Biology subjects

Jandrasits, K.

Publications and source records attributed to Jandrasits, K..

11 recordsLinked to original sources

bioRxiv2026

RHO GTPase of Plants contributes to robust establishment of cellular asymmetry during development from a single cell

A fundamental question in developmental biology is how highly complex, yet reproducible multicellular body plans form from a single cell. The multicellular haploid body of the land plant Marchantia polymorpha develops from a single isolated cell - the spore - that divides asymmetrically. This produces a small terminally differentiating basal cell, and a large proliferative apical cell that gives rise to the multicellular sporeling body. The genetic basis for the establishment of asymmetry, first within the spore, and later within the sporeling body has remained virtually unknown. Here, we show that the plant specific RHO-type GTPase - RHO OF PLANTS (ROP) - polarises to the spore basal pole to ensure spore division is highly and reproducibly asymmetric. We demonstrate this highly asymmetric division is necessary to specify the terminal differentiation of the basal cell. Furthermore, we show that ROP-mediated polarised outgrowth is required to establish asymmetry within the sporeling body derived from the apical cell. Our discovery highlights how ROP function confers developmental robustness and contributes to the establishment of asymmetry during plant development from a single isolated cell.

plant biology↗

bioRxiv2025

The cytochrome P450 enzyme MpCYP78E1 inhibits meristem initiation and activity in Marchantia polymorpha

Plant shoot branches are formed by the initiation and activation of generative centres known as meristems. In dichotomously branching plants, such as many bryophytes and lycophytes, new meristems are formed when a pre-existing meristem splits into two daughter meristems. These meristems may be active and produce shoot branches or may be inactive. Here, we show that in conditions where meristem inactivation occurs, such as simulated shade, the position of the inactive meristem alternated between either side of the plant body in the liverwort Marchantia polymorpha. Using this predictable pattern, we generated transcriptomes of active and inactive meristems and identified the cytochrome P450 monooxygenase, MpCYP78E1, as a novel regulator of meristem activity. MpCYP78E1 reporter expression was higher in active meristems than inactive meristems. More meristems were active in loss of function mutants than wild type, and fewer meristems were active in gain of function mutants, indicating that MpCYP78E1 inhibits meristem activity. Furthermore, unlike wild type, Mpcyp78e1 loss of function mutants produced supernumerary meristem from the centre of the mature plant body. We conclude that MpCYP78E1 inhibits both meristem initiation and activity to modulate shoot branching architecture.

plant biology↗

bioRxiv2025

A TNL receptor mediates microbiome feedbacks in Arabidopsis

Plant performance depends on the soil microbiome. While microbiome feedbacks are well documented, the mechanisms by which plants perceive and mediate these feedbacks remain unclear. We established a framework using two distinct microbiomes in the same soil, where one led to enhanced growth of the Arabidopsis thaliana accession Col-0. Screening 410 accessions revealed substantial variation in growth feedbacks, which we used for genome-wide association mapping. We identified the immune receptor Mediator of Microbiome Feedback 1 (MMF1) as a candidate gene involved in microbiota feedbacks. Characterisation in the reference accession Col-0 revealed that mmf1 mutants lost the beneficial growth feedback, had an altered root bacterial community, and failed to induce a defence-related transcriptional response observed in wild-type plants. The discovery of MMF1 implies that integration of microbial signals optimises host microbiome composition and immune status to enhance growth.

plant biology↗

bioRxiv2024

Population genomics of Marchantia polymorpha subspecies ruderalis reveals evidence of climate adaptation

Sexual reproduction results in the development of haploid and diploid cell states during the life cycle. In bryophytes the dominant multicellular haploid phase produces motile sperm that swim through water to the egg to effect fertilization from which a relatively small diploid phase develops. In angiosperms, the reduced multicellular haploid phase produces non-motile sperm that is delivered to the egg through a pollen tube to effect fertilization from which the dominant diploid phase develops. These different life cycle characteristics are likely to impact the distribution of genetic variation among populations. However, little is known about the distribution of genetic variation among populations of bryophytes. To understand how genetic variation is distributed among populations of a bryophyte and to establish the foundation for population genetics research in bryophytes, we described the genetic diversity of collections of Marchantia polymorpha subspecies ruderalis, a cosmopolitan ruderal liverwort. We explored genetic diversity of this species using 78 genetically unique (non-clonal) accessions from a total of 209 collected from 37 sites in Europe and Japan. There was no detectable population structure among European populations but significant genetic differentiation between Japanese and European populations. By associating genetic variation across the genome with global climate data, we identified summer temperature and precipitation as climate factors influencing the frequency of adaptative alleles. We speculate that the requirement for water through which motile sperm swim imposes a constraint on the life cycle to which the plant genetically adapts.

plant biology↗

bioRxiv2024

The three-dimensional anatomy and dorsoventral asymmetry of the mature Marchantia polymorpha meristem develops from a symmetrical gemma meristem

Meristems are three-dimensional generative structures that maintain a population of stem cells whilst producing new organs and tissues. Meristems develop in all land plants, however we know relatively little about the spatial and temporal regulation of meristem structure in lineages such as the bryophytes. Here we describe the three-dimensional anatomy of the meristem during the development of the liverwort, Marchantia polymorpha. Using optical reconstructions of the frontal, sagittal and transverse planes through the mature meristem, we show that the apical stem cell is sub-apical, ventral, and located in the outer cell layer. The anatomy of the mature meristem is therefore asymmetrical in the dorsoventral axis, which is reflected by the domain specific protein localisation of Marchantia Class III and Class IV Homeodomain-Leucine-Zippers (MpC3HDZ and MpC4HDZ) and promoter activity of MpYUCCA2. The dorsoventral asymmetry that defines the mature meristem is absent in the juvenile meristems of the asexual propagules known as gemmae. We discovered that anatomical dorsoventral asymmetry of the meristem forms after two days of gemmaling growth and is accompanied by expression of the dorsal identity reporter, MpC3HDZ. We conclude that the gemma meristem is in a state of arrested development and undergoes anatomical rearrangement to develop the three-dimensional meristem structure of the mature plant.

plant biology↗

bioRxiv2022

Epigenetic variation in the Lombardy poplar along climatic gradients is independent of genetic structure and persists across clonal reproduction

- Environmental changes can trigger phenotypic variation in plants through epigenetic mechanisms, but strong genetic influences make it difficult to isolate and study epigenetic effects. Clonal trees with low genetic variation, such as the Lombardy poplar (Populus nigra cv. Italica Duroi), offer a unique system to study epigenetic variation associated with the environment. - We collected cuttings (ramets) of Lombardy poplar along a wide geographical range in Europe. We performed whole-genome-bisulfite sequencing of 164 ramets grown in a common garden and of a subset of 35 of the original parental individuals. Using historical bioclimatic data, we tested the relationship between DNA methylation and climatic gradients. - We found that average methylation levels in TEs and promoter regions correlate with biologically relevant climatic variables. Furthermore, we observed that DNA methylation was transmitted to the next clonal generation, but a fraction of the methylome changed relatively fast when comparing the parental individuals with the clonal offspring. - Our results suggest that the poplar methylome is a dynamic layer of information that can be transmitted to the clonal offspring and potentially affect how poplars acclimate to new environmental conditions.

ecology↗

bioRxiv2022

Meristem dormancy in a dichotomous branching system is regulated by a liverwort-specific miRNA and a clade III SPL gene in Marchantia polymorpha

The shape of modular organisms depends on branching architecture, which in plants is determined by the fates of generative centres called meristems. The branches of the liverwort Marchantia polymorpha are derived from two adjacent meristems that develop at thallus apices. These meristems may be active and develop branches or may be dormant and do not form branches. The relative number and position of active and dormant meristems defines overall shape and form of the thallus. We show that the clade III SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) transcription factor, MpSPL1, is required for meristem dormancy. The activity of MpSPL1 is regulated by the liverwort-specific Mpo-MR13 miRNA which in turn is regulated by PIF-mediated phytochrome signaling. An unrelated miRNA, MIR156, represses a different SPL gene (belonging to clade IV) that inhibits branching during the shade avoidance response in Arabidopsis thaliana. This suggests that a conserved mechanism of phytochrome signaling modulates branching architecture in liverworts and angiosperms and therefore likely operated in the last common ancestor. However, PIF-mediated phytochrome signaling represses the expression of different miRNA genes with different SPL targets during dichotomous, apical branching in liverworts and during lateral, subapical branching in angiosperms. We speculate that the mechanism that acts downstream of light and regulates meristem dormancy evolved independently in liverworts and angiosperms.

plant biology↗

bioRxiv2022

Reduced coenzyme Q synthesis confers non-target site resistance to the herbicide thaxtomin A

Herbicide resistance in weeds is a growing threat to global crop production. Non-target site resistance is problematic because a single resistance allele can confer tolerance to many herbicides (cross resistance), and it is often a polygenic trait so it can be difficult to identify the molecular mechanisms involved. Most characterized molecular mechanisms of non-target site resistance are caused by gain-of-function mutations in genes from a few key gene families - the mechanisms of resistance caused by loss-of-function mutations remain unclear. In this study, we first show that the mechanism of non-target site resistance to the herbicide thaxtomin A conferred by loss-of-function of the gene PAM16 is conserved in Marchantia polymorpha, validating its use as a model species with which to study non-target site resistance. To identify mechanisms of non-target site resistance caused by loss-of-function mutations, we generated 107 UV-B mutagenized M. polymorpha spores and screened for resistance to the herbicide thaxtomin A. We isolated 13 thaxtomin A-resistant mutants and found that 3 mutants carried candidate resistance-conferring SNPs in the MpRTN4IP1L gene. Mprtn4ip1l mutants are defective in coenzyme Q biosynthesis and accumulate higher levels of reactive oxygen species (ROS) than wild-type plants. Mutants are also defective in thaxtomin A metabolism, consistent with the hypothesis that loss of MpRTN4IP1L function confers non-target site resistance. We conclude that loss of MpRTN4IP1L function is a novel mechanism of non-target site herbicide resistance, and propose that other mutations which increase ROS levels or decrease thaxtomin A metabolism could confer thaxtomin A resistance in the field. AUTHOR SUMMARYModern agriculture relies on herbicides to control weed populations. However, herbicide resistance in weeds threatens the efficacy of herbicides and global crop production, similar to how antibiotic resistance poses a global health threat. Understanding the molecular mechanisms behind herbicide resistance helps to prevent resistance from evolving and to better manage herbicide resistant weeds in the field. Here, we use a forward genetic approach in the model species Marchantia polymorpha to discover novel mechanisms of herbicide resistance. We report the discovery of a novel mechanism of herbicide resistance caused by loss-of-function mutations in the MpRTN4IP1L gene. We find that Mprtn4ip1l mutants are resistant to the herbicides thaxtomin A and isoxaben, accumulate higher levels of reactive oxygen species than wild type plants, and are defective in thaxtomin A metabolism. We predict that loss-of-function mutations or treatments that increase reactive oxygen species production could contribute to thaxtomin A tolerance.

plant biology↗

bioRxiv2021

Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates

Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible field-based model species for genetics and epigenetics. The availability of a high quality reference genome is vital for understanding pennycress physiology and for clarifying its evolutionary history within the Brassicaceae. Here, we present a chromosome-level genome assembly of var. MN106-Ref with improved gene annotation, and use it to investigate gene structure differences between two accessions (MN108 and Spring32-10) that are highly amenable to genetic transformation. We describe small RNAs, pseudogenes, and transposable elements, and highlight tissue specific expression and methylation patterns. Resequencing of forty wild accessions provides insights into genome-wide genetic variation as well as QTL regions for flowering time and a seedling color phenotype. Altogether, these data will serve as a tool for pennycress improvement in general and for translational research across the Brassicaceae.

plant biology↗

bioRxiv2021

Plant-derived benzoxazinoids act as antibiotics and shape bacterial communities

Plants synthesize and release specialized metabolites into their environment that can serve as chemical cues for other organisms. Metabolites that are released from the roots are important factors in determining which microorganisms will colonize the root and become part of the plant rhizosphere. Root exudates can be converted by soil microorganisms, which can result in the formation of toxic compounds. How individual members of the plant rhizosphere respond to individual compounds and how the differential response of individual microorganisms contributes to the response of a microbial community remains an open question. Here, we investigated the impact of derivatives of benzoxazinoids, a class of plant root exudates released by important crops such as wheat and maize, on a collection of 180 root-associated bacteria. Phenoxazine, derived in soil from benzoxazinoids, inhibited the growth of root-associated bacteria in vitro in an isolate-specific manner, with sensitive and resistant isolates present in most of the studied clades. Using synthetic communities, we show that community stability is a consequence of the resilience of its individual members, with communities assembled from tolerant isolates being overall more tolerant to benzoxazinoids. However, the performance of an isolate in a community context was not correlated with its individual performance but appeared to be shaped by interactions between isolates. These interactions were independent of the overall community composition and were strain-specific, with interactions between different representatives of the same bacterial genera accounting for differential community composition.

plant biology↗

bioRxiv2020

araDEEPopsis: From images to phenotypic traits using deep transfer learning

Linking plant phenotype to genotype, i.e., identifying genetic determinants of phenotypic traits, is a common goal of both plant breeders and geneticists. While the ever-growing genomic resources and rapid decrease of sequencing costs have led to enormous amounts of genomic data, collecting phenotypic data for large numbers of plants remains a bottleneck. Many phenotyping strategies rely on imaging plants, which makes it necessary to extract phenotypic measurements from these images rapidly and robustly. Common image segmentation tools for plant phenotyping mostly rely on color information, which is error-prone when either background or plant color deviate from the underlying expectations. We have developed a versatile, fully open-source pipeline to extract phenotypic measurements from plant images in an unsupervised manner. O_SCPLOWARAC_SCPLOWO_SCPLOWDEEPC_SCPLOWO_SCPLOWOPSISC_SCPLOW was built around the deep-learning model DeepLabV3+ that was re-trained for segmentation of Arabidopsis thaliana rosettes. It uses semantic segmentation to classify leaf tissue into up to three categories: healthy, anthocyanin-rich, and senescent. This makes O_SCPLOWARAC_SCPLOWO_SCPLOWDEEPC_SCPLOWO_SCPLOWOPSISC_SCPLOW particularly powerful at quantitative phenotyping from early to late developmental stages, of mutants with aberrant leaf color and/or phenotype, and of plants growing in stressful conditions where leaf color may deviate from green. Using our tool on a panel of 210 natural Arabidopsis accessions, we were able to not only accurately segment images of phenotypically diverse genotypes but also to map known loci related to anthocyanin production and early necrosis using the O_SCPLOWARAC_SCPLOWO_SCPLOWDEEPC_SCPLOWO_SCPLOWOPSISC_SCPLOW output in genome-wide association analyses. Our pipeline is able to handle images of diverse origins, image quality, and background composition, and could even accurately segment images of a distantly related Brassicaceae. Because it can be deployed on virtually any common operating system and is compatible with several high-performance computing environments, O_SCPLOWARAC_SCPLOWO_SCPLOWDEEPC_SCPLOWO_SCPLOWOPSISC_SCPLOW can be used independently of bioinformatics expertise and computing resources. O_SCPLOWARAC_SCPLOWO_SCPLOWDEEPC_SCPLOWO_SCPLOWOPSISC_SCPLOW is available at https://github.com/Gregor-Mendel-Institute/aradeepopsis.

plant biology↗