Organisation: JGU > Faculty 10 > Institute of Organismic and Molecular Evolution (IomE) > AG Xu

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We study evolutionary genetics of plant biotic interactions. We aim to understand how organisms evolve in multitrophic communities using integrative tools from genomics, molecular biology and chemical ecology.

The group originated in 2012 at the Max-Planck Institute for Chemical Ecology (in the department of Molecular Ecology). In 2018, the group moved to the University of Münster. Since April 2022, we are at the University of Mainz.

We are an INTER³group: International, interdisciplinary and intellectual. To learn more, please check our research, team and publications.

We aim to understand how organisms evolve and survive in nature using integrative tools from genomics, molecular biology, single-cell omics, chemical ecology, experimental evolution, and synthetic biology.

Current Projects

In nature, organisms live in communities and form complex trophic interactions. Understanding how multitrophic communities evolve and respond to environmental changes is a fundamental and pressing challenge in face of global change. While research in evolutionary biology revealed that a warming climate can drive adaptive evolution of individual organisms in the community, studies from community ecology showed that a warming climate can alter trophic interactions and community structure, which in turn changes the (co)evolutionary trajectory of interacting species. Thus, integrating evolutionary and ecological responses is crucial to understand the climate responses of individual species and communities. However, methodological challenges have hampered empirical studies until now. This project will address these challenges by experimentally evolving populations of three interacting species (aphid, duckweed, and daphnia) in their native communities using outdoor mesocosms with different climate conditions.

We will quantify how warming shapes the function and evolution of the multitrophic community in real-time. By manipulating climate-driven plant evolution, we will determine whether plant evolution alters the community’s response to climate change. We will also assess whether the interacting species coevolve in the community by quantifying the reciprocal selection imposed from their evolutionary changes. We will investigate the molecular mechanisms underlying (co)evolution using state-of-the-art genetic tools. Using a combination of experimental evolution, community manipulation, and cutting-edge genetic and analytic tools, this project will push the research boundaries of evolutionary ecology by revealing the mechanisms and processes of community evolution at work.

Many plant specialized metabolites (PSMs) function as defenses and abrogating particular pathway steps can lead to the accumulation of toxic intermediates, indicating that in addition to defense-based functional selection, autotoxicity avoidance plays a key role in the evolution of the PSM biochemistry. However, we currently do not know to which extent and how autotoxicity protection mechanisms evolve in concert with defensive functions.

These challenging questionsrequire a multi-species and -organ approach integrating gene -and PSM-level information (multiomics atlases) to test, using both functional and evolutionary studies, three key predictions of autotoxicity avoidance-driven evolution: that 1) strong signatures of positive selection for a PSM pathway should be detected for genes participating in autotoxicity prevention; 2) expression of those genes should likely be enriched in specific cell types associated with cell growth and/or differentiation; and that 3) similar organ-level signatures of selection should be detected among closely-related species harboring a given PSM innovation, since the selection imposed by intrinsic cellular functions is likely to be less dynamic than ecological selections. Here, by building on our recent breakthrough on the biosynthesis and (auto)toxicity mechanisms of diterpene glycosides (DTG) in tobacco as well as on other groups’ work on the biosynthesis of steroidal glycoalkaloids (SGA), two prominent Solaneaceae PSM defenses, we will implement a state-of-the-art integration of computational metabolomics, transcriptomics, single-cell genomics and genetic manipulation tools to address this challenge.

We aim to

(i) establish integrated metabolomics-transcriptomics atlases for eight solanaceous species to pinpoint on biochemical innovations in the DTG and SGA pathways;

(ii) retrace the molecular evolution of these pathways and characterize genes with signatures of strong positive selection;

(iii), as a case-study, functionally decipher the contribution of autotoxicity avoidance for SGAs’ evolution using a combination of single-cell genomics and genetic manipulations. The outcomes of this work will allow us to evaluate whether autotoxicity prevention is a key selection pressure driving the chemodiversification in Solanaceae.

This is a joint project together with Prof. Emmanuel Gaquerel from the University of Strasbourg, funded by DFG and ANR.

Related publications:

The Colorado potato beetle (Leptinotarsa decemlineata) is a powerful model for studying rapid evolutionary innovation. This project investigates how new cellular defense strategies emerge and diversify in an agricultural pest that repeatedly adapts to challenging environments.

