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bioRxiv2024

TOTEM: A web TOol for Tissue-EnrichMent analysis on gene lists

Analysis of spatiotemporal patterns of gene expression is crucial to decode biological systems responses. High-throughput sequencing allows in-depth transcriptome analyses and experimental designs, providing valuable reference expression atlases. Specifically, testing overrepresentations of tissue-specific genes based on these atlases can provide valuable insights; however, such an approach is not accessible to inexperienced users. Here, we introduce TOTEM (TOol for Tissue-EnrichMent), a web tool designed to calculate enrichment values per tissue by identifying tissue-specific genes from an organ/organism of interest given a user gene list. Results are visually represented, and users gene classified. The utility of TOTEM is manifest when using integrated single cell expression atlases, enabling the study of complicated tissues, with the maximum possible resolution. Its effectiveness is validated by the study of BRL3 role in stress specifically from the vascular tissues. Finally, TOTEMs modular design allows for continual integration of new experiments. TOTEM can be freely accessed at: https://totemwebtool.com.

plant biology↗

bioRxiv2021

The desert green algae Chlorella ohadii thrives at excessive high light intensities by exceptionally enhancing the mechanisms that protect photosynthesis from photoinhibition

Although light is the driving force of photosynthesis, excessive light can be harmful. One of the main processes that limits photosynthesis is photoinhibition, the process of light-induced photodamage. When the absorbed light exceeds the amount that is dissipated by photosynthetic electron flow and other processes, damaging radicals are formed that mostly inactivate photosystem II (PSII). Damaged PSII must be replaced by a newly repaired complex in order to preserve full photosynthetic activity. Chlorella ohadii is a green micro-alga, isolated from biological desert soil crusts, that thrives under extreme high light and is highly resistant to photoinhibition. Therefore, C. ohadii is an ideal model for studying the molecular mechanisms underlying protection against photoinhibition. Comparison of the thylakoids of C. ohadii cells that were grown under low light versus extreme high light intensities, found that the alga employs all three known photoinhibition protection mechanisms: i) massive reduction of the PSII antenna size; ii) accumulation of protective carotenoids; and iii) very rapid repair of photo-damaged reaction center proteins. This work elucidated the molecular mechanisms of photoinhibition resistance in one of the most light-tolerant photosynthetic organisms and shows how photoinhibition protection mechanisms evolved to marginal conditions, enabling photosynthesis-dependent life in severe habitats. One Sentence HighlightAnalysis of the photosynthetic properties of a desert algae that thrives at extreme high light intensities revealed protection from photoinhibition driven by the remarkable enhancement of three protection mechanisms.

plant biology↗

bioRxiv2024

Palynological studies on selected members of Fabaceae

The investigation into pollen biology encompasses various stages such as pollen production, transfer to stigma, and the ensuing interactions leading to fertilization. Stigma plays a crucial role in providing an optimal environment for pollen germination and subsequent tube growth. However, conducting in vivo studies presents challenges due to the complexities of pistillate tissues, thus necessitating a reliance on in vitro cultures to comprehend pollen physiology. This study focuses on assessing pollen viability and germination in a selection of Fabaceae species, including Canavalia gladiata, Centrosoma pubescens, Clitoria ternatea, Crotalaria pallida, Glyricidia maculata, Pueraria phaseoloides, and Vigna unguiculata, utilizing tetrazolium testing and hanging drop culture methods. Results demonstrate a range of variability in pollen viability (from 19.38% to 80.78%) and germination (ranging from 23.90% to 79.81%), with Crotalaria pallida exhibiting the highest rates of viability and germination, whereas Clitoria ternatea and Pueraria phaseoloides displayed the lowest rates. This investigation contributes valuable insights into the pollen characteristics of Fabaceae species, hinting at possible connections between pollen viability/germination and seed/fruit set percentages.

plant biology↗

bioRxiv2020

Cucumber Mosaic Virus and their associated satellite RNAs infecting banana (Musa sp. Genomic group AAA) in Cote dIvoire : A molecular characterization.

