Biology subjects

Provart, N. J.

Publications and source records attributed to Provart, N. J..

At least 19 recordsLinked to original sources

bioRxiv2026

Zea Lip: An atlas of glycerolipid profiles across leaf development in maize

Lipids are the predominant building blocks of plant membranes and are essential for plant growth and development. They are crucial for survival during times of stress as lipids are involved in multiple signaling pathways, and their relative abundances can change in response to environmental factors. To better characterize the lipid composition of the vital food crop maize, we generated a comprehensive glycerolipid atlas using ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. We surveyed the lipid profiles of three different maize genotypes: B73, a temperate inbred; CML312, a subtropical inbred; and Palomero Toluqueno, an open-pollinated variety from the Mexican highlands. We collected leaf samples from 4 developmental stages and 6 leaves. From one growth stage, we also sampled along with three leaf zones: base, center, and tip. The genotype and leaf number were the major drivers of lipid differences. Phosphatidylcholine, lysophosphatidylcholine, and triacylglycerol genotypic differences were particularly high. We generated an eFP browser to be integrated into the maize genome browser, as well as a separate web interface to easily browse and compare lipid levels across tissues and genotypes, available at https://bar.utoronto.ca/~dev/efp_maize_lipid/cgi-bin/efpWeb.cgi and https://rrellan.shinyapps.io/Zea-Lip/ respectively. SIGNIFICANCE STATEMENTThis work creates a spatial map of lipids in maize leaves across four growth stages for three genotypes: a lowland, a sub-tropical, and a highland. The resources generated here will directly benefit both the maize and lipid communities by creating a large dataset that can be used to generate new hypotheses in understanding lipid metabolism and environmental responses in maize.

plant biology↗

bioRxiv2025

The plant circadian clock exerts stronger control over the diel proteome than the transcriptome

AbstractThe plant circadian clock is a genetic circuit composed of multiple mutually-regulating transcription factors that together synchronize internal biological rhythms to the [~]24-hour period of planetary rotation. While it has been known for over a decade that nearly 40% of the transcriptome in the model plant Arabidopsis oscillates with a circadian rhythm, it is yet unclear to what extent this translates to the proteome. Here, through parallel quantitative proteome and transcriptome time-course profiling of Arabidopsis wild-type plants and a panel of clock deficient plant lines, we show that specific clock genes exercise extensive control over diel proteome rhythmicity, and to a much greater extent than they do the transcriptome. This control results in a clock-dependent synchronization of rhythmic proteins along a bimodal phase distribution that is lost in circadian clock deficient plants. This suggests pervasive post-translational control of gene expression by specific elements of the circadian system, notably the morning expressed LHY/CCA1 module. Our findings imply that the circadian clock exercises much greater control of gene expression through proteostasis mechanisms than previously recognised, necessitating a recalibration of our current understanding of clock proteins as primarily transcriptional regulators.

plant biology↗

bioRxiv2024

A pangenome and pantranscriptome of hexaploid oat

Oat grain is a traditional human food rich in dietary fiber that contributes to improved human health. Interest in the crop has surged in recent years owing to its use as the basis for plant-based milk analogs. Oat is an allohexaploid with a large, repeat-rich genome that was shaped by subgenome exchanges over evolutionary timescales. In contrast to many other cereal species, genomic research in oat is still at an early stage, and surveys of structural genome diversity and gene expression variability are scarce. Here, we present annotated chromosome-scale sequence assemblies of 33 wild and domesticated oats along with an atlas of gene expression across six tissues of different developmental stages in 23 accessions. We describe the interplay of gene expression diversity across subgenomes, accessions and tissues. Gene loss in the hexaploid is accompanied by compensatory up-regulation of the remaining homeologs, but this process is constrained by subgenome divergence. Chromosomal rearrangements have significantly impacted recent oat breeding. A large pericentric inversion associated with early flowering explains distorted segregation on chromosome 7D and a homeologous sequence exchange between chromosomes 2A and 2C in a semidwarf mutant has risen to prominence in Australian elite varieties. The oat pangeome will promote the adoption of genomic approaches to understanding the evolution and adaptation of domesticated oats and will accelerate their improvement.

genomics↗

bioRxiv2023

A high-resolution gene expression atlas of the medial and lateral domains of the gynoecium of Arabidopsis

Angiosperms are characterized by the formation of flowers, and in their inner floral whorl, one or various gynoecia are produced. These female reproductive structures are responsible for fruit and seed production, thus ensuring the reproductive competence of angiosperms. In Arabidopsis thaliana, the gynoecium is composed of two fused carpels with different tissues that need to develop and differentiate to consolidate a mature gynoecium and thus the reproductive competence of Arabidopsis. For these reasons, they have become the object of study for floral and fruit development. However, due to the complexity of the gynoecium, specific spatio-temporal tissues expression patterns are still scarce. In this study, we used precise laser-assisted microdissection and high-throughput RNA sequencing to describe the transcriptional profiles of the medial and lateral domain tissues of the Arabidopsis gynoecium. We provide evidence that the method used is reliable and that, in addition to corroborating gene expression patterns of previously reported regulators of these tissues, we found genes whose expression dynamics point to being involved in cytokinin and auxin homeostasis and in cell cycle progression. Furthermore, based on differential gene expression analyses, we functionally characterized several genes and found that they are involved in gynoecium development. This new resource is available via the Arabidopsis eFP browser and will serve the community in future studies on developmental and reproductive biology.

plant biology↗

bioRxiv2023

The transcriptome landscape of developing barley seeds reveals H3K27me3 dynamics in endosperm tissues

Cereal grains are an important food and feed. To provide comprehensive spatiotemporal information about biological processes in developing seeds of cultivated barley, we performed a transcriptomic study of the embryo, endosperm, and seed maternal tissues collected from 4 to 32 days after pollination. Weighted gene co-expression network and motif enrichment analyses pointed out specific groups of genes and transcription factors with possible impacts on regulating barley seed tissue development. We defined a set of tissue-specific marker genes and families of transcription factors for functional studies of the pathways controlling barley grain development. Assessment of selected groups of chromatin regulators revealed that epigenetic processes are highly dynamic and likely to play a major role during barley endosperm development. Repressive modification H3K27me3 is globally reduced in endosperm tissues and at specific developmental and storage compound genes. Altogether, this atlas uncovers the complexity of the developmental regulation of gene expression in barley grains. TeaserSpatiotemporal profiling of developing barley seeds revealed loss of H3K27me3 and changes in gene expression in endosperm.

plant biology↗

bioRxiv2023

The aerial epidermis is a major site of quinolizidine alkaloid biosynthesis in narrow-leafed lupin

Lupins are promising legume crops that accumulate toxic alkaloids in the seeds, complicating their use as high-protein crops. The alkaloids are synthesized in green organs (leaves, stems, and pods) and a subset of them is transported to the seeds during fruit development. The exact sites of biosynthesis and accumulation remain unknown, however mesophyll cells have been proposed as sources, and epidermal cells have been suggested as sinks. We examined the spatial localization of the alkaloids in biosynthetic organs of narrow-leafed lupin using mass spectrometry-based imaging (MSI). The alkaloids that accumulate in seeds ("core" alkaloids) were evenly distributed across tissues, however their esterified versions accumulated primarily in the epidermis. In addition, we generated a tissue-specific RNAseq dataset of biosynthetic organs using laser-capture microdissection. The dataset revealed that alkaloid biosynthetic genes are strongly expressed in the epidermis. To confirm the biosynthetic capacity of the leaf epidermis, we combined precursor feeding studies with mass spectrometry imaging, which showed that the lower epidermis is highly biosynthetic. Our work challenges the current assumptions on the precise sites of lupin alkaloid biosynthesis, with direct implications for the elucidation of the alkaloid biosynthesis pathway and the long-distance transport network from source to seed.

plant biology↗

bioRxiv2023

A laser capture microdissection transcriptome of M. truncatula roots responding to rhizobia reveals spatiotemporal tissue expression patterns of genes involved in nodule signaling and organogenesis

We report a public resource for examining the spatiotemporal RNA expression of 54,893 M. truncatula genes during the first 72 hours of response to rhizobial inoculation. Using a methodology that allows synchronous inoculation and growth of over 100 plants in a single media container, we harvested the same segment of each root responding to rhizobia in the initial inoculation over a time course, collected individual tissues from these segments with laser capture microdissection, and created and sequenced RNA libraries generated from these tissues. We demonstrate the utility of the resource by examining the expression patterns of a set of genes induced very early in nodule signaling, as well as two gene families (CLE peptides and nodule specific PLAT-domain proteins) and show that despite similar whole root expression patterns, there are tissue differences in expression between the genes. Using a rhizobial response data set generated from transcriptomics on intact root segments, we also examined differential temporal expression patterns and determined that, after nodule tissue, the epidermis and cortical cells contained the most temporally patterned genes. We circumscribed gene lists for each time and tissue examined and developed an expression pattern visualization tool. Finally, we explored transcriptomic differences between the inner cortical cells that become nodules and those that do not, confirming that the expression of ACC synthases distinguishes inner cortical cells that become nodules and provide and describe potential downstream genes involved in early nodule cell division.

plant biology↗

bioRxiv2022

Chromosome-level genome assembly of Euphorbia peplus, a model system for plant latex, reveals that relative lack of Ty3 transposons contributed to its small genome size

Euphorbia peplus (petty spurge) is a small, fast-growing plant that is native to Eurasia and has become a naturalized weed in North America and Australia. E. peplus is not only medicinally valuable, serving as a source for the skin cancer drug ingenol mebutate, but also has great potential as a model for latex production owing to its small size, ease of manipulation in the laboratory, and rapid reproductive cycle. To help establish E. peplus as a new model, we generated a 267.2 Mb HiC-anchored PacBio HiFi nuclear genome assembly with an embryophyta BUSCO score of 98.5%, a genome annotation based on RNA-seq data from six tissues, and publicly accessible tools including a genome browser and an interactive organ-specific expression atlas. Chromosome number is highly variable across Euphorbia species. Using a comparative analysis of our newly sequenced E. peplus genome with other Euphorbiaceae genomes, we show that variation in Euphorbia chromosome number is likely due to fragmentation and rearrangement rather than aneuploidy. Moreover, we found that the E. peplus genome is relatively compact compared to related members of the genus in part due to restricted expansion of the Ty3 transposon family. Finally, we identify a large gene cluster that contains many previously identified enzymes in the putative ingenol mebutate biosynthesis pathway, along with additional gene candidates for this biosynthetic pathway. The genomic resources we have created for E. peplus will help advance research on latex production and ingenol mebutate biosynthesis in the commercially important Euphorbiaceae family. Significance statementEuphorbia is one of the five largest genera in the plant kingdom. Despite an impressive phenotypic and metabolic diversity in this genus, only one Euphorbia genome has been sequenced so far, restricting insights into Euphorbia biology. Euphorbia peplus has excellent potential as a model species due to its latex production, fast growth rate and production of the anticancer drug ingenol mebutate. Here, we present a chromosome-level E. peplus genome assembly and publicly accessible resources to support molecular research for this unique species and the broader genus. We also provide an explanation of one reason the genome is so small, and identify more candidate genes for the anticancer drug and related compounds.

plant biology↗

bioRxiv2022

Characterization and visualization of global metabolomic responses of Brachypodium distachyon to environmental changes

Plant responses to environmental change are mediated via changes in cellular metabolomes. However, <5% of signals obtained from tandem liquid chromatography mass spectrometry (LC-MS/MS) can be identified, limiting our understanding of how different metabolite classes change under biotic/abiotic stress. To address this challenge, we performed untargeted LC-MS/MS of leaves, roots and other organs of Brachypodium distachyon, a model Poaceae species, under 17 different organ-condition combinations, including copper deficiency, heat stress, low phosphate and arbuscular mycorrhizal symbiosis (AMS). We used a combination of information theory-based metrics and machine learning-based identification of metabolite structural classes to assess metabolomic changes. Both leaf and root metabolomes were significantly affected by the growth medium. Leaf metabolomes were more diverse than root metabolomes, but the latter were more specialized and more responsive to environmental change. We also found that one week of copper deficiency shielded the root metabolome, but not the leaf metabolome, from perturbation due to heat stress. Using a recently published deep learning based method for metabolite class predictions, we analyzed the responsiveness of each metabolite class to environmental change, which revealed significant perturbations of various lipid classes and phenylpropanoids such as cinnamic acids and flavonoids. Co-accumulation analysis further identified condition-specific metabolic biomarkers. Finally, to make these results publicly accessible, we developed a novel visualization platform on the Bioanalytical Resource website, where significantly perturbed metabolic classes can be readily visualized. Overall, our study illustrates how emerging chemoinformatic methods can be applied to reveal novel insights into the dynamic plant metabolome and plant stress adaptation.

plant biology↗

bioRxiv2021

Marchantia polymorpha gene expression atlas reveals the hierarchy of abiotic stress responses and conservation of diurnal gene expression

Abiotic stresses negatively impact ecosystems and the yield of crops, and climate change will increase their frequency and intensity. Despite progress in understanding how plants respond to individual stresses, our knowledge of plant acclimatization to combined stresses-typically occurring in nature is still lacking. Here, we used a plant with minimal regulatory network redundancy, Marchantia polymorpha, to study how seven abiotic stresses, alone and in 19 pairwise combinations, affect the phenotype, gene expression, and activity of cellular pathways. We found a high divergence of transcriptomic stress responses between Arabidopsis and Marchantia, suggesting that the stress-specific gene regulatory networks (GRNs) between bryophytes and angiosperms are not strongly conserved. The reconstructed high-confidence GRNs demonstrated that the response to specific stresses dominates those of others by relying on a large ensemble of transcription factors. We also showed that a regression model could accurately predict the gene expression under combined stresses, indicating that Marchantia performs arithmetic addition to respond to multiple stresses. Finally, we provide two online resources (https://conekt.plant.tools and http://bar.utoronto.ca/efp_marchantia/cgi-bin/efpWeb.cgi) to facilitate the study of gene expression in Marchantia exposed to abiotic stresses.

plant biology↗

bioRxiv2021

Temporal Gene Expression in Apical Culms Shows Early Changes in Cell Wall Biosynthesis Genes in Sugarcane

Multiple genes in sugarcane control sucrose accumulation and the biosynthesis of cell wall components; however, it is unclear how these genes are expressed in its apical culms. To better understand this process, we sequenced mRNA from +1 stem internodes collected from four genotypes with different concentrations of soluble solids. Culms were collected at four different time points, ranging from six to 12-month-old plants. Here we show differentially expressed genes related to sucrose metabolism and cell wall biosynthesis, including genes encoding invertases, sucrose synthase and cellulose synthase. Our results showed increased expression of invertases in IN84-58, the genotype with lower sugar and higher fiber content, as well as delayed expression of secondary cell wall-related cellulose synthase for the other genotypes. Interestingly, genes involved with hormone metabolism were differentially expressed across time points in the three genotypes with higher soluble solids content. A similar result was observed for genes controlling maturation and transition to reproductive stages, possibly a result of selection against flowering in sugarcane breeding programs. These results indicate that carbon partitioning in apical culms of contrasting genotypes is mainly associated with differential cell wall biosynthesis, and may include early modifications for subsequent sucrose accumulation. Co-expression network analysis identified transcription factors related to growth and development, showing a probable time shift for carbon partitioning occurred in 10-month-old plants.

genomics↗

bioRxiv2021

ePlant in 2021: New Species, Viewers, Data Sets, and Widgets

ePlant was introduced in 2017 for exploring large Arabidopsis thaliana data sets from the kilometre to nanometre scales. In the past four years we have used the ePlant framework to develop ePlants for 15 agronomically-important species: maize, poplar, tomato, Camelina sativa, soybean, potato, barley, Medicago truncatula, eucalyptus, rice, willow, sunflower, Cannabis sativa, wheat and sugarcane. We also updated the interface to improve performance and accessibility, and added two new views to the Arabidopsis ePlant - the Navigator and Pathways viewers. The former shows phylogenetic relationships between homologs in other species and their expression pattern similarities, with links to view data for those genes in the respective ePlants. The latter shows Plant Reactome metabolic reactions. We also describe new Arabidopsis data sets including single cell RNA-seq data from roots, and how to embed ePlant eFP expression pictographs into any web page.

bioinformatics↗

bioRxiv2021

AGENT: the Arabidopsis Gene Regulatory Network Tool for Exploring and Analyzing GRNs

Gene regulatory networks (GRNs) are complex networks that capture multi-level regulatory events between one or more regulatory macromolecules, such as transcription factors (TFs), and their target genes. Advancements in screening technologies such as enhanced yeast-one-hybrid screens have allowed for high throughput determination of GRNs. However, visualization of GRNs in Arabidopsis has been limited to ad hoc networks and are not interactive. Here, we describe the Arabidopsis GEne Network Tool (AGENT) that houses curated GRNs and provides tools to visualize and explore them. AGENT features include expression overlays, subnetwork motif scanning, and network analysis. We show how to use AGENTs multiple built-in tools to identify key genes that are involved in flowering and seed development along with identifying temporal multi-TF control of a key transporter in nitrate signaling. AGENT can be accessed at https://bar.utoronto.ca/AGENT.

bioinformatics↗

bioRxiv2021

A 'Variant Viewer' for investigating population-level variation in Arabidopsis thaliana

High throughput sequencing has opened the doors for investigators to probe genetic variation present in large populations of organisms. In plants, the 1001 Genomes Project (1001genomes.org) is one such effort that sought to characterize the extant worldwide variation in Arabidopsis thaliana for future analyses to compare and draw upon. We developed a web application that accesses the 1001 Genomes database called The Variant Viewer, for investigators to view variants in any A. thaliana gene and within gene families. These variants may be visualized in the context of alignments of queried genes, across splice isoforms of these genes and in relation to conserved domains.

bioinformatics↗

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↗

bioRxiv2020

Innovation, conservation and repurposing of gene function in plant root cell type development

Plant species have evolved myriads of solutions to adapt to dynamic environments, including complex cell type development and regulation. To understand this diversity, we profiled tomato root cell type translatomes and chromatin accessibility. Using xylem differentiation in tomato, relative to Arabidopsis, examples of functional innovation, repurposing and conservation of transcription factors are described. Repurposing and innovation of genes are further observed within an exodermis regulatory network and illustrate its function. Translatome analyses of rice, tomato and Arabidopsis tissues suggest that root meristems are more conserved, and that the functions of constitutively expressed genes are more conserved than those of cell type/tissue-enriched genes. These observations suggest that higher-order properties of cell type and pan-cell type regulation are conserved between plants and animals. One Sentence SummaryPan-species cell type translatome and chromatin accessibility data reveal novelty, conservation and repurposing of gene function.

genomics↗

bioRxiv2019

The Tung Tree (Vernicia Fordii) Genome Provides A Resource for Understanding Genome Evolution and Oil Improvement

Tung tree (Vernicia fordii) is an economically important woody oil plant that produces tung oil containing a high proportion of eleostearic acid ([~]80%). Here we report a high-quality, chromosome-scale tung tree genome sequence of 1.12 Gb with 28,422 predicted genes and over 73% repeat sequences. Tung tree genome was assembled by combining Illumina short reads, PacBio single-molecule real-time long reads and Hi-C sequencing data. Insertion time analysis revealed that the repeat-driven tung tree genome expansion might be due to long standing long terminal repeat (LTR) retrotransposon bursts and lack of efficient DNA deletion mechanisms. An electronic fluorescent pictographic (eFP) browser was generated based on genomic and RNA-seq data from 17 various tissues and developmental stages. We identified 88 nucleotide-binding site (NBS)-encoding resistance genes, of which 17 genes may help the tung tree resist the Fusarium wilt shortly after infection. A total of 651 oil-related genes were identified and 88 of them were predicted to be directly involved in tung oil biosynthesis. The fewer phosphoenolpyruvate carboxykinase (PEPC) genes, and synergistic effects between transcription factors and oil biosynthesis-related genes may contribute to high oil content in tung seeds. The tung tree genome should provide valuable resources for molecular breeding and genetic improvement.

bioinformatics↗

bioRxiv2019

Transcriptomics at maize embryo/endosperm interfaces identify a novel transcriptionally distinct endosperm sub-domain adjacent to the embryo scutellum (EAS)

Seeds are complex biological systems comprising three genetically distinct tissues nested one inside another (embryo, endosperm and maternal tissues). However, the complexity of the kernel makes it difficult to understand inter compartment interactions without access to spatially accurate information. Here we took advantage of the large size of the maize kernel to characterize genome-wide expression profiles of tissues at embryo/endosperm interfaces. Our analysis identifies specific transcriptomic signatures in two interface tissues compared to whole seed compartments: The scutellar aleurone layer (SAL), and the newly named endosperm adjacent to scutellum (EAS). The EAS, which appears around 9 days after pollination and persists for around 11 days, is confined to one to three endosperm cell layers adjacent to the embryonic scutellum. Its transcriptome is enriched in genes encoding transporters. The absence of the embryo in an embryo specific (emb) mutant can alter the expression pattern of EAS marker genes. The detection of cell death in some EAS cells together with an accumulation of crushed cell walls suggests that the EAS is a dynamic zone from which cell layers in contact with the embryo are regularly eliminated, and to which additional endosperm cells are recruited as the embryo grows.

plant biology↗