Using comparative genomics, transcriptomics, cell-level analyses, and functional experiments, we aim to understand how defensive traits originate, how they are regulated, and how they contribute to ecological success. While the mechanistic details of this ongoing project remain confidential, our broader goal is to reveal how evolution generates novel cellular functions and how these innovations shape the adaptive potential of pest species.

This project is part of SPP 2349.

Rapid increase in fecundity is one of the major traits associated with the evolution of agricultural pests. Insect fecundity is strongly affected by the ovariole number, which is genetically controlled, but can be influenced by environmental factors, such as temperature and food quality.

In Drosophila, evolutionary changes in ovariole number are associated with the number of terminal filament cells (TFCs) in the terminal filament (TF), a stack of 9-10 disc-shaped cells located at the anterior tip of each ovariole. The regulation of both TFC and TF numbers is dependent on the Hippo signalling pathway, an evolutionarily conserved regulator of organ growth and cell fate that also regulates haematopoiesis in Drosophila. However, the genetic mechanism underlying the increased ovariole number in agricultural pests remains unclear.

To identify the genetic mechanisms underlying ovariole number variations in CPB, we will perform quantitative trait loci (QTL) analysis using the established mapping populations. We will also compare the small RNA profiles and single-cell transcriptomes of the TF between the two genotypes that differ in their ovariole numbers. The outcomes will provide new insights into the cellular regulation of cell fate, e.g., via small RNAs, involved in controlling ovariole numbers in CPB. Furthermore, we will use the population genomics approach to characterize the signature of selection in CPB and investigate whether the evolution of the toxin and ovariole number in CPB was under natural selection.

This project is part of the GenEvo Research Training Programme.

The Colorado Potato Beetle (CPB), Leptinotarsa decemlineata produces a neurotoxin, leptinotarsin in its hemolymph, which is lethal to other insects and vertebrates. This project aims to investigate the evolutionary and molecular mechanisms underlying leptinotarsin production and self-tolerance in CPB using a combination of functional neurobiology and evolutionary genetics approaches.

This project is part of the GenEvo Research Training Programme.

Flowering plants produce some of the most diverse reproductive structures in nature, yet the core developmental program required to build a flower remains poorly understood. Duckweeds provide a unique opportunity to address this question: they are among the smallest and fastest-growing flowering plants, with highly reduced body plans and extremely simple flowers.

In this project, we establish Lemna aequinoctialis as a tractable model for minimal flower development. We combine chromosome-level genomics, single-nucleus RNA sequencing, whole-mount in situ validation, and genetic transformation tools to identify the cell types, regulatory genes, and developmental trajectories that generate flowers inside the duckweed frond. By studying how duckweeds retain, modify, or lose components of canonical flowering pathways, we aim to define the minimal genetic toolkit required for sexual reproduction in flowering plants.

This work will provide new insight into the evolution of plant reproductive development and create a compact experimental platform for studying flower formation, genome evolution, and synthetic biology in plants.

Europe’s strategic vulnerability is rooted in its dependency on imported raw materials. Pharmaceutical supply chains rely on non-EU sources for key chemical precursors, while the EU also imports vast quantities of protein feeds and vegetable oils. In recent geopolitical tensions, or epidemic outbreaks, such dependencies translate into shortages, price spikes, and loss of autonomy.

This project explores duckweed as a green, scalable platform for producing valuable biological raw materials for medicine, food, and renewable bio-based products within Europe. Duckweeds grow rapidly in contained aquatic systems, require little land, and can be integrated with nutrient-recycling approaches, making them attractive for decentralized and sustainable production. Building on our expertise in duckweed biology and plant synthetic biology, we aim to develop this system as a model for future low-footprint biomanufacturing, contributing to more resilient European supply chains and reduced environmental impact.

This project is supported by Mainzer-wissenschaftsstiftung.

This project investigates how host choice shapes rapid adaptation in the Colorado potato beetle, a globally important agricultural pest. We combine behavioural assays, experimental evolution, population genetics, and modelling to test how oviposition and feeding preferences influence adaptation to insecticide-treated host plants. By linking niche choice with resistance evolution, the project aims to clarify how pest populations respond to strong human-imposed selection and why different behavioural and genetic strategies can coexist within populations. These insights will improve our understanding of rapid host adaptation and may inform more sustainable approaches to pest management.

This project is part of SFB-TRR 212

This project investigates how host choice shapes rapid adaptation in the Colorado potato beetle, a globally important agricultural pest. We combine behavioural assays, experimental evolution, population genetics, and modelling to test how oviposition and feeding preferences influence adaptation to insecticide-treated host plants. By linking niche choice with resistance evolution, the project aims to clarify how pest populations respond to strong human-imposed selection and why different behavioural and genetic strategies can coexist within populations. These insights will improve our understanding of rapid host adaptation and may inform more sustainable approaches to pest management.