In Cote dIvoire, banana (Musa sp.) ranks third among exportation products and represents 3% of the Gross Domestic Product with a national production up to 500000 tons in 2019. Banana is subject to numerous disease agents among which viruses cause significant losses. To figure out the impact of viruses in Ivorian industrial banana fields, surveys were conducted in the 7 main banana production departments. A total of 260 leaf fragments presenting viral symptoms were collected and analyzed. From the 65 leaf fragments used for biological indexing, 14 showed symptoms related to Cucumber mosaic virus (CMV). CMV presence was confirmed by double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) using CMV polyclonal antibodies. CMV strains we isolated, appeared to be highly infectious and to produce various symptoms like mosaic, chlorosis, and necrotic spots on Cucumis sativus, Cucurbita pepo, and Nicotiana tabacum. Satellite RNAs (SatRNAs) associated with CMV isolates were also detected using reverse transcription polymerase chain reaction (RT-PCR) with a degenerate primer pair. CMVs coat protein as well as satRNAs was sequenced. Novel Ivorian coat proteins and satRNAs were compared to publicly available sequences. We noticed a single amino acid substitution (Serine to Leucine) at position 73 of the novel coat protein that allowed us to divide Ivorian CMV strains into two groups. Molecular and phylogenetic analysis suggested that Ivorian strains might be classified into CMV Subgroup IA. We also discovered that satellite RNA associated with Ivorian CMVs form a separate clade.

plant biology↗

bioRxiv2024

Mechanical stress orients stomata division to form tissue scale alignments.

The last stomatal division aligns with the leafs main axis in many species [1]. Understanding how cellular events such as these are coordinated across organ scales remains a challenge in developmental biology. In Arabidopsis, polarised proteins guide the asymmetric divisions in the early stomatal lineage. These proteins show organ scale alignment and may be sensitive to mechanical stress [2]. In contrast, what determines the orientation and alignment of the critical final division is unknown [3]. Here we use an artificial system where every cell adopts the fate of a stomata pore [4] making it easy to visualise their alignment. Combining this system with simultaneous time-lapse imaging on both sides of the cotyledon we are able to compare the stomatal orientation relative to the organ axis, the cell major axis, and the principal directions of growth. Using finite element modelling on a realistic template enabled us to identify differential growth-derived stress patterns as a factor coordinating stomata division at the organ scale. Mechanical perturbation confirmed the influence of tensile stress on stomata division orientation. Through this study, we have identified a mechanism that can explain this nearly century-old observation.

plant biology↗

bioRxiv2026

Spatial expression evolution of duplicated genes post-whole genome duplication in cultivated tomato

The mechanisms by which whole genome duplication contributes to expression divergence of duplicate genes, which can impact the evolution of form and function, has been a long-standing question in evolutionary biology. We compared expression patterns of paralogs derived from the most recent Solanaceae-specific genome triplication event across 23 tissues and inferred ancestral expression states to investigate patterns of expression evolution. While the partitioning of ancestral expression states is traditionally considered the second most common (after the gene loss) trajectory of duplicate expression evolution, we found that the ancestral expression states tended to be retained by most (~66%) duplicates, with ~6% of gene lineages experiencing expression gain events and ~20% experiencing expression losses. The genes that gained expression in fruit tissues are significantly enriched with functions associated with fruit quality. Notably, asymmetrical expression divergence is prevalent among duplicates, especially when ancestral genes were either not expressed or were highly expressed. Our study demonstrates the utility of integrating paralog expression comparisons with phylogenetic analyses to document the potential evolutionary history of spatial expression patterns and gain insight into how expression divergence contributes to the evolution of function across tissues.

plant biology↗

bioRxiv2024

Heat-Triggered Transcriptional Reprogramming in Microspores Disrupts Progression of Pollen Development in Brassica napus L.

