VIB-UGent Center for Plant Systems Biology

VIB-UGent Center for Plant Systems Biology

Table of contents 4 Research strategy 6 Research groups 27 Center in numbers 28 2

Expertise & technologies

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Technology transfer

38

Training

40 Committees 42

Outreach

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PhDs & alumni

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Research strategy Building the plant molecular framework for a resilient and sustainable future

Using different model systems such as Arabidopsis thaliana, Marchantia polymorpha, Physcomitrium patens, and duckweed, and crops like maize, wheat, soybean, poplar, and tomato, the VIB-UGent Center for Plant Systems Biology (PSB) aims to develop climate-smart plants through state-of-the-art technologies, with the goal of positively impacting biodiversity, promoting a plant-based society, and supporting sustainable agriculture.

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Biod ive rsi ty Advanced Live Imaging

Metabolomics

ased socie b t n ty a l P

Single Cell Analysis Genomics

Proteomics Phenomics

Computational Biology & AI

Technologies

Spatial Transcriptomics Genome Editing

Molecular Plant Biotechnology

Approaches

Model Systems

Plant Models and Crops

Comparative Genomics

C li m a t e At PSB, our mission focuses on addressing climate change, advancing sustainable agriculture, and conserving biodiversity through innovative plant research. Our goal is to help create a sustainable future where ecological equilibrium is maintained.

We study fundamental plant processes through innovative methods and state-of-the-art technologies, using experimental and computational approaches. Our climate-smart research is developing resilient plant varieties to withstand extreme climates and enhance carbon capture.

In agriculture, we aim to reduce resource use by creating crops that require fewer inputs for

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Network Biology

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Lab, Greenhouse and Field

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Cells, Tissues and Organs

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higher yields and championing environmentally friendly farming practices to ensure long-term food security. We study plant genomes, plant diversity, and plant evolution and adaptation, vital for understanding biodiversity and ecological resilience. We engage the public through education, fostering a community dedicated to environmental sustainability. In short, we are committed to science-based solutions for a world where development and conservation go together, ensuring a green and secure future for all.

Yves Van de Peer, Science Director

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VIB VIB’s research is structured in thematic research centers, each center comprising several research groups. Each of these groups has a specific expertise, but given the complexity and multidisciplinary nature of life sciences research today, there is a strong need for groups to collaborate within the center and even across (university) borders The VIB centers perform world-leading basic research on some of the most poignant biological questions of our time. It is VIB’s firm conviction that basic scientific research – often guided by serendipity – can result in major, sometimes unforeseen, breakthroughs.

However, scientific research should benefit society as a whole. That is why each research group is also encouraged and supported in framing their work in a socially relevant and applicable context. As such, each group has a substantial interest in a translational research line, where they aim to develop their basic findings in a way that can make a big impact on important societal challenges.

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Research groups

In the presentation of the research groups below, it will become clear that each group in the VIB-UGent Center for Plant Systems Biology (PSB) performs trailblazing basic research that leads to significant translational potential. By leveraging their expertise in various aspects of plant biology, the teams can significantly contribute to the development of novel crop varieties, specifically aimed at meeting oncoming challenges such as climate change and food production demands.

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Inge De Clercq Inter-organelle stress signalling In a world facing rapid climate change, ensuring that plants can withstand environmental and pathogen-induced stresses is essential for global food security. While most people think of organelles like mitochondria and chloroplasts as the 'powerhouses' of the cell, they are also key environmental sensors. These small structures within plant cells play a central role in detecting changes, responding to stress, and helping plants survive challenging conditions.

Although their importance in human diseases such as cancer and neurodegenerative disorders is well-recognized, the role of organelles in plant stress responses is still poorly understood. During stressful situations, like high light intensities or pathogen attacks, organelles don’t stay still. They move dynamically within the cell, cluster at stress sites, and even interact with one another. This behavior highlights their importance in helping plants cope with both environmental and cellular challenges.

The De Clercq lab is particularly interested in uncovering the molecular mechanisms by which organelles 'communicate' during stressful conditions. Specifically, we study the communication happening through dynamic interactions and physical connection points, called inter-organelle contact sites during both pathogen-related and environmental stresses To achieve this, our group is establishing advanced live-cell imaging tools to track these inter-organelle contact sites and cutting-edge proteomic tools to identify the proteins involved in steering organelle interactions. In addition, we explore how pathogens manipulate organelle functions to their advantage, undermining plant defenses. By identifying the proteins

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pathogens use to attack organelles, our team aims to uncover weak points in the plant’s immune system and develop strategies to enhance crop resistance.

Ultimately, the goal of the De Clercq lab is to unlock the hidden roles of organelles in stress sensing and signaling. By understanding these often overlooked players, we will develop innovative strategies to create plants that are more resilient to climate challenges and make crops better equipped to resist diseases.

Polina Novikova Ecological genomics The Novikova Lab is assessing the global genetic diversity of different model systems to understand the mechanisms underlying adaptation. We apply population genetics approaches to assess the change of allelic frequencies under various environmental conditions driving natural selection, which could be external (e.g., abiotic or biotic stress) or internal (e.g., polyploidy or cancer).

Polyploidy, or a whole genome duplication, is one of our favorite phenomena because it can act as a selection force and a phenotype being selected. Polyploidy is often associated with extreme environments and, although abundant, is non-randomly distributed across the Tree of Life. We aim to understand how environment and genetics affect the initial formation of polyploids, what determines the success of establishing new polyploid lineages, and what processes underlie the return to a diploid state over a long evolutionary time.

To address each of these phases of a polyploid cycle, we work on different model systems, usually covering vast geographical territories with various environments. We believe that understanding why some organisms are more prone or tolerant to whole-genome duplications than others, why some environments promote polyploidy and some limit it, and why some polyploids spread more successfully and some go extinct immediately can deliver ground-breaking advances relevant across biology, agriculture, and medicine. At the same time, polyploidy provides a setup with a complexity of internal and external factors and forces, which we use as a model to understand fundamental principles shaping global diversity.

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Tom Beeckman Root development Plant roots serve a multitude of functions. They anchor plants and supply them with water and nutrients and exchange various growth substances with the shoots. At the root-soil interface, numerous interactions between plants and their environment take place. The diversity of functions and the broad range of interactions with the environment render the biology of roots complicated.