This project is part of SFB-TRR 212

Shuqing Xu obtained his PhD from ETH Zürich under the supervision of Prof. Florian Schiestl and Prof. Alex Widmer in 2011. His PhD thesis focused on the evolution of floral signals in a specialized pollination system. Between 2012 and 2017, he moved to Max Planck Institute for Chemical Ecology in Jena as a project group leader in the Department of Molecular Ecology (led by Prof. Ian Baldwin), where he worked on the evolutionary genetics of plant defences. In 2018, he was appointed as an associate professor (W2) at the University of Münster. Since April 2022 he is the department chair of evolutionary plant sciences at the University of Mainz. He is a father of three children.

Christian Uhink is responsible for teaching the Botanical Identification Exercises and the Basic Botanical Exercises in the undergraduate programs. He received his PhD working at the Institute of Special Botany at JGU Mainz on the systematics and biogeography of alpine plant groups. He also works as a study manager for the faculty of biology.

Martin joined the group in May 2018. He received his PhD from the University of Jena for his work at the Max-Planck Institute for Chemical Ecology (Prof. Ian Baldwin) in 2015. He has extensive experience with analytic chemistry and is interested in studying the mechanisms and functions of plant chemical defences. He is currently in charge of the molecular and analytic platforms in the group. He is also working on an ongoing project that investigates whether and how aphid herbivory on duckweed affects the evolution of aquatic communities.

Nijat joined the group in June 2022. He received his PhD in community and behavioural ecology at the University of Koblenz-Landau, Germany in 2022. He is interested in understanding the mechanisms and consequences of animal behaviour. He is currently working on the role of niche choice on host plant adaptation in Colorado potato beetles. His project is part of the NC3 initiative.

Abhisek joined the group in April 2024. He received his PhD in computational genomics at the Indian Institute of Science Education and Research Bhopal, India in December, 2023. During his PhD, he used a multi-omics approach to understand the adaptive evolution of biological pathways in Eukaryotic organisms. His postdoctoral research at JGU Mainz focuses on revealing the role of autotoxicity protection for defense metabolism innovations in Solanaceae using a multi-omics approach.

Thomas joined the group in January 2026. He recently completed his dissertation at Leibniz Institute on Aging in Jena. His postdoctoral research at JGU Mainz focuses on the evolution and function of horizontally transferred genes in Colorado potato beetle.

Zhiyao joined the group in May 2026 as a postdoc. He obtained his PhD from Zhejiang University in 2025, studying molecular mechanisms underlying plant-herbivore interactions. In AG Xu, he will develop and state-of-the-art molecular biology tools to understand the biosynthesis and function of plant specialised metabolites

Sara joined the group in September 2021. She received her master's degree from the International Center for Advanced Mediterranean Agronomic Studies in Bari, Italy.
She is interested in understanding how microbes affect the function and evolution of plant defences. She has been working on the plant experimental project.

Léonore joined the group in July 2022, after receiving her master's degree at Pierre and Marie Curie University in Paris. She is currently working on the evolution of a neurotoxin in Colorado potato beetles. Her project is part of the GenEvo research training group. She is co-supervised by Prof. Marion Silies.

Himrekha joined the group in May, 2023 after receiving her master's degree from the University of Mumbai, India. She is working on the mechanisms underlying neurotoxin self-tolerance and its evolution in Colorado Potato Beetles. She is co-supervised by Prof. Marion Silies.. Her project is a part of the GenEvo Research Training group.

Philippa joined the group in June 2024 after receiving her master’s degree from the Johannes Gutenberg University in Mainz, Germany. She is interested in understanding animal behavior and currently working on investigating the evolution of niche choice behavior and its effects on the fitness of Colorado potato beetles.

Anna joined the group in January 2025 after earning her master’s degree from Ruprecht-Karls University Heidelberg, Germany. Her research focuses on molecular mechanisms underlying plant-microbe interactions, with a particular interest in developing a transformation method for Lemna aequinoctialis.

Boya joined the group in April 2026 as a GenEvo student. He obtained his Master’s thesis in 2024 from the Institute of Botany, Jiangsu Province, and the Chinese Academy of Sciences. Later, he worked as a research assistant at the Zhejiang University School of Medicine. His PhD project aims to understand how selection drives the evolution of gene expression among different organs in the Colorado potato beetle.

