperm starch content. The gene underlying LYS3 was identified by genetic mapping and mutations in this gene were identified in all four barley lys3 alleles. LYS3 encodes a transcription factor called Prolamin Binding Factor (PBF). Its role in controlling embryo size was confirmed using wheat TILLING mutants. To understand how PBF controls embryo development, we studied its spatial and temporal patterns of expression in developing grains. The PBF gene is expressed in both the endosperm and the embryos, but the timing of expression in these organs differs. PBF expression in wild-type embryos precedes the onset of embryo enlargement in lys3 mutants, suggesting that PBF suppresses embryo growth. We predicted the down-stream target genes of PBF in wheat and found them to be involved in a wide range of biological processes, including organ development and starch metabolism. Our work suggests that PBF may influence embryo size and endosperm starch synthesis via separate gene control networks. HIGHLIGHTSO_LILYS3 encodes a transcription factor called Prolamin Binding Factor (PBF) that is expressed in grains only. C_LIO_LIWheat and barley LYS3/PBF mutants have enlarged embryos suggesting that this gene suppresses embryo growth. C_LIO_LIThe down-stream target genes of PBF in wheat are predicted to be involved in a wide range of biological processes including organ development and starch metabolism. C_LI

plant biology↗

bioRxiv2023

Canonical and ETT-mediated auxin signalling pathways synergistically promote gynoecium development in Arabidopsis thaliana

Gynoecium polarity establishment is regulated by auxin, a phytohormone whose signal is transduced through several pathways. The relationship between the ETT and canonical TIR1/AFB pathways, and their relevance for carpel development beyond Arabidopsis thaliana, have not been investigated. The data presented here show that the expression patterns of canonical and ETT-mediated signalling components, and phenotypes of higher order mutants are shared between Arabidopsis and Capsella rubella. tir1 afb2 ett mutants partially phenocopy ett arf4 double mutants, suggesting a role for AUXIN RESPONSE FACTOR 4 (ARF4) in the integration of canonical and ETT-mediated signalling. Comparative transcriptomics revealed that the auxin-independent mis-regulation of YABBY genes correlate with patterning defects observed in Arabidopsis ett arf4 mutants. Together, the data presented suggest conserved synergism between canonical and ETT-mediated pathways in gynoecium polarity establishment in the Brassicaceae. Finally, the data suggest that ETT/ARF4 function to prevent the auxin-induced expression of a range of targets in Arabidopsis, consistent with activator-repressor ARF antagonism, and implying that the maintenance of auxin insensitivity by repressive ARFs is important for a range of biological processes. Summary StatementHere the relationship between canonical and ETT-mediated auxin signalling machineries is investigated in Arabidopsis and Capsella revealing conserved synergism between these two pathways in Brassicaceae with distinct fruit shapes.

plant biology↗

bioRxiv2018

Drought frequency predicts life history strategies in Heliophila

Explaining variation in life history strategies is a long-standing goal of evolutionary biology. For plants, annual and perennial life histories are thought to reflect adaptation to environments that differ in the frequency of stress events such as drought. Here we test this hypothesis in Heliophila (Brassicaceae), a diverse genus of flowering plants native to Africa, by integrating 34 years of satellite-based drought measurements with 2192 herbaria occurrence records. Consistent with predictions from classic life history theory, we find that perennial Heliophila species occur in environments where droughts are significantly less frequent compared to annuals. These associations are predictive while controlling for phylogeny, lending support to the hypothesis that drought related natural selection has influenced the distributions of these strategies. Additionally, the collection dates of annual and perennial species indicate that annuals escape drought prone seasons during the seed phase of their life cycle. Together, these findings provide empirical support for classic hypotheses about the drivers of life history strategy in plants - that perennials out compete annuals in environments with less frequent drought and that annuals are adapted to environments with more frequent drought by escaping drought prone seasons as seeds.

evolutionary biology↗

bioRxiv2026

Genetic analysis of grapevine wood composition identifies glycosyltransferases involved in the biosynthesis of stilbene glycosides

Although wood extractives may play important roles in defense against pathogens, few studies have explored the genetic determinism of their accumulation. In this work, we have used a non-targeted metabolomic approach to perform a genetic analysis of grapevine (Vitis vinifera) wood extractive composition in a progeny from a cross between Riesling and Gewurztraminer. Metabolic quantitative trait loci (mQTL) analyses of cane and trunk wood extractives revealed a number of mQTLs. Analysis of one of these mQTL has led to the identification of a cluster of six UDP glycosyltransferase (UGT) genes linked to the accumulation of resveratrol-glucoside (piceid) in both canes and trunks. Detailed biochemical and structural characterization of these six UGTs highlighted a surprising functional diversity among this small gene family, as well as one UGT gene as a key determinant of the constitutive accumulation of piceid in lignified grapevine tissues. Molecular evolution analyses showed that the UGTs in this gene cluster were globally under strong purifying selection, suggesting important biological roles of the corresponding proteins. Moreover, the functional characterization showed that distinct UGT genes were involved in the biosynthesis of cis- and trans- isomers of piceid, suggesting that these isomers may play different biological roles in grapevine.

plant biology↗

bioRxiv2022

The circadian clock controls temporal and spatial patterns of floral development in sunflower

Biological rhythms are ubiquitous. They can be generated by circadian oscillators, which produce daily rhythms in physiology and behavior, as well as by developmental oscillators such as the segmentation clock, which produces modular developmental units in a periodic fashion. Here, we show that the circadian clock controls the timing of late-stage floret development, or anthesis, in domesticated sunflower. In these plants, what appears to be a single inflorescence consists of up to thousands of individual florets tightly packed onto a capitulum disk. While early floret development occurs continuously across capitula to generate iconic spiral phyllotaxy, during anthesis floret development occurs in discrete ring-like pseudowhorls with up to hundreds of florets undergoing simultaneous maturation. We demonstrate circadian regulation of floral organ growth and show that the effects of light on this process are time-of-day dependent. Disruption of circadian rhythms in floral organ development causes loss of pseudowhorl formation. Thus, we show that the sunflower circadian clock acts in concert with environmental response pathways to tightly synchronize the anthesis of hundreds of florets each day, generating spatial patterns on the developing capitulum disk. This coordinated mass release of floral rewards at predictable times of day likely promotes pollinator visits and plant reproductive success.

plant biology↗

bioRxiv2018

Switching toxic protein function in life cells

Toxic proteins are prime targets for molecular farming and efficient tools for targeted cell ablation in genetics, developmental biology, and biotechnology. Achieving conditional activity of cytotoxins and their maintenance in form of stably transformed transgenes is challenging. We demonstrate here a switchable version of the highly cytotoxic bacterial ribonuclease barnase by using efficient temperature-dependent control of protein accumulation in living multicellular organisms. By tuning the levels of the protein, we were able to control the fate of a plant organ in vivo. The on-demand-formation of specialized epidermal cells (trichomes) through manipulating stabilization versus destabilization of barnase is a proof-of-concept for a robust and powerful tool for conditional switchable cell arrest. We present this tool both as a potential novel strategy for the manufacture and accumulation of cytotoxic proteins and toxic high-value products in plants or for conditional genetic cell ablation.

plant biology↗

bioRxiv2026

Single-cell transcriptomic landscapes reveal cell-type-specific regulatory mechanisms of nutrient accumulation and transport in wheat grain

To elucidate the transcriptional regulatory mechanisms underlying wheat grain development, we constructed single-cell transcriptomic atlases of wheat grains at 4 and 8 days after pollination (DAP) using single-nucleus RNA sequencing. A total of 58,546 high-quality nuclei were clustered into 16 distinct cell populations representing all major seed tissues, including the embryo, aleurone layer, transfer cells, endosperm, inner pericarp, seed coat, and embryo surrounding region. Comparative analysis revealed a dynamic transcriptional reprogramming from growth-related pathways at DAP 4 to nutrient accumulation at DAP 8, which coincided with shifts in the expression of hormone signaling and organ development genes, as well as starch and storage protein genes. Pseudotime trajectory analysis identified two major differentiation branches, highlighting distinct roles in nutrient storage and support. Notably, the transcription factor TaMADS58 was found to regulate pericarp cell number while simultaneously enhancing protein content and processing quality. Concurrently, TaJEKLL, specifically expressed in nucellar projection cells, was demonstrated to influence nucellar projection development and nutrient transport. Natural variation in TaMADS58 and TaJEKLL revealed their potential to decouple yield from quality traits, offering promising applications for crop improvement. Collectively, this study provides a high-resolution single-cell resource for wheat seed biology and demonstrates that investigating gene expression with spatiotemporal precision at the single-cell level can facilitate the discovery of key genes for precisely regulating individual traits.

plant biology↗

bioRxiv2026

LeafContourEFD: a reproducible workflow for elliptic Fourier analysis with orientation normalization and lateral asymmetry

PremiseElliptic Fourier analysis is widely used to quantify leaf shape variation, but inconsistent normalization and orientation alignment can introduce biologically irrelevant variation. In addition, a reproducible workflow from raw images to normalized elliptic Fourier descriptors (EFDs) is still lacking. Methods and ResultsWe developed LeafContourEFD, a GUI application for reproducible leaf morphometrics. It integrates image segmentation, contour extraction, EFD calculation, and an extended normalization framework, termed oriented true EFD normalization, based on a user-defined biological reference axis. Analyses of Quercus serrata, Q. crispula, and Triadica sebifera showed that existing normalization methods can introduce orientation-related variance when the first-harmonic major axis does not match the leaf base-to-tip axis. In contrast, oriented true normalization removed these artifacts, yielding clearer shape transitions along principal components allowing shape variation among leaves to be captured while preserving biologically meaningful lateral asymmetry. ConclusionsLeafContourEFD improves interpretability and reproducibility in outline-based morphometrics and provides transparent outputs and metadata for data sharing and cross-study comparisons.

plant biology↗

bioRxiv2018

Widespread inter-individual gene expression variability in Arabidopsis thaliana

A fundamental question in biology is how gene expression is regulated to give rise to a phenotype. However, transcriptional variability is rarely considered and could influence the relationship between genotype and phenotype. It is known in unicellular organisms that gene expression is often noisy rather than uniform and this has been proposed to be beneficial when environmental conditions are unpredictable. However, little is known about transcriptional variability in plants. Using transcriptomic approaches, we analysed gene expression variability between individual Arabidopsis thaliana plants growing in identical conditions over a 24 hour time-course. We identified hundreds of genes that exhibit high inter-individual variability and found that many are involved in environmental responses. We also identified factors that might facilitate gene expression variability, such as gene length, the number of transcription factors regulating the genes and the chromatin environment. These results shed new light on the impact of transcriptional variability in gene expression regulation in plants.

plant biology↗