The Beeckman group studies how and when roots branch to create an effective root system that is optimally adapted to the soil environment. In addition, our group studies the impact of the availability versus shortage of key plant nutrients such as nitrogen and phosphorus on root development and plant growth in general. Understanding this is of major relevance to assist agriculture in the search for alternative crops, new varieties, or approaches that can help plants cope with less favorable environmental conditions, such as drought and nutrient shortage.

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Wout Boerjan Bioenergy and bio-aromatics It is well recognized that burning fossil resources is a major contributor to climate change and that plant biomass can serve as a renewable and potentially carbon-neutral raw material for producing fuels and various other bio-based products that are currently derived from oil.

The primary long-term goal of the Boerjan group is to engineer plant cell wall composition for more cost-effective conversion of plant biomass into pulp, fermentable sugars, or aromatic building blocks, without adversely affecting plant yield.

Since the cell wall polymer lignin plays a central role in these conversion processes, our team focuses on understanding lignin biosynthesis, polymerization, and structure, and applies this knowledge to develop plants with improved properties. For example, by reducing lignin content, poplar trees have been engineered to facilitate pulp and bioethanol production.

Our team also investigates how lignin biosynthesis integrates with plant metabolism and development by exploring the potential bioactive properties of metabolites involved in or derived from the lignin biosynthesis pathway and by studying their modes of action. In addition to metabolites destined to lignin, plant biomass also contains thousands of molecules whose structures — and therefore properties — remain unknown. Our group's main activity is to characterize these metabolites and their biosynthetic pathways by integrating mass spectrometry, systems biology, metabolite-based GWAS, and reverse genetics.

The team uses Arabidopsis, maize, and poplar as model systems for gene discovery and conducts field trials to assess the new traits in a relevant environment. In summary, research in the Boerjan group supports the transition from a fossil-based to a bio-based economy.

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Geert De Jaeger Functional interactomics The De Jaeger group is a technology-driven research team that obtained international visibility with their state-of-the-art affinity purification and proximity labeling approaches to map protein interaction networks in plant cells and tissues, both from the model species Arabidopsis and from crop plants. The platform is accessible to fellow researchers from academia or companies.

More recently, these tools have been applied to gather knowledge on the relationship between nutrient signaling and plant growth. Signaling pathways involving key growth regulators such as sugar and nitrogen are studied based on protein interaction networks built, comprising the antagonistic target of rapamycin (TOR) and SNF1-related (SnRK1) kinases, two master regulators that integrate nutrient signaling with plant growth. As such, we generate targeted data on the function and regulation of those two metabolic hubs in carbon and nitrogen signaling. Our protein interaction networks are rich resources for hypothesis-driven research.

Currently, we are studying the function of upstream regulators and downstream targets of TOR and SnRK1 activity we recently isolated. We are also translating our network data into beneficial phenotypes. We engineer Arabidopsis plants intending to enhance growth, stress resilience, or nitrogen use efficiency to contribute knowledge to help develop a more sustainable agriculture.

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Bert De Rybel Vascular development Plants rely on directed cell elongation and cell division to generate a full 3D structure. Intrinsic polarity cues and cellular communication provide spatial information to plant cells and establish their position relative to the tissue context and the growth axis. This framework allows cells to integrate available information and orient their divisions to enable structured growth. The mechanisms that control cell division orientation and cell proliferation are key questions in developmental biology, but remain poorly understood.

These concepts are particularly important during vascular development, as many highly controlled oriented divisions are required to establish distinct vascular cell identities during primary growth. Next, proliferation is crucial to allow the massive expansion in the number of cell files during secondary growth, resulting in lateral expansion.

The main research objective of the De Rybel team is to understand how plant cells control the proliferation and orientation of their cell divisions. These processes are crucial for tissue growth in general and vascular development in specific. Understanding vascular proliferation is of great interest as vascular tissues have the specific ability to undergo a tremendous amount of these divisions and the additional cell files created this way generate almost all of the tissues that make up wood in trees, are crucial for source-to-sink transport throughout the plant, and make up many edible structures such as fruits, roots, and tubers. Moreover, vascular architecture has been linked to the efficiency of water uptake and water storage in dry conditions. As such, our research lays the groundwork to understand and exploit how vascular proliferation and architecture can ensure optimal plant growth in a changing environment.

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Ive De Smet Functional phosphoproteomics To fully understand plant growth and development, also in the context of environmental changes, we need to identify novel components and require insight into the underlying network.

The De Smet lab tackles this using mass spectrometry-based approaches that capture structural changes and post-translational modifications of proteins. Concerning the latter, temporary and reversible phosphorylation of proteins is essential in regulating intracellular biological processes.

Phosphorylation has a major influence on various cellular responses and affects all aspects of a protein, including folding, localization, interactions, function, and the regulation of enzymatic activities.

While the knowledge of post-translational regulation of proteins in plants is growing because of its crucial importance in plant molecular networks, it remains an underexplored and challenging area.

Nevertheless, our team believes the time has come to move beyond laboratory species, such as Arabidopsis thaliana, and to also investigate signaling cascades in crop species, such as soybean and wheat.

As a biological question, our team investigates the impact of high temperatures on plant growth and development. Using well-established mass spectrometry-based pipelines (limited proteolysis mass spectrometry and phosphoproteomics), the researchers identify and characterize early signaling components associated with a temperature change, both in Arabidopsis and in wheat.

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Lieven De Veylder Cell cycle Plants cannot move, so they need to be able to adapt quickly to a changing environment. The De Veylder lab aims to understand how plants adjust their growth at the level of the cell cycle.

Identifying the mechanisms that control cell cycle progression in response to environmental cues can help develop climate-resilient crops and innovative crop management practices.

One line of research focuses on wound-induced regeneration. Plants have a unique ability to regenerate, allowing them to survive severe stresses such as injury, herbivory, and changing weather conditions. Previously, our team identified a key molecular component that controls stem cell replenishment after apoptosis. Based on these observations, the De Veylder lab aims to understand the pathways that activate plant regeneration, knowledge that could help the regeneration process of recalcitrant plants.

In another line of research, our team aims to map the mechanisms that allow plants to maintain cell cycle activity and genome integrity under growth conditions that cause DNA damage. This includes the study of proliferation-arresting proteins that control the transition between cell division and differentiation, knowledge that could be used to increase plant resilience to climate change.

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Daniel Van Damme Advanced live cell imaging The discovery of fluorescent proteins allowed the visualization of intracellular processes in real-time and introduced dynamics, interactions, and transitions as novel parameters that could be measured by microscopic imaging. The Van Damme group uses various tools, including temperature modulation, root tip tracking, and microfluidics, to achieve dynamic and long-term live cell imaging of intracellular processes in plants.

The main research question in our group concerns understanding how plant cells orchestrate intracellular trafficking of proteins within the endomembrane system and how this contributes to the cellular response to abiotic stress

situations such as drought and elevated temperature. Within the endomembrane trafficking routes, the focus lies on endocytosis, which is the pathway that controls the homeostasis of the outer cellular membrane, and the interplay between endocytosis and autophagy, which is a catabolic recycling pathway that is highly upregulated under stress conditions. Generating knowledge on how endocytosis functions in plants and how it connects with autophagic degradation will provide a framework for the development of novel tools to control cellular homeostasis and intercellular communication. Ultimately, this will allow generating plants with increased tolerance to stress conditions.

Our team combines state-of-the-art cell biological, genetic, structural, and proteomic approaches to achieve our research goals. As model systems, we use Nicotiana tabacum Bright Yellow-2 culture cells, Arabidopsis thaliana PSB-D culture cells, Arabidopsis thaliana plants, and Nicotiana benthamiana epidermal leaf cells.

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Alain Goossens Specialized metabolism The plant kingdom synthesizes thousands of unique and bioactive specialized metabolites that have important roles in plant survival and often valuable applications for humans. Yet, this impressive metabolic machinery is still hardly exploited, mainly because of the limited molecular insight into plant (specialized) metabolism. Nature has invented strict, yet not fully understood, regulatory networks that control plant metabolism. These networks safeguard plant fitness in a continuously changing environment. By investigating the reprogramming of plant metabolism by developmental and environmental cues, the Goossens group aims to advance our fundamental understanding of the mechanisms that steer plant metabolism.

Our team specifically focuses on jasmonate, the phytohormone that steers the delicate balance between growth and defense programs across the plant kingdom. Understanding when, where, how, and why the JA (jasmonic acid) signal is

produced and transmitted in planta, how it interacts with other environmental and developmental cues, and how it is transduced to the onset of cell-specific specialized metabolism will allow capture of the regulatory networks that steer the plant metabolic networks. In parallel, this will enable unlocking plant-specialized metabolism for numerous human applications, given that our findings serve simultaneously as a novel resource for engineering tools that will facilitate the creation of plant-based synthetic biology platforms for the sustainable production of high-value plant metabolites and increased crop productivity by improvement of plant fitness in a changing environment.

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Hilde Nelissen Plant growth dynamics Plants continuously produce new organs in a highly coordinated manner, determining their final shape and yield under varying conditions.

The cellular mechanisms and molecular networks driving these growth processes are precisely regulated in space and time.

The Nelissen team aims to unravel the spatio-temporal regulation of plant growth, paving the way for climate-smart plants—a vital solution for sustainable agriculture. We explore how genetic and environmental changes, both in the greenhouse and the field, influence growth processes.

By mapping molecular and cellular dynamics from the cell to the canopy level, we develop tools to translate this knowledge into targeted network modifications. Together, we are engineering plants for a more resilient and sustainable future.

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Thomas Jacobs Plant genome editing The Jacobs group develops and optimizes genome editing tools for plants. We use CRISPR given its simple design and multitude of modifications, and collaborate with many academic and industrial groups that need to develop or optimize a new gene editing technology or simply want to use a reported technique. We design, test, and validate genome editing systems in a wide range of plant species. The primary objective is to make plant genome editing simple at scale; it should be easy to use, work in any plant species, and produce any desired genetic outcome.

One of the fundamental lines of research is the creation or curation of a collection of genome editing (CRISPR) reagents and protocols for various plant systems. A catalog of CRISPR reagents (nucleases, base editors, etc.) has been integrated into a standard modular vector system for ease of use and adoptability. These vectors are made available to the community via the VIB Vector Vault https://vectorvault.vib.be/. To increase gene editing frequencies and improve the recovery of useful gene-edited plants, our group is focused on the entire gene-editing workflow, from optimizing protocols, vector components, downstream analysis, and isolation of mutants of interest.

a couple of things: (1) a general understanding of which genes, and combinations of genes, are essential for plant growth and development, (2) the ability to make targeted large-scale structural changes to plant chromosomes, and (3) the ability to precisely install or write new DNA elements into a plant genome. To address point 1, the Jacobs group collaborates with several other PSB groups and collaborators at the Flemish research institute ILVO to develop CRISPR screens for plant research. The ERC OMEGA project is also developing novel technologies to enable large-scale modifications of plant genomes.

Within the next 5-10 years, the ability to make precise changes to individual plant genes will be routine. We think the next big challenge will be to manipulate genomic DNA at the chromosomal scale, that is 100s of kilobases, or even megabases, at a time. To do this we need

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Frank Van Breusegem Oxidative stress signaling Suboptimal growth conditions caused by drought, temperature, salt, and pathogen-related stresses are leading to worldwide yield losses in cultivated crops. These issues are anticipated to become even bigger in the future, as climate change will cause more temperature and drought stress. In the meantime, the demand for plants for food, feed, and bio-energy is increasing. This encouraged the search and development of appropriate breeding strategies and has made crop stress tolerance a major objective in plant biotechnology research.

The Van Breusegem group studies how plants regulate their stress responses, with special attention to the signaling network underlying oxidative stress responses.

Reactive oxygen species (ROS), causing oxidative stress, were long considered as harmful by-products of (diseased) metabolism. However, recently they have emerged as important regulators of plant stress responses. Through combined top-down and bottom-up genomics and redox proteomics approaches, we are dissecting the molecular networks governing ROS signal transduction in plants. Our team seeks to pinpoint pathways that are potential targets for innovative molecular breeding strategies to develop stress-tolerant crops.

The Van Breusegem lab also has a longstanding interest in a group of proteases called metacaspases and their function and regulation during cell death in Arabidopsis thaliana. Metacaspases cut a wide range of protein substrates, involved in immune, growth, and developmental processes.

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Moritz Nowack Programmed cell death Programmed cell death (PCD) is a fundamental biological process. PCD has its evolutionary origins billions of years ago in bacteria that defended their clonal communities against viral attacks by sacrificing individual cells for the greater good of the colony. With the evolution of complex multicellular organisms, PCD has adopted multiple functions in physiological and pathological contexts. In both animals and plants, defects in the molecular control of PCD can cause severe developmental aberrations and diseases. in diverse developmental contexts.

The significance of PCD for human health was recognized decades ago. In plants, however, we know comparatively little about PCD, even though different forms of PCD occur throughout plant life, and many of them are critical for plant health and fitness, as well as for successful growth and reproduction.

The Nowack lab is exploring the molecular control of plant PCD during vegetative and reproductive development. Dozens of different cell types, tissues, and organs execute tightly regulated, actively controlled cell death programs during their differentiation and development. Our team has identified several commonly expressed, evolutionary conserved PCD signature genes, suggesting that a plant PCD core machinery controls the initiation and execution of cell death

Using the latest molecular-, cell-, and systems-biology approaches, our team is unraveling the mechanisms that control the preparation, initiation, and execution of plant PCD as an inherent part of cellular differentiation. Most research is performed in the framework of vegetative and reproductive development of the model plant Arabidopsis thaliana. However, we are also investigating PCD during fertilization and kernel development of maize (Zea mays) as an important seed-producing crop plant.

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investigate the subcellular localization, mobility, transport routes, and binding interactions of various brassinosteroid enzymes and signaling components.

Jenny Russinova Brassinosteroids The main focus of the Russinova group is the function of the plant growth-promoting steroidal hormones known as brassinosteroids.

Brassinosteroid-deficient mutants exhibit dramatic developmental defects. These hormones regulate the expression of numerous genes, influence the activity of complex metabolic pathways, contribute to the regulation of cell division and differentiation, and help control overall development. Brassinosteroids have a broad spectrum of activities that positively impact both the quantity and quality of crops, while also increasing plant resistance to stress and pathogens.

The brassinosteroid pathway is one of the best-characterized signal transduction pathways in plants. Brassinosteroids are perceived by a plasma membrane-localized receptor complex, which transduces the signal from the cell surface to the nucleus via an intracellular cascade of phosphorylation-mediated protein-protein interactions.

Our primary objective is to combine genetic, molecular, and cell biology tools to study the mechanisms of brassinosteroid biosynthesis, transport, distribution, and signaling. We use genetics, chemical genomics, and proteomics to

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The potential application of brassinosteroids in agriculture is based not only on their ability to increase crop yields but also on their capacity to enhance resistance to various stress conditions, such as high salinity, drought, and fungal and viral infections. Therefore, unraveling the regulatory mechanisms of brassinosteroid signaling or identifying chemicals that influence this activity can enable the development of targeted strategies for cultivating high-yielding plants.

Steven Maere Evolutionary systems biology The Maere lab develops computational biology methods to study the wiring and evolution of molecular systems.

A major interest of our lab is to unravel how plants respond molecularly and phenotypically to combined stresses under field conditions. Most single-stress studies performed under controlled laboratory conditions are of limited predictive value for plant phenotypes in the field. To get a view of the complex interactions between plant stress response pathways and their effect on yield phenotypes, we want to harness natural gene expression and phenotype variation among genetically identical field-grown plants, based on the premise that each plant is subject to subtle deviations of several micro-environmental factors from the field average.

Our team is currently developing methods to use individual plant datasets for reverse engineering stress response pathways, their interaction, and their impact on yield-related phenotypes, focusing on rapeseed, maize, and soybean as model crops. Understanding how stress pathways are wired and how they interact is essential to developing crops with enhanced yield and tolerance to field stress conditions, which will be crucial to coping with the challenges presented by climate change and a rising world population.

The Maere lab is also active in the field of molecular evolution. For the past few decades, molecular evolution research has largely focused on the evolution of individual gene families and overall genome structure. Analogous to the transition from reductionist to system-scale approaches in molecular biology, the logical next step is to study the evolution of genes in the context of the systems in which they function.

One way to study how systems of interacting components evolve is to simulate the evolution of suitably abstracted model systems in silico.

Given recent developments in the field of high-performance computing, it is now possible to simulate the evolution of molecular systems at an unprecedented level of mechanistic detail.

Our group uses mathematical models to map the genotype of artificial transcriptional regulatory systems to their expression phenotype. These are then used to study how transcriptional regulatory systems evolve. One evolutionary question of particular interest to the lab is how whole-genome duplications, which are common in plants, impact the evolution of regulatory systems in the short and long term. In this context, our lab is also developing a methodology to detect ancient whole-genome duplications in plant genomes.

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Sofie Goormachtig Rhizosphere The Goormachtig lab focuses on how interactions between plant roots and neighboring organisms positively influence plant growth. The emphasis is on the symbiosis between legumes and rhizobia, resulting in the formation of new root organs, the nodules, in which the rhizobia reside and fix atmospheric nitrogen for the plant, making plant growth independent of nitrogen fertilizers. Our group studies developmental and environmental control of nodule organogenesis in the model legume Medicago truncatula and soybean.

The group takes great initiatives to introduce soybeans as a new crop in Flanders through collaborative citizen and farmer science projects.

Our research extends beyond leguminous plants.

Plants engage in numerous interactions with

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both beneficial and harmful soil organisms. These can be bacteria and fungi, but also other plants, such as Orobanchaceae sp. It is thus of great importance for plants to attract friends and repel foes. This intra- and interkingdom communication occurs through molecular signaling pathways involving the secretion and sensing of various metabolites and proteins. Our team combines root microbiome analysis with proteomics, transcriptomics, genetic approaches, and highthroughput phenotyping to elucidate the mechanisms by which microbes communicate with plant roots, resulting in beneficial effects for the plants.

Yves Van de Peer Bioinformatics and evolutionary genomics The Van de Peer lab has long been an active collaborator in numerous international plant genome projects. In recent years, however, our research focus has shifted predominantly toward polyploidy and whole-genome duplication.

Members of our group are dedicated to creating computational tools for detecting remnants of polyploidy and dating ancient paleopolyploidy events.

To explore the mechanistic reasons behind the selective advantages of polyploidy, particularly evident during periods of environmental stress, we use both computational and experimental strategies. Computational methods include simulating digital organisms that replicate biological populations with single and duplicated genomes. In contrast, experimental efforts involve long-term evolution studies using two model organisms: the unicellular alga Chlamydomonas reinhardtii and the rapidly growing duckweed Spirodela polyrhiza. These organisms are ideal for

such studies due to their high vegetative growth rates, relatively small genome sizes, minimal space requirements, ease of laboratory culture establishment, and established roles as model systems for researching the functional impacts of whole genome evolution.

In addition to conducting various evolution experiments with both biological and digital organisms, our group is also developing eco-evolutionary models to elucidate the short-term establishment processes of polyploids. Furthermore, in collaboration with ILVO, our group is leveraging new insights into polyploidy to enhance the breeding of more resilient and robust polyploid crops.

Overall, a deeper understanding of the 'rules' governing polyploidy at various levels will provide significant insights into polyploid evolution and will have far-reaching implications for the burgeoning field of evolutionary cell biology.

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Klaas Vandepoele Computational regulomics The objective of the Vandepoele group is to extract biological knowledge from large-scale experimental data sets using -omics data integration, comparative sequence & expression analysis, network biology, and artificial intelligence (AI).

Through the development of novel computational methods, we identify new aspects of genome biology, especially in the area of gene regulation and function prediction.

Our research is centered at the intersection of plant genomics, biotechnology, and computational biology. We analyze expression and chromatin accessibility data, in both bulk and single-cell variants to unravel plant gene regulatory networks.

Both (sc)RNA-Seq data and (sc)ATAC-Seq data are leveraged by the MINI-EX and MINI-AC toolkits, resulting in a deeper understanding of the interplay between gene expression and epigenomics, DNA motifs, and transcription factors. We perform systematic regulatory gene annotations in diverse plant and diatom species and characterize regulatory sequences in crop

species with complex genomes. More recently, our group started implementing AI-guided approaches for the analysis of noncoding DNA sequences and the inference of the underlying regulatory grammar. These findings facilitate the modification of native plant promoters and the design of novel synthetic promoters.

Comparative functional genomics forms a second line of inquiry. Plant genomes contain an extremely large number of genes, both in the number of gene families as well as in copy number. Consequently, searching for individual genes with conserved biological functions is challenging. Therefore, comparing expression data across species offers a valuable approach, complementary to protein similarity, to identify functional orthologs and characterize genes with unknown functions. This is an essential step for the translation of detailed biological knowledge on gene functions and networks from model species to crops (e.g. PLAZA platform).

Taken together, the Vandepoele group demonstrates how computational and experimental approaches can synergize to unravel the complexities of plant and diatom genomes.

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Center in numbers

(on average/year 2022-2024)

PSB attracts a lot of international PhD students and postdocs. On average 40 different nationalities work at PSB, with the Chinese community being the largest of all foreign researchers.

65 publications in Tier 5 journals

Belgian PhD students

49

140 total publications

international PhD students

25

54

PhD graduations

5 patents filed

2 spin-offs founded 1 in 2021 1 in 2025

25 Belgian Postdocs

46 International income

4800 K€

international Postdocs

Industrial income

3160 K€

275 FTE 27

Expertise & technologies

The forward-looking research at the VIB-UGent Center for Plant Systems Biology allows its members to build significant expertise in using new and up-and-coming technologies and methods. Since the center has a strong social component as well, the present expertise is channeled into several expertise clusters that can assist both PSB members and others to implement the best possible technologies in their work.

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Metabolomics Core

Screening Core For more than 20 years, the VIB-UGent Center for Plant Systems Biology has been applying chemical biology approaches to study plant biology. In 2007, this led to the establishment of the VIB Screening Core. The VIB Screening Core advises and assists researchers in the process of assay development.

After successful assay development, the team provides services for high-throughput screening of compound or siRNA collections. For more information, feel free to contact Dominique Audenaert (dominique.audenaert@vib.be).

The VIB-UGent Center for Plant Systems Biology has developed strong expertise in plant metabolite profiling in the past, which is now further advanced by the VIB Metabolomics Core Ghent. Established in 2016 and hosted within PSB, the core provides high-quality metabolomics services and specializes in both primary and specialized (secondary) metabolism. The core offers cutting-edge technology and expertise for high-impact research, specializing in discovery and targeted metabolomics. Its services include ultra-performance liquid chromatography and gas chromatography coupled with high-resolution mass spectrometry (GC- and UPLC-HRMS), along with advanced data processing, statistical analysis, and molecular networking. The team helps researchers explore metabolic pathways, uncover gene functions, and identify novel compounds through compound purification for subsequent NMR analysis. For more information or requests, visit metabolomicscore-gent.sites.vib.be or contact Geert Goeminne at geert.goeminne@ vib.be.

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Fluorescence-based imaging in plants PSB possesses extensive knowledge and numerous tools on various aspects of plant cell biology using predominantly stable transformants of Arabidopsis thaliana as well as Nicotiana benthamiana transient leaf expression as model systems, while efforts are made to expand intracellular imaging to crops such as maize, wheat, and tomato. Expertise present in the center includes live-cell, dynamic, and long-term imaging. This includes root growth tracking to enable studying cell death and regeneration, as well as the effect of chemicals and biocontrol agents on plant growth at organ, tissue, and cellular resolution. Visual multicolor subcellular tracing using an extensive set of fluorescent marker lines allows the study of the effects of chemical compounds and growth-promoting or antifungal bacteria on the cytoskeleton, cell division, cell death, biosensors, and endomembrane trafficking. Finally, 3D and 4D visualization and quantification of growth effects at the cellular level are regularly performed.

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Introducing the plant phenotyping installations PSB has several plant phenotyping platforms for the automated imaging and precise irrigation of plants. The combination of automated plant handling with non-invasive imaging methods yields a variety of physiological, morphological, and plant growth-related variables during plant development. In addition to the study of different genotypes, the platforms also allow the investigation of different soil types/growth substrates, multiple irrigation schemes, biological/chemical irrigation, biological/chemical spraying applications, and more. Depending on the species, traits, and developmental stage of interest, the most suitable platform is selected.

IGIS The In Vitro Growth Imaging System (IGIS) was built to monitor the growth parameters of small seedlings, like Arabidopsis, with a high temporal resolution. The basic setup consists of a rotating metal disk, which can accommodate up to ten

Petri dishes, and a camera, which captures top-view pictures of the developing seedlings with high temporal resolution. Images can be acquired both during the light and dark periods.

WIWAM XY (396 plants) WIWAM xy is a robot for the high-throughput and reproducible phenotyping of seedlings and small plants, like Arabidopsis, grown in soil. Plants are grown in individual pots, which are picked up by the overlying robotic arm. Pots are brought to the imaging position, with an RGB camera, and the weighing-watering station, with a precision of up to 0.1mL. The system is located in a growth room, equipped with dimmable LED illumination.

The environment is monitored by integrating light, temperature, and humidity sensors for a detailed recording of the experimental growth conditions.

WIWAM Line (156 plants) and Rhizoline (300 plants) On these platforms, plants are positioned in tables, which are sorted in rows. The robot arm pushes the tables aside to create the required space in between the rows, so that the robot arm can pick plants from the side, making the systems suitable for caulescent plants, such as small maize plants. For imaging and irrigation, pots are taken to a designated area in the back of the growth chamber, where plants are rotated in front of an RGB camera for multiple-angle imaging. The Rhizoline is also equipped with a line scanner for imaging roots in transparent pots.

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PHENOVISION (392 plants) PHENOVISION is a greenhouse infrastructure for automated, high-throughput phenotyping of crops up to 2m in height. Pots are transported in carriers on a conveyor belt system. The imaging cabinets are equipped with RGB, thermal, and hyperspectral imaging systems. Three weighing and watering stations ensure accurate soil humidity levels throughout the experiment.

For further information or possible collaboration, contact: Hilde Nelissen (hilde.nelissen@psb. vib-ugent.be)

VIB AGRO-INCUBATOR The Center’s phenotyping capacities are tightly linked with the activities at the VIB AgroIncubator, where plant research, technological engineering, and computational developments are combined to drive innovation toward a green and sustainable future. The VIB Agro-Incubator is a plant science and agricultural technology incubator that houses an automated phenotyping facility, four lab units, a test field of two hectares, and a robotic sprayer, allowing for testing the plant response to crop protection agents, biologicals, and biostimulants. The VIB AgroIncubator is part of the distributed plant

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phenotyping infrastructure EMPHASIS and takes the lead in establishing the central hub. For more information, see https://agro-incubator.sites.vib. be/en

ILVO For over a decade, PSB has gained experience with field evaluations of phenotypic traits. In collaboration with ILVO, which is responsible for the field management, PSB organizes field trials to assess the agronomic relevance of promising germplasm in current agricultural and managerial practices. In addition, the center performs comparative studies between the field and the controlled conditions in the greenhouse, at the molecular and phenotypic levels, to increase the success rate of converting our lab-based findings to agricultural applications.

CROP GENOME ENGINEERING FACILITY The growing demand for crop transformation in the research community is driven by the rise of CRISPR/Cas9 gene editing. At the Crop Genome Engineering Facility (CGEF), we provide stateof-the-art maize and soybean transformation services to academic and industry partners, accelerating innovation in plant biotechnology.

Our transformation pipeline uses Agrobacterium tumefaciens to generate transgenic maize and soybean lines. For maize, we transform immature embryos of the inbred line B104, producing an average of 10 independent transgenic events within three to four months. These plants mature in our greenhouses and are pollinated with either wild-type or self-crossed pollen to produce T1 transgenic seeds that are ready for shipment in seven to eight months. For soybeans, we offer a half-seed transformation of W82 and an early-maturing genotype. Heritable modifications are evaluated in the T1 generation and T2 seeds are delivered to the end-user within 14 months.

Beyond transformation, the facility offers expertise in construct and gRNA design, cloning, T-DNA copy number determination, and downstream analyses, including the evaluation of gene editing outcomes. Through our partnership with the VIB Agro Incubator, we support large-scale projects enabling multigenerational seed scaling and/or phenotyping services.

The CGEF welcomes research collaborations to explore the transformation of other maize genotypes or crops, alternative delivery systems, novel selection strategies, and the development of new gene editing systems.

The facility is led by Lennart Hoengenaert, who is happy to discuss collaborative opportunities (Lennart.Hoengenaert@psb.ugent.be).

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PLANT PROTEOMICS FACILITY Interactomics service

Phosphoproteomics service

We offer the plant research community and companies access to our latest interactomics approaches, covering AP-MS and PL-MS (Turbo-ID) as complementary approaches. We also offer service for XL-MS based on tandem affinity purification of stable protein complexes.

We offer the plant research community and companies access to our latest phosphoproteomics approaches. In addition to global phosphoproteome analyses, we also offer targeted analyses of protein phosphorylation status, and we perform mass spectrometry-based assays on (putative) kinase-substrate pairs.

For AP-MS, we prefer to use Protein A/G-based tags. Alternatively, AP-MS based on GFP or other tags can be requested. For proximity labeling, we follow the Turbo-ID approach. We also have ample experience with tandem affinity purification for the isolation of stable protein complexes at high purity. The latter we can apply in cross-linking experiments that deliver structural analysis of the protein complex based on the identification of cross-linked peptides.

Experiments are performed under the Research Service Agreement, following well-established protocols for all (plant) species of interest.

More details and conditions are provided after consulting ive.desmet@psb.vib-ugent.be.

Experiments are performed under the Research Service Agreement, following well-established protocols for all (plant) species of interest. For cell cultures, we start from delivered bait clones.

For experiments in plants, we start from delivered plant tissue.

More details and conditions are provided after consulting geert.dejaeger@psb.vib-ugent.be.

Back row: Ive De Smet and Geert De Jaeger Front row: Jelle Van Leene, Eveline Van De Slijke, and Geert Persiau

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PLANT SINGLE CELL PLATFORM The Plant Single Cell Platform provides the plant research community with access to its advanced single-cell transcriptomics expertise and is free to use for PSB scientists. The Plant Single Cell Accelerator program runs in parallel to accelerate the implementation of single-cell approaches in crop species and foster interactions between PSB and industrial partners. Both the research community and industrial partners have access to experimental services and consultancy tailored to their needs. Our expertise is supported by well-established protocols applicable to a wide range of species, including Arabidopsis thaliana and various crop species (e.g., maize, rice, and soybean). We are continuously extending the portfolio of methods and technologies to study plant processes at a single cell/nucleus level, with methods such as transcriptome fixation and long-read sequencing. Our team has extended knowledge of plant sample preparation for singlecell and nuclei isolation, flow cytometry, single-cell platforms, and data analysis, allowing for rapid and robust data processing, cell clustering, cluster annotation, and visualization. This way, we can assist researchers with an end-to-end pipeline.

Additionally, we focus on technology development

and platform testing in targeted and untargeted spatial transcriptomics, which can be used to study cell types in their spatial context. We have optimized paraffin and cryo-sectioning on various plant species and tissues, and we assist in optimizing others. For more information, please contact freya.persyn@psb.vib-ugent.be or scplatform@ psb.vib-ugent.be.

Back row: Jonah Nolf, Thomas Eekhout, Bert De Rybel Front row: Jolien De Block, Freya Persyn

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Tech transfer Since its inception, the VIB-UGent Center for Plant Systems Biology (PSB) has been dedicated to translating its outstanding fundamental research into impactful contributions to the economy and society.

PSB continuously seeks opportunities to collaborate with industry, offering worldclass expertise in various fields of plant biotechnology.

Our team of highly skilled scientists specializes in areas such as plant growth and development, secondary metabolism, biotic and abiotic stress resilience, wood formation, oxidative stress, and plant resilience. Our experts provide new insights that spark creative ideas with potential economic and societal benefits. Through active scouting, we share these ideas with companies to find partners for further development.

The center also boasts advanced technology platforms and direct access to VIB service facilities. These include plant phenotyping through imaging robots, various omics techniques (proteomics, metabolomics, transcriptomics, up to single-cell analysis), bioinformatics and biostatistics support, and more. Our collective expertise allows companies to study the mode of action of their compounds, genes, or traits of interest from the cellular level to the canopy, across a variety of plant species.

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In addition, PSB actively pursues patenting strategies for technologies with commercial potential. VIB manages an extensive patent portfolio and files new patent applications annually.

Most of these patents are licensed to various partners or used to establish spin-off companies.

PSB has a long-standing tradition of transforming basic science into successful industrial ventures.

Inspired by the pioneering work of VIB founders Marc Montagu and Jeff Schell, the first Belgian biotech company, Plant Genetic Systems, was founded in Ghent in 1982. This company is now known as BASF Agricultural Solutions Belgium NV (formerly Bayer Crop Science).

PSB's research has also led to the creation of several other start-ups, including CropDesign (now a BASF Plant Science company), Devgen (now Syngenta), Agrosavfe (now Biotalys), Aphea.

Bio, Protealis, and recently Rainbow Crops.

Aphea.Bio, founded in 2017, is a spin-off that develops sustainable agricultural products based on natural microorganisms to increase crop yields and protect them against specific fungal diseases.

The company leverages resources and expertise in plant-bacteria interactions from PSB and microbiome know-how from the VIB-KU Leuven Center for Microbiology.

Protealis, founded in 2021, focuses on breeding protein-rich legume crops such as soybean and yellow pea. This company combines PSB’s experience in nitrogen-fixing rhizobia with complementary expertise from KU Leuven and ILVO in seed coating and legume breeding.

Rainbow Crops, founded in 2025, engineers complex traits to improve crop genetics via multiplex genome editing, breeding, and AI, based on the expertise in genome editing, phenotyping, and AI at PSB.

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Training

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To foster innovation and creativity in the life sciences, it is crucial to provide students with an educational program that integrates cutting-edge knowledge in their field of interest and stimulates their scientific curiosity and creativity. Therefore, delivering up-to-date education in plant developmental biology, biotechnology, genetics, and bioinformatics is a key objective of VIB-UGent Center for Plant Systems Biology.

PSB is part of the Department of Plant Biotechnology and Bioinformatics at Ghent University. This department provides teachers for various courses in the Bachelor's, Master's, and Master after Master's programs.

For instance, the Master of Science in Plant Biotechnology encompasses all aspects of modern plant biotechnology, including state-of-the-art technologies, plant growth and development, abiotic stress and biotic interactions, intellectual property, and safety regulations. Additionally, we support the interfaculty Master of Science in Bioinformatics, offering three tracks tailored to students' specific interests and backgrounds, preparing them for diverse job profiles in the bioinformatics domain.

Beyond teaching, PSB hosts weekly seminars featuring internationally renowned speakers who present their latest research. Furthermore, PhD jurors are invited to deliver lectures on their work when they come to assess PhD students at the center.

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03 - Translating science into solutions

PSB communities

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PhD Committee @PSB

The PhD committee represents the PhD students of PSB in several management committees at VIB and UGent. They have started numerous initiatives at PSB to help the working environment be both a fun and scientifically collaborative workplace.

Contact address: phdcommittee@psb.ugent.be

Back row: (left to right): Lotte Dhaese, Geng Sun, Arthur Cleyman Front row (left to right): Elisa Drijvers, Cedric De Smet, Eline Verhelst

Postdoc Committee @PSB

Left to right: Elena Sanchez Martin-Fontecha, Božena Klodová; Antoine Davière, Freya Persyn, Wouter Smagghe. Missing on the picture: Veronica Sondervan.

The local PSB postdoc committee is dedicated to building a supportive network for all postdocs at PSB. They provide a channel to communicate different needs and wishes from the postdoc community to the different departmental meetings. Additionally, they organize social events and informational sessions to support current and future opportunities.

Contact address: bozena.klodova@psb.vib-ugent.be

Tech Committee @PSB

The tech committee (Techcom) is the voice of technicians across PSB. We're a team of experienced technicians who represent our group in staff meetings and act as a bridge between technicians and management.

Whether it's raising concerns, sharing ideas, or simply being there to listen, we're here to support our colleagues and help create a better workplace for everyone.

Contact address: tcom@psb.ugent.be

Back row: Evelien Mylle; Davy Opdenacker, Isabelle Vanhoutte Front row: Robin Pottie, Ilse Vercauteren, Els Van Lerberghe, Jonas Nolf, Annelore Natran

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03 - Translating science into solutions

Outreach

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Science is not just for scientists. Quite the contrary, it is of interest to everyone. To do their work, scientists often receive funds from governmental sources, which, in turn, derive from the public. Scientific researchers are happy to engage with the general public to show what they are doing and why it is worthwhile. PSB scientists frequently give lectures for non-scientists on the benefits of biotechnology for agriculture.

Furthermore, they are actively engaged in the ongoing discussion on genome editing for the development of a sustainable, climate-resilient agriculture.

WETENSCHAP OP STAP: Members of VIB-UGent Center for Plant Systems Biology also participate in 'Science on the road', a VIB program that introduces youngsters from the fifth and sixth grades of elementary school to life in the laboratory.

MICROCAST AND MORE PSB is backing numerous initiatives conceived by our PhD students and postdocs to expand the reach of our scientific research. One such initiative is the podcast 'Microcast,' available on Spotify. It's both fun and engaging. Give it a listen!

SOY IN 1000 GARDEN AND 60 FIELDS Through VIB's Grand Challenge Program, PSB is actively involved in introducing protein crops to Northwestern Europe. Over a thousand citizens have been invited to grow soybeans in their gardens to identify local soil microbes capable of forming symbiotic relationships and fixing nitrogen for this new crop. This project has sparked many engaging discussions between citizens and scientists. Several bacterial strains identified will now be tested in farmers' agricultural fields.

This citizen and farmer science initiative helps us disseminate our research and collaboratively move towards a more plant-based society and sustainable agriculture.

ECOTEAM The VIB-UGent EcoTeam is dedicated to reducing the ecological footprint within the institute and beyond. Rooted in a strong ecological philosophy, the team’s mission aligns closely with the principles of plant biotechnology and the broader

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goals of PSB. Through a range of initiatives, the EcoTeam encourages more sustainable daily practices, such as minimizing waste during experiments, correctly sorting laboratory waste, switching off unused equipment, and promoting eco-friendly commuting and travel options.

Beyond everyday actions, the EcoTeam actively engages in strategic discussions with management to implement long-term, structural ecological improvements. These include optimizing greenhouse lighting, reducing the building’s overall energy consumption, and introducing outdoor green spaces with bee-friendly flowering plants.

The EcoTeam also plays an important role in public outreach, raising awareness about the vital connection between biodiversity and biotechnology. As part of these efforts, they have partnered with Natuurpunt, a Flemish nature conservation organization. By supporting Rijvissche, the nature reserve located near PSB’s research facilities, the team underscores its commitment to both science and sustainability.

INCREASING BIODIVERSITY LOCALLY Biodiversity, including diversity within species, between species, and across ecosystems, representing the genetic makeup of plants, animals, microorganisms, and the complexity of ecosystems, underpins all life on Earth. Healthy communities are sustained by well-functioning ecosystems, which provide critical services such as clean air, fresh water, natural medicines, and food security. Such ecosystems also regulate diseases and help stabilize the climate.

Biodiversity loss is occurring at an alarming rate, with recent estimates showing that species extinctions are currently ten to hundreds of times higher than the natural baseline and it is generally assumed that we are currently experiencing the

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next major mass extinction, caused by human activities, such as deforestation, habitat fragmentation, and climate change.

Locally, PSB tries to create awareness of the loss of biodiversity by working with Natuurpunt to improve biodiversity in a local forest and grassland area, the Hutsepotbos.

By implementing these actions, nature reserves such as the Hutsepotbos can foster a healthy and diverse ecosystem, benefiting both wildlife and the local community.

PSB GARDEN PSB also maintains a community garden that provides students, postdocs, and staff with the opportunity to explore the cultivation of various plants and crops. This space allows us to experiment with different varieties of promising and often-overlooked crops.

PhDs & alumni The VIB-UGent Center for Plant Systems Biology is proud to have seen 336 of its talented young scientists get awarded a PhD degree over the past 3 years, with more starting and undertaking this academic journey.

Their work was critical to the vast publication track record of PSB in leading journals and several technology transfer projects coordinated by the department.

Several of the PhD graduates have gone on to secure prestigious research fellowships in Belgium and abroad, including FWO, EMBO, and Marie-Curie post-doctoral fellowships.

Who better than the people themselves to give a testimony to the role VIB has played in their career?

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03 - Translating science into solutions

My time at PSB was one of the most transformative experiences of my life. PSB stands out as a leading institute in plant science, offering a strong foundation and state-of-the-art facilities that were instrumental in my scientific research. The supportive and multicultural environment provided me a unique opportunity to grow both personally and professionally, while the cutting-edge research opportunities prepared me for future challenges.

Tian Wu Associate researcher at the Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences PhD student from 2020-2024

PSB was the ideal place to pursue my postdoctoral research, as it is undoubtedly one of the world's leading institutes for plant science. The institute's support greatly facilitated my integration and enhanced the efficiency of my research endeavors.

Nicolas Doll Permanent researcher position from the CNRS, at the ENS de Lyon.

Postdoc from 2020-2023

What I appreciated during my postdoc at PSB, besides the opportunity to carry out cutting-edge research, was the focus on professional development. Thanks to careful mentorship, excellent training opportunities, and a vibrant international community full of inspiring people, PSB gave me a chance to grow tremendously as a scientist and a leader.

Matous Glanc Director at Czexapts in Science Postdoc from 2019-2023

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At PSB, you have the opportunity to engage in plant science at the highest level. The whole environment is set up to support research excellence: from top administration, through state-of-the-art facilities, to extensive scientific networks. With its vibrant international community, PSB provides the chance to connect with leading scientists in the field, grow as a researcher, and maximize scientific output.

Elia Lacchini Senior Research Fellow, Department of Plant Molecular Biology, University of Lausanne, Switzerland Postdoc from 2018-2024

My time at PSB was truly transformative. The well-equipped facilities, collaborative learning environment, and dedicated faculty provided me with the perfect foundation to grow both academically and professionally. PSB fosters an inspiring atmosphere where students are encouraged to innovate, collaborate, and strive for excellence. I am grateful for the invaluable experience and support I received, which have played a crucial role in shaping my professional journey.

Xiangyu Xu Postdoctoral fellow at UC Berkeley in the Department of Plant & Microbial Biology in the USA PhD student from 2017-2023

I have wonderful memories from my time as a postdoc at PSB! It’s a fantastic place for plant science, where great ideas easily turn into top-level collaborative projects and meaningful discoveries. I grew a lot scientifically, which greatly benefited my academic career. Hard work was well balanced with fun in the vibrant city of Ghent, but most importantly, it was about building lasting friendships and connections that today continue to shape my personal and professional life.

Andrés Ritter Junior Professor at the Roscoff Marine Station (CNRS - Sorbonne University), France Postdoc from 2019-2023

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VIB-UGent Center for Plant Systems Biology UGent-VIB Research Building FSVM Technologiepark 71 9052 Ghent Belgium

+32 9 331 38 00 +32 9 331 38 09 www.psb.ugent.be