Pascal Blaschke (BSc student)
Aleksandra Varenikova (TA & research assistant)
Dr. Patrycja Baraniecka (postdoc in the group)
Dr. Pablo Duchen (postdoc/group leader in the group)
Prof. Antonino Malacrinò (postdoc in the group)
Prof. Wenwu Zhou (postdoc in the group)
Dr. Martin Höfer (PhD student)
Dr. Yangzi Wang (PhD student)
Víctor Cáceres Singh (MSc student)
Julia Michaela Held (BSc student)
Jonas Joachim Biroth (MSc student)
Kris Künemund (research assistant)
Dr. Alitha Edison (PhD student)
Laura Böttner (co-supervised PhD student)
Anna Viola Rauschkolb (BSc student)
Nesma Mohamed (guest scientist)
Dr. Ling Lin (guest scientist)
Lanlan Ke (guest scientist)
Uschi Martiné (Technical assistant)
Dr. Zhihao Lin (PhD student)
Dr. Thomas Brockmöller (PhD student)
Marina Hölter (MSc student)
Annika Pins (BSc student)
Hanna Kertzel (BSc student)
Maximilian Hackhausen (BSc student)
Jonas Nikolaus Bachofer (BSc student)
Luise Schmidt (BSc student)
Thomas Schacker (BSc student)
Pauline Prüsener (BSc student)
Samuel Wink (BSc student)
Fabio Dudenhausen (BSc student)
Milena Harnisch (BSc student)
Maximilian Schiefer (BSc student)
Joachim Rikus (BSc student)
Pia te Heesen (BSc student)
Dr. Matthiew Durren (Internship student)

Siadjeu C, Chakraborty A, Xu S

2026

Xu S, Gaquerel E

2025

Schäfer M, Malacrinò A, Walcher C, Spaak P, Serwaty-Sárazová M, Käser S, Bulas T, Dambone-Bösch C, Dexter E, Hottinger K, Böttner L, Vorburger C, Ebert E, & Xu S,

2025

Li J, Halitschke R, Li D, Paetz C, Su H, Heiling S, Xu S*, Baldwin IT*

2021

Xu S*, Stapley J, Gablenz S, Boyer J, Appenroth KJ, Sree KS, Gershenzon J, Widmer A, Huber M*

2019

Xu S*#, Brockmöller T*#, Navarro-Quezada A, Kuhl H, Gase K, Ling ZH, Zhou WW, Kreitzer C, Stanke M, Tang HB et al & Baldwin IT*

2017

Zhou W, Kugler A, McGale E, Haverkamp A, Knaden M, Guo H, Beran F, Yon F, Li R, Lackus N et al & Xu S*

2017

Xu S*, Kreitzer C, McGale E, Lackus ND, Guo H, Kollner TG, Schuman MC, Baldwin IT, Zhou WW*

2017

Full publication list can be found here:

To address the multifaceted questions arising from our research, we employ a broad and diverse range of methodologies. This includes a wide variety of equipment for molecular biological studies, protein analyses, histology, and microscopy, as well as facilities for the cultivation of plants and other model organisms.

Our group has state-of-the-art analytic instruments. This includes a Shimazu Triple Quadrupole LC-MS/MS 8060 (funded by DFG). This machine can quantify small molecules, such as phytohormones, with very highly sensitive and precision. For more details, please see here: https://www.shimadzu.de/lcms-8060-triple-quadrupole-ms

If you are interested in using our analytic instrument, please contract:

Dr. Martin Schäfer (mschaefer@uni-mainz.de)
or
Prof. Shuqing Xu (shuqing.xu@uni-mainz.de)

The NanoJect III is a precision microinjection system designed for the controlled delivery of small volumes of liquids into cells and other biological samples. It enables accurate and reproducible injections, making it particularly suitable for applications in molecular and cellular biology, such as the microinjection of DNA, RNA, proteins, or other reagents.

If you are interested in using our Microinjector please contract Prof. Shuqing Xu (shuqing.xu@uni-mainz.de) or Dr. Siân Stockton (sstockto@uni-mainz.de)

The Axio Zoom V16 is a high-performance digital microscope designed for advanced industrial and scientific inspection. It combines a motorized zoom system with high-resolution imaging, allowing users to inspect and document fine details efficiently. The system is particularly suitable for quality control, failure analysis, research, and precision inspection, where accurate visualization and reproducible results are important.

If you are interested in using our high-performance digital microscope please contract: