Biology subjects

Greb, T.

Publications and source records attributed to Greb, T..

15 recordsLinked to original sources

bioRxiv2026

Reference genome assembly of the tetraploid tuber crop Tropaeolum tuberosum

Tropaeolum tuberosum is a tuber-forming crop native to the Andes, valued for its nutritional content, pest resistance and adaptation to high-altitude environments. Despite its contribution to food security and sustainable agriculture, it remains an underutilized species with scarce genomic resources, limiting genetic and functional studies. To address this gap, we generated a reference genome assembly for a European ex situ tetraploid accession of T. tuberosum using PacBio HiFi sequencing. The assembly spans 1.3 Gb in 1,805 contigs (contigs N50 = 32.2 Mb, longest contig = 60 Mb) and recovers 87% of the estimated genome size. We assessed assembly completeness and accuracy using Benchmarking Universal Single-Copy Orthologs, which detected 98.5% complete genes (21.7% single-copy, 76.8% duplicated), 0.7% fragmented, and 0.7% missing, demonstrating near-complete gene space recovery consistent with a high-quality tetraploid genome. To evaluate transferability, we resequenced a field-collected Colombian genotype of economic relevance using Oxford Nanopore technology. Read mapping showed 99.7% of primary alignments to the reference (weighted mean coverage = 16.4x, 96.1% at [≥]5x), confirming broad sequence conservation between accessions and validating the suitability of the ex situ reference as an anchor for in situ germplasm. Repetitive elements accounted for 71.3% of the genome. Using ANNEVO, we annotated 56,354 high-confidence protein-coding genes, achieving 98.3% complete BUSCOs, a PSAURON score of 97.2, and 90.5% taxonomic consistency with the rosid lineage (OMArk). This high-quality reference genome establishes a foundational resource for comparative genomics, population genomics and functional analyses on T. tuberosum, supporting future breeding and conservation of this important food resource. Significance statementT. tuberosum is an underutilized Andean tuber crop that combines highly nutritious tubers with remarkable disease resistance and UV tolerance, supporting Andean smallholder livelihoods under harsh high-altitude conditions. Beyond its role as a food crop, it is cultivated widely as an ornamental due to its abundant, brightly colored flowers closely resembling those of its relative nasturtium. Despite this dual relevance, genomic resources have been entirely lacking, limiting efforts to understand its domestication history, adaptation, and potential as a climate-resilient alternative to potato with higher nutraceutical properties. Our reference genome assembly provides the first genome-scale resource for T. tuberosum, creating a foundation for dissecting polyploid genome organization, key agronomic and nutritional traits, and interactions with biotic and abiotic stress. By enabling evolution, domestication, comparative genomics, breeding, conservation, and functional studies, this resource unlocks T. tuberosum as a model for resilient, diversified cropping systems globally.

plant biology↗

bioRxiv2026

WUSCHEL modulates jasmonate signaling to control the balance between growth and defense in the shoot apical meristem

The growth-defense trade-off is an essential survival strategy for plants under environmental stress. However, how this balance is maintained at the meristematic level remains unclear. Here, we show that wounding of rosette leaves systemically inhibits inflorescence stem growth, associated with reduced cell proliferation in the inner cell layers of the shoot apical meristem (SAM), but not in the apical stem cell domain. Mechanistically, this selective cell behavior is dependent on the interplay between the growth-repressing jasmonate (JA) signaling and the growth-promoting stem cell regulator WUSCHEL (WUS). WUS mitigates wounding-induced growth inhibition by repressing JA-responsive gene expression via promoting the accumulation of JASMONATE-ZIM DOMAIN 3 (JAZ3), which encodes a JA signaling repressor. WUS on the one hand induces JAZ3 mRNA accumulation and on the other hand directly competes with the JA receptor CORONATINE INSENSITIVE1 (COI1) for JAZ3 binding, thereby inhibiting JAZ3 protein degradation. Our findings identify a WUS-JAZ3-COI1 regulatory module that coordinates the growth-defense balance in the SAM upon systemic wounding, revealing a cell-type-specific mechanism for sustaining developmental robustness of the meristem during stress response.