Rising temperatures due to climate change pose significant threats to global food security, particularly by impacting crop fertility and yield. Despite the known susceptibility of male reproductive development to heat stress, the specific adaptive mechanisms and critical regulatory genes involved in the stage-specific heat stress response in crops are still not well understood. This study examines the impact of acute heat stress on pollen development in Brassica napus (Canola), an essential oilseed crop, with a focus on the uninucleate microspore stage. We demonstrate that a brief exposure to 40{degrees}C during the uninucleate microspore stage results in loss of cellular polarity, failed asymmetric cell division, loss of cytoplasm, and pollen abortion, leading to a significant decline in pollen viability. Transcriptome analysis reveals the complexity of heat-induced transcriptional reprogramming in microspores, identifying 8.1% (6,245) of the expressed genes as responsive to high temperature, with a higher degree of downregulation. Fourteen differentially expressed transcription factors (TFs) belonging to diverse TF families were identified in heat-stressed microspores, with overrepresented target genes. The differential regulation of cell cycle control genes in heat-stressed microspores supports our microscopic observations and details the transcriptional reprogramming underlying the failure of heat-stressed microspores to undergo the first and second pollen mitotic divisions (PMI and PMII), resulting in aberrant pollen development in B. napus. Heat stress disrupts key biological pathways such as transcription, mRNA processing, translational control, protein homeostasis, autophagy, phytohormone signaling, and reactive oxygen species (ROS) homeostasis. Heat stress alters the intricate network of multiple signaling pathways, potentially disrupting the regulatory pathways underlying pollen development, with evident crosstalk underscoring the complexity of the heat stress response in pollen development. These findings underscore the critical vulnerability of the microspore stage to heat stress in Canola. Understanding the identified heat-responsive genes and regulatory networks provides valuable insights for breeding climate-resilient Canola varieties, thereby contributing to global food security amidst changing climatic conditions. HighlightsO_LIAcute heat stress during microspore stage in Brassica napus disrupts pollen development. C_LIO_LIHeat stress induces complex transcriptional reprogramming in microspores, with higher degree of downregulation. C_LIO_LITranscriptional control, RNA processing, coordination of protein homeostasis and translational control is altered in heat-stressed microspores C_LIO_LIMisregulation of cell cycle control genes supports the loss of cellular polarity and failure to undergo asymmetric cell division in heat stressed microspores. C_LI

plant biology↗

bioRxiv2020

Using karyotyping and achene morphology to accurately identify Sonchus oleraceus (Asteraceae) in the context of its biological control

In weed biocontrol, accurate identification of the target weed is essential to select effective and host-specific biocontrol agents. This study focuses on the biocontrol of an invasive weed species in Australia, native from Europe, the common sowthistle, Sonchus oleraceus L. (Asteraceae). During field surveys, the distinction between S. oleraceus and a morphologically related species (S. asper L.) was difficult because of specimens bearing intermediate morphological features. These observations raised questions about the reliability the morphological characters used for distinguishing between these species and the identity of the intermediate phenotypes. First, cytological analyses coupled with morphological comparisons were carried out on specimens collected in Europe and Australia. Results showed that specimens morphologically described as S. oleraceus and S. asper possessed, in accordance with literature 32 and 18 chromosomes, respectively. Specimens with intermediate morphotypes had 32 chromosomes, showing that they belong to S. oleraceus species. The variability of characters used for diagnosis is discussed and for a particular feature, achene ornamentation, an inquiry among 30 people was carried out to determine how this character might be relevant for distinguishing the two species herein considered. The successful identification rate was 92.2% (SE {+/-} 0.77) showing the practical interest of this feature for diagnosis.

plant biology↗

bioRxiv2021

Comparative Transcriptome Profiling of High and Low oil yielding Santalum album L.

East Indian Sandalwood (Santalum album L.) is highly valued for its heartwood and its oil. There have been no efforts to comparative study of high and low oil yielding genetically identical sandalwood trees grown in similar climatic condition. Thus we intend to study a genome wide transcriptome analysis to identify the corresponding genes involved in high oil biosynthesis in S. album. In this study, 15 years old S. album (SaSHc and SaSLc) genotypes were targeted for analysis to understand the contribution of genetic background on high oil biosynthesis in S. album. A total of 28,959187 and 25,598869 raw PE reads were generated by the Illumina sequencing. 2.12 million and 1.811 million coding sequences were obtained in respective accessions. Based on the GO terms, functional classification of the CDS 21262, & 18113 were assigned into 26 functional groups of three GO categories; (4,168; 3,641) for biological process (5,758;4,971) cellular component and (5,108;4,441) for molecular functions. Total 41,900 and 36,571 genes were functionally annotated and KEGG pathways of the DEGs resulted 213 metabolic pathways. In this, 14 pathways were involved in secondary metabolites biosynthesis pathway in S. album. Among 237 cytochrome families, nine groups of cytochromes were participated in high oil biosynthesis. 16,665 differentially expressed genes were commonly detected in both the accessions (SaHc and SaSLc). The results showed that 784 genes were upregulated and 339 genes were downregulated in SaHc whilst 635 upregulated 299 downregulated in SaSLc S. album. RNA-Seq results were further validated by quantitative RT-PCR. Maximum Blast hits were found to be against Vitis vinifera. From this study we have identified additional number of cytochrome family in SaHc. The accessibility of a RNA-Seq for high oil yielding sandalwood accessions will have broader associations for the conservation and selection of superior elite samples/populations for further genetic improvement program.

plant biology↗

bioRxiv2024

Niche-Based Priority Effects Predict Microbe Resistance to Erwinia amylovora in Pear Nectar

Fire blight is a devastating disease affecting pome fruit trees that is caused by Erwinia amylovora and leads to substantial annual losses worldwide. While antibiotic-based management approaches like streptomycin can be effective, there are concerns over evolved resistance of the pathogen and non-target effects on beneficial microbes and insects. Using microbial biological control agents (mBCAs) to combat fire blight has promise, but variable performance necessitates the discovery of more effective solutions. Here we used a niche-based predictive framework to assess the strength of priority effects exerted by prospective mBCAs, and the mechanisms behind growth suppression in floral nectar. Through in vitro and in vivo assays, we show that antagonist impacts on nectar pH and sucrose concentration were the primary predictors of priority effects. Surprisingly, overlap in amino acid use, and the degree of phylogenetic relatedness between mBCA and Erwinia did not significantly predict pathogen suppression in vitro, suggesting that competition for limited shared resources played a lesser role than alterations in the chemical environment created by the initial colonizing species. We also failed to detect an association between our measures of in vitro and in vivo Erwinia suppression, suggesting other mechanisms may dictate mBCA establishment and efficacy in flowers, including priming of host defenses.

plant biology↗

bioRxiv2023

Compensation of compromised PRC2 regulation by a miRNA ensures robustness of Arabidopsis leaf development

Robustness is pervasive throughout biological systems, enabling them to maintain persistent outputs despite perturbations in their components. Here, we reveal a novel mechanism contributing to leaf morphology robustness in the face of genetic perturbations. In Arabidopsis, leaf shape is established during early development through the quantitative action of the CUP-SHAPED COTYLEDON2 (CUC2) gene that is negatively regulated by the co-expressed MICRORNA164A (MIR164A) gene. Compromised epigenetic regulation due to defective Polycomb Repressive Complex 2 (PRC2) function results in the transcriptional derepression of CUC2 but has no impact on CUC2 protein dynamics or early morphogenesis. We solve this apparent paradox by showing that compromised PRC2 function simultaneously activates a compensatory mechanism involving another member of the MIR164 gene family, the MIR164B gene. This mechanism dampens CUC2 protein levels, thereby compensating for compromised PRC2 function and canalizing early leaf morphogenesis. Furthermore, we show that this compensation mechanism is active under different environmental conditions. Our findings shed light on how the interplay between different types of transcriptional regulation can contribute to developmental robustness.

plant biology↗

bioRxiv2022

Reversible restriction of electron flow across cytochrome b6f in dark acclimated cells limited for downstream electron sinks

Photosynthetic organisms frequently experience abiotic stresses that restrict their growth and development. Under such circumstances, most absorbed solar energy cannot be used for CO2 fixation and can cause the photoproduction of reactive oxygen species (ROS) that can damage the photosynthetic reaction centers, photosystems I and II (PSI and PSII), resulting in a decline in primary productivity. This work describes a biological switch in the green alga Chlamydomonas reinhardtii that reversibly restricts photosynthetic electron transport (PET) at the cytochrome b6f complex when reductant and ATP generated by PET are in excess of the capacity of carbon metabolism to utilize these products; we specifically show a restriction at this switch when sta6 mutant cells, which cannot synthesize starch, are limited for nitrogen (growth inhibition) and subjected to a dark-to-light transition. This restriction, which may be a form of photosynthetic control, causes diminished electron flow to PSI, which prevents PSI photodamage. When electron flow is blocked the plastid alternative oxidase (PTOX) may also become activated, functioning as an electron valve that dissipates some of the excitation energy absorbed by PSII thereby lessening PSII photoinhibition. Furthermore, illumination of the cells following the dark acclimation gradually diminishes the restriction at cytochrome b6f complex. Elucidating this photoprotective mechanism and its modulating factors may offer new insights into mechanisms associated with photosynthetic control and offer new directions for optimizing photosynthesis.

plant biology↗

bioRxiv2021

A mathematical framework for analyzing wild tomato root architecture

The root architecture of wild tomato, Solanum pimpinellifolium, can be viewed as a network connecting the main root to various lateral roots. Several constraints have been proposed on the structure of such biological networks, including minimizing the total amount of wire necessary for constructing the root architecture (wiring cost), and minimizing the distances (and by extension, resource transport time) between the base of the main root and the lateral roots (conduction delay). For a given set of lateral root tip locations, these two objectives compete with each other -- optimizing one results in poorer performance on the other -- raising the question how well S. pimpinellifolium root architectures balance this network design trade-off in a distributed manner. Here, we describe how well S. pimpinellifolium roots resolve this trade-off using the theory of Pareto optimality. We describe a mathematical model for characterizing the network structure and design trade-offs governing the structure of S. pimpinellifolium root architecture. We demonstrate that S. pimpinellifolium arbors construct architectures that are more optimal than would be expected by chance. Finally, we use this framework to quantify structural differences between arbors grown in the presence of salt stress, classify arbors into four distinct architectural ideotypes, and test for heritability of variation in root architecture structure.

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↗

bioRxiv2019

Integrative Multi-Omics Analysis of Barley Genotypes Shows Differential Salt-Induced Osmotic Barriers and Response Phases Among Rootzones

The mechanisms underlying rootzone-localised responses to salinity stress during early stage of barley development remains fragmentary and elusive. Here, we performed a comprehensive detection of the multi-root-omes (transcriptomes, metabolomes, lipidomes) of a domesticated barley cultivar (Clipper) and a landrace (Sahara) with seedling root growth maintained and restricted in response to salt stress, respectively. Novel generalized linear models were designed to determine differentially expressed genes (DEG) or abundant metabolites (DAM) specific to salt treatments, genotypes, or rootzones (meristematic Z1, elongation Z2, maturation Z3). Based on pathway over-representation of the DEG and DAM, phenylpropanoid biosynthesis is the most statistically over-represented biological pathways among all salinity responses observed. Together with the histological evidence, an intense salt-induced lignin impregnation was found only at the stelic cell wall of Clipper Z2, comparing to a unique elevation of suberin deposition across Sahara Z2. This suggests two differential salt-induced modulations of apoplastic flow between the genotypes. Based on global correlation network construction of the DEG and DAM, callose deposition that potentially adjusted the symplastic flow in roots was almost independent of salinity in rootzones of Clipper, but was markedly decreased in that of Sahara. Through closer examinations of molecular and hormonal clues, we further demonstrate that the salinity response in rootzones of Clipper were mostly at recovery phase, comparing to Sahara with rootzones retained at quiescence. Taken together, we propose that two distinctive salt tolerance mechanisms could exist in Clipper (growth-sustaining) and Sahara (salt-shielding), providing important clues for improving crop plasticity to cope with the deteriorating global salinization of soil.

plant biology↗

bioRxiv2020

Genome-Wide Identification and Characterization of MLO Gene Family in Octoploid Strawberry

Powdery mildew (PM) caused by Podosphaera aphanis is a major fungal disease in cultivated strawberry. Mildew Resistance Locus O (MLO) is a gene family described for having conserved seven-transmembrane domains. Induced loss-of-function in specific MLO genes can confer durable and broad resistance against PM pathogens. However, the underlying biological role of MLO genes in strawberry is still unknown. In the present study, the genomic structure of MLO genes were characterized in both diploid (Fragaria vesca) and octoploid strawberry (Fragaria xananassa), and the potential sources of MLO-mediated susceptibility were identified. Twenty MLO-like sequences were identified in F. vesca, with sixty-eight in F. xananassa. Phylogenetic analysis divides strawberry MLO genes into eight different clades, in which three FveMLO and ten FaMLO genes were grouped together with the functionally known MLO susceptibility. Out of ten FaMLO genes, FaMLO17-2 and FaMLO17-3 showed the highest similarity to the known susceptibility MLO proteins. Gene expression analysis of FaMLO genes was conducted using a multi-parental segregating population. Three expression quantitative trait loci (eQTL) were substantially associated with MLO transcript levels in mature fruits, suggesting discrete genetic control of susceptibility. These results are a critical first step in understanding allele function of MLO genes, and are necessary for further genetic studies of PM resistance in cultivated strawberry.

plant biology↗

bioRxiv2021

Transcriptome Dynamics of Floral Organs Approaching Blooming in the Flowering Cherry (Cerasus x yedoensis) Cultivar 'Somei-Yoshino'

To gain insights into the genetic mechanisms underlying blooming and petal movement in flowering cherry (Cerasus x yedoensis), we performed time-course RNA-seq analysis of the floral buds and open-flowers of the most popular flowering cherry cultivar, Somei-Yoshino. Independent biological duplicate samples of floral buds and open-flowers were collected from Somei-Yoshino trees grown at three different locations in Japan. RNA-seq reads obtained from floral bud and open-flower samples collected in the current study (in 2019) and in a previous study (in 2017) were aligned against the genome sequence of Somei-Yoshino to quantify gene transcript levels. Clustering analysis of RNA-seq reads revealed dynamic changes in the transcriptome, with genes in seven modules predominantly expressed at specific time points, ranging from 5 weeks before flowering to 2 weeks after flowering. Based on the identified gene modules and Gene Ontology (GO) terms enriched at different floral stages, we speculate that the genetic mechanisms underlying petal movement and flower opening in cherry involve the processes of development, cell wall organization, reproduction, and metabolism, which are executed by genes encoding transcription factors, phytohormones, transporters, and polysaccharide metabolic enzymes. Furthermore, we propose a method for cherry bloom forecasting, based on gene expression levels at different time points before flowering as RNA markers.

plant biology↗

bioRxiv2020

EARLY FLOWERING 3 controls temperature responsiveness of the circadian clock

Predictable changes in light and temperature during a diurnal cycle are major entrainment cues that enable the circadian clock to generate internal biological rhythms that are synchronized with the external environment. With the average global temperature predicted to keep increasing, the intricate light-temperature coordination that is necessary for clock functionality is expected to be seriously affected. Hence, understanding how temperature signals are perceived by the circadian clock has become an important issue, especially in light of climate change scenarios. In Arabidopsis, the clock component EARLY FLOWERING 3 (ELF3) not only serves as an essential light Zeitnehmer, but also functions as a thermosensor participating in thermomorphogenesis. However, the role of ELF3 in temperature entrainment of the circadian clock is not fully understood. Here, we report that ELF3 is essential for delivering temperature input to the clock. We demonstrate that in the absence of ELF3, the oscillator was unable to properly respond to temperature changes, resulting in an impaired gating of thermoresponses. Consequently, clock-controlled physiological processes such as rhythmic growth and cotyledon movement were disturbed. Together, our results reveal that ELF3 is an essential Zeitnehmer for temperature sensing of the oscillator, and thereby for coordinating the rhythmic control of thermoresponsive physiological outputs.

plant biology↗