plant biology↗

bioRxiv2025

Robust division orientation of cambium stem cells requires cortical division zone components but not the preprophase band

The control of cell division plane orientation is fundamental for organizing developmental processes and shaping bodies of multicellular organisms. In plants, radial organ growth is mediated by the cambium, a stem cell niche deeply embedded in expanding organs and continuously producing xylem and phloem in a strictly bidirectional manner. Cambium stem cells (CSCs) are unique in comparison to other plant stem cells as they consistently divide along their longest axis clearly overriding the commonly found short axis rule. Despite the topological consistency of CSC divisions and the functional importance of proper division plane orientation for CSC derivatives, the regulatory mechanisms behind this consistency remain unknown. Here, we characterized microtubule organization during CSC divisions in Arabidopsis thaliana and found that division plane orientation is established independently from spindle orientation and the preprophase band (PPB). This conclusion is based on the remarkable variability of spindle orientation during metaphase and the robustness of CSC divisions in PPB-deficient mutants. Instead, the orientation of division planes depends on the cortical division zone (CDZ) and CDZ-related PHRAGMOPLAST ORIENTING KINESIN (POK) proteins. Our results highlight the importance of wood-forming CSCs and their subcellular characterization as an instructive example for the determination of cell division orientation in plants.

plant biology↗

bioRxiv2025

The Cell Wall Controls Stem Cell Fate in the Arabidopsis Shoot Apical Meristem

At the basis of plant developmental plasticity are continuously active pluripotent stem cells, which fuel the life-long post-embryonic formation of new organs. Since plant cells are encased in cell walls and thus immotile, their individual fate-specification program is dependent on their relative position within the organism. It is assumed that the cell wall and its mechanical properties are under surveillance, linking cell wall state to intracellular gene-regulatory networks. However, the role of these cell wall signalling pathways in plant development and the contribution of cell wall properties to cell behaviour and identity are unclear. Here, we show that control of cell wall properties is essential for the perpetuation of stem cell populations and pattering in the shoot apical meristems. The expression of pectin methylesterases (PMEs), which modify homogalacturonan methylesterification and thereby modulate cell wall mechanics, is maintained at low levels in stem cells by the stem cell specifying transcription factor WUS. Low PME expression is required for stemness, auxin patterning and stem cell-specific mechanical properties. Conversely, WUS depletion reduces wall stiffness in the meristem centre, reinforcing its role in maintaining mechanical homeostasis. Together, our findings show that WUS-mediated control of cell wall-modifying enzymes is essential for sustaining stem cell identity and SAM organization. These results demonstrat that the plant cell wall is not only involved in cell differentiation, but also exerts feedback control on developmental transitions, contributing to our understanding how the immediate physical environment is able to guide cell fate decisions in plants.

plant biology↗

bioRxiv2024

Mechanical forces instruct division plane orientation of cambium stem cells during radial growth in Arabidopsis thaliana

Precise regulation of cell division is central for the formation of complex multicellular organisms and a hallmark of stem cell activity. In plants, due to the absence of cell migration, correct placement of newly produced cell walls during cell division is of eminent importance for generating functional tissues and organs. In particular, during radial growth of plant shoots and roots, concerted cell divisions in the cambium are essential to produce adjacent xylem and phloem tissues in a strictly bidirectional manner. While several intercellular signaling cascades have been identified to instruct tissue organization during radial growth, a role of mechanical forces in guiding cambium stem cell activity has been frequently proposed but, so far, not been functionally investigated on the cellular level. Here, we coupled anatomical analyses with a cell-based vertex model to analyze the role of mechanical stress in radial plant growth at the cell and tissue scale. Simulations based on segmented cellular outlines of radially growing Arabidopsis hypocotyls revealed a distinct stress pattern with circumferential stresses in cambium stem cells which coincided with the orientation of cortical microtubules. Integrating stress patterns as a cue instructing cell division orientation was sufficient for the emergence of typical cambium-derived cell files and agreed with experimental results for stress-related tissue organization in confining mechanical environments. Our work thus underlines the significance of mechanical forces in tissue organization through self-emerging stress patterns during the growth of plant organs.

plant biology↗

bioRxiv2023

Strigolactones optimise plant water usage by modulating vessel formation

Wood formation is fundamental for the remarkable growth of plant bodies by continuously providing cells for long-distance transport of water and nutrients1-3. Vessel elements, the water transporting units within woody tissues, are generated from a cylindrical domain of cambium stem cells (CSCs) producing different vascular cell types in a bidirectional manner4-6. However, knowledge on the regulation of CSC activity is limited with unclear cell fate trajectories as the most obscure aspect in this context. Here, via revealing transcriptome signatures of CSCs and their derivatives with single cell resolution in Arabidopsis thaliana, we discover that the strigolactone (SL) signalling pathway modulates cell type composition in vascular tissues and thereby increases drought resistance. In particular, we find that SL signalling negatively regulates vessel element formation and thereby plant water usage. SL signalling is generally associated with differentiating vascular tissues but low in developing vessels and in CSCs implying a local role during fate decisions in CSC-derived cells. Highlighting the importance of vascular tissue composition for the overall plant water balance, alteration of vessel element formation has a direct impact on transpiration rates through leaf stomata. Our results demonstrate the importance of structural alignment of water transporting tissues to unstable water regimes and provide perspectives for a long-term modulation of drought resistance in plants.

plant biology↗

bioRxiv2021

Strigo-D2 - a bio-sensor for monitoring the spatio-temporal pattern of strigolactone signaling in intact plants

Strigolactones (SLs) are a class of plant hormones modulating developmental programs in response to endogenous and exogenous stimuli and mediating biotic interactions. However, a comprehensive view on the spatio-temporal pattern of SL signaling has not been established and tools for a systematic in planta analysis do not exist. Here, we present Strigo-D2, a genetically encoded ratiometric SL signaling sensor, allowing the examination of SL signaling distribution with cellular resolution and its rapid response to altered SL levels in intact plants. By monitoring the abundance of a truncated and fluorescently labeled SUPPRESSOR OF MAX2 1-LIKE 6 (SMXL6) protein, a proteolytic target of the SL signaling machinery, we show that all cell types investigated have the capacity to respond to changes in SL levels but with very different dynamics. In particular, SL signaling is pronounced in vascular cells but low in guard cells and the meristematic region of the root. We also show that other hormones leave Strigo-D2 activity unchanged indicating that initial SL signaling steps work in isolation from other hormonal signaling pathways. Specificity and spatio-temporal resolution of Strigo-D2 underline the value of the sensor for monitoring SL signaling in a broad range of biological contexts and with highly instructive analytical depth.

plant biology↗

bioRxiv2021

A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data

Identity and functions of plant cells are influenced by their precise cellular location within the plant body. Cellular heterogeneity in growth and differentiation trajectories results in organ patterning. Therefore, assessing this heterogeneity at molecular scale is a major question in developmental biology. Single-cell transcriptomics (scRNA-seq) allows to characterize and quantify gene expression heterogeneity in developing organs at unprecedented resolution. However, the original physical location of the cell is lost during the scRNA-seq procedure. To recover the original location of cells is essential to link gene activity with cellular function and morphology. Here, we reconstruct genome-wide gene expression patterns of individual cells in a floral meristem by combining single-nuclei RNA-seq with 3D spatial reconstruction. By this, gene expression differences among meristematic domains giving rise to different tissue and organ types can be determined. As a proof of principle, the data are used to trace the initiation of vascular identity within the floral meristem. Our work demonstrates the power of spatially reconstructed single cell transcriptome atlases to understand plant morphogenesis. The floral meristem 3D gene expression atlas can be accessed at http://threed-flower-meristem.herokuapp.com

plant biology↗

bioRxiv2020

A novel pathway controlling cambium initiation and -activity via cytokinin biosynthesis in Arabidopsis

Plant secondary growth, also referred to as wood formation, includes the production of secondary xylem, which is derived from meristematic cambium cells embedded in vascular tissues. Despite the importance of secondary xylem in plant growth and wood formation, the molecular mechanism of secondary growth is not yet well understood. Here we identified an important role for the Arabidopsis thaliana (Arabidopsis) AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED 15 (AHL15) gene, encoding for a putative transcriptional regulator, in controlling vascular cambium activity and secondary xylem formation. Secondary xylem development was significantly reduced in inflorescence stems of the Arabidopsis ahl15 loss-of-function mutant, whereas AHL15 overexpression led to extensive secondary xylem formation. AHL15 expression under a vascular meristem-specific promoter also enhanced the amount of interfascicular secondary xylem. Moreover, AHL15 appeared to be required for the enhanced secondary xylem formation in the Arabidopsis double loss-of-function mutant of the SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1) and FRUITFULL (FUL) genes. A well-known central regulator of cambial activity is the plant hormone cytokinin. We showed that the expression of two cytokinin biosynthesis genes (ISOPENTENYL TRANSERASE (IPT) 3 and 7) is decreased in ahl15 loss-of-function mutant stems, whereas the secondary xylem deficiency in these mutant stems can be resorted by cambium-specific expression of the Agrobacterium tumefaciens IPT gene, indicating that AHL15 acts through the cytokinin pathway. These findings support a model whereby AHL15 acts as a central factor inducing vascular cambium activity downstream of SOC1 and FUL and upstream of IPT3, IPT7 and LOG4, LOG5 governing the rate of secondary xylem formation in Arabidopsis inflorescence stems.

plant biology↗

bioRxiv2020

Tissue-specific transcriptome profiling of the Arabidopsis thaliana inflorescence stem reveals local cellular signatures.

Genome-wide gene expression maps with a high spatial resolution have substantially accelerated molecular plant science. However, the number of characterized tissues and growth stages is still small because of the limited accessibility of most tissues for protoplast isolation. Here, we provide gene expression profiles of the mature inflorescence stem of Arabidopsis thaliana covering a comprehensive set of distinct tissues. By combining fluorescence-activated nucleus sorting and laser-capture microdissection with next generation RNA sequencing, we characterize transcriptomes of xylem vessels, fibers, the proximal and the distal cambium, phloem, phloem cap, pith, starch sheath, and epidermis cells. Our analyses classify more than 15,000 genes as being differentially expressed among different stem tissues and reveal known and novel tissue-specific cellular signatures. By determining transcription factor binding regions enriched in promoter regions of differentially expressed genes, we furthermore provide candidates for tissue-specific transcriptional regulators. Our datasets predict expression profiles of an exceptional amount of genes and allow generating hypotheses toward the spatial organization of physiological processes. Moreover, we demonstrate that information on gene expression in a broad range of mature plant tissues can be established with high spatial resolution by nuclear mRNA profiling. One sentence summaryA genome-wide high-resolution gene expression map of the Arabidopsis inflorescence stem is established.

plant biology↗

bioRxiv2020

Computational modelling of cambium activity provides a regulatory framework for simulating radial plant growth

Precise organization of growing structures is a fundamental process in developmental biology. In plants, radial growth is mediated by the cambium, a stem cell niche continuously producing wood (xylem) and bast (phloem) in a strictly bidirectional manner. While this process contributes large parts to terrestrial biomass, cambium dynamics eludes direct experimental access due to obstacles in live cell imaging. Here, we present a cell-based computational model visualizing cambium activity and integrating the function of central cambium regulators. Performing iterative comparisons of plant and model anatomies, we conclude that the receptor- like kinase PXY and its ligand CLE41 are part of a minimal framework sufficient for instructing tissue organization. By integrating tissue-specific cell wall stability values, we moreover probe the influence of physical constraints on tissue geometry. Our model highlights the role of intercellular communication within the cambium and shows that a limited number of factors is sufficient to create radial growth by bidirectional tissue production. Impact statementRadial plant growth produces large parts of terrestrial biomass and can be computationally simulated with the help of an instructive framework of intercellular communication loops.

plant biology↗

bioRxiv2019

OBERON3 and SUPPRESSOR OF MAX2 1-LIKE proteins form a regulatory module specifying phloem identity

Spatial specificity of cell fate decisions is central for organismal development. The phloem tissue mediates long-distance transport of energy metabolites along plant bodies and is characterized by an exceptional degree of cellular specialization. How a phloem-specific developmental program is implemented is, however, unknown. Here we reveal that the ubiquitously expressed PHD-finger protein OBE3 forms a central module with the phloem- specific SMXL5 protein for establishing phloem identity in Arabidopsis thaliana. By protein interaction studies and phloem-specific ATAC-seq analyses, we show that OBE3 and SMXL5 proteins form a complex in nuclei of phloem stem cells where they establish a phloem-specific chromatin profile. This profile allows expression of OPS, BRX, BAM3, and CVP2 genes acting as mediators of phloem differentiation. Our findings demonstrate that OBE3/SMXL5 protein complexes establish nuclear features essential for determining phloem cell fate and highlight how a combination of ubiquitous and local regulators generate specificity of developmental decisions in plants.

plant biology↗

bioRxiv2019

SUPPRESSOR OF MAX2 1-LIKE 5 promotes secondary phloem formation during radial stem growth

As a prerequisite for constant growth, plants can produce vascular tissues at different sites in their postembryonic body. In particular, the formation of vascular tissues during longitudinal and radial expansion of growth axes differs fundamentally with respect to its anatomical configuration. This raises the question to which level regulatory mechanisms of vascular tissue formation are shared throughout plant development. Here, we show that, similar as primary phloem formation during longitudinal growth, the cambium-based formation of secondary phloem depends on the function of SMXL genes. Using promoter reporter lines, we observe that SMXL4 and SMXL5 activities are associated with different stages of secondary phloem formation in Arabidopsis stems and the specific loss of SMXL5 function results in the absence of secondary phloem. Interestingly, the additional disruption of SMXL4 activity increases cell proliferation rates in the cambium region without that secondary phloem is formed. Based on genome-wide transcriptional profiling and expression analyses of phloem-related markers we conclude that early steps of phloem formation are impaired in smxl4;smxl5 double mutants and that additional cambium-derived cells fail in establishing any phloem-related feature. Our results show that molecular mechanisms determining primary and secondary phloem share important features but differ slightly with SMXL5 playing a more dominant role in the formation of secondary phloem.

plant biology↗

bioRxiv2018

A Comprehensive Tool Set for Inducible, Cell Type-Specific Gene Expression in Arabidopsis

Understanding the context-specific role of gene function is a key objective of modern biology. To this end, we generated a resource for inducible cell-type specific trans-activation based on the well-established combination of the chimeric GR-LhG4 transcription factor and the synthetic pOp promoter. Harnessing the flexibility of the GreenGate cloning system, we produced a comprehensive set of GR-LhG4 driver lines targeting most tissues in the Arabidopsis shoot and root with a strong focus on the indeterminate meristems. We show that, when combined with effectors under control of the pOp promoter, tight temporal and spatial control of gene expression is achieved. In particular, inducible expression in F1 plants obtained from crosses of driver and effector lines allows rapid assessment of the cell type-specific impact of an effector with high temporal resolution. Thus, our comprehensive and flexible toolbox is suited to overcome the limitations of ubiquitous genetic approaches, the outputs of which are often difficult to interpret due to widespread existence of compensatory mechanisms and the integration of diverging effects in different cell types.\n\nOne sentence summary: A set of lines enabling spatio-temporal control of gene expression in Arabidopsis.

plant biology↗

bioRxiv2017

Spatial Specificity Of Auxin Responses Coordinates Wood Formation

Spatial organization of signaling events of the phytohormone auxin is fundamental for maintaining a dynamic transition from plant stem cells to differentiated descendants. The cambium, the stem cell niche mediating wood formation, fundamentally depends on auxin signaling but its exact role and spatial organization is obscure. Here, we show that, while auxin signaling levels increase in differentiating cambium descendants, a moderate level of signaling in cambial stem cells is essential for cambium activity. We identify the auxin-dependent transcription factor ARF5/MONOPTEROS to cell-autonomously restrict the number of stem cells by attenuating the activity of the stem cell promoting WOX4 gene. In contrast, ARF3 and ARF4 function as cambium activators in a redundant fashion from outside of WOX4-expressing cells. Our results reveal an influence of auxin signaling on distinct cambium features by specific signaling components and allow the conceptual integration of plant stem cell systems with distinct anatomies.

plant biology↗