Pierre Baduel
team PEpiTE
- Polyploidy, Epigenetics, and TEs -
Background
Understanding how natural populations adapt to their environment and determining the molecular basis of these adaptations are two long-standing challenges in evolutionary biology, with major implications in today’s context of brutal climate change. Our team focuses on the contribution of transposable elements (TEs) in generating and transmitting heritable phenotypic variation in plants, and how polyploidy may influence these mechanisms.
We use Arabidopsis thaliana as our model system as the advanced tools available for genome, epigenome, and ploidy manipulation in this species make it a unique platform to dissect the interplay between TEs, polyploidy, and their impact on phenotypic variation.
Given the prevalence of polyploidy in plants, especially domesticated and invasive species, and the recognized role of TEs in generating heritable variation (through both mutagenic and epimutagenic effects), we expect our work to bring new insights into the molecular mechanisms contributing to the adaptation, and eventually the evolution, of species.
Research questions
Transgenerational Epigenetic Inheritance at TEs
In plants, loss of DNA methylation at TEs can be epigenetically inherited, but the determinants and significance of this additional system of inheritance are still unclear, in large part because of the confounding effects of DNA sequence polymorphisms.
To investigate the inheritance properties of DNA methylation loss at TEs in the absence of DNA sequence variation, we generate mutant lines that are deficient in DNA methylation at TEs and assess the transgenerational stability of the induced epigenetic variants when reintroduced in a genetically wild-type background. In parallel, we mine the genomes and epigenomes of natural A. thaliana strains collected from across the world to explore the scope, dynamics, and biological implications of TE-mediated transgenerational epigenetic inheritance in nature (Baduel et al., Science, 2025).
Impact of polyploidy on the epigenetic control of TEs
Whole genome duplication (WGD), which gives rise to polyploidy, is a recurrent event throughout eukaryote evolution, yet its impacts on the genome and the epigenome remain poorly understood. In particular, little is known on how polyploidy affects the epigenetic control of TEs, although TEs, because of their ability to generate large-effect mutations, have a unique potential to contribute to the rapid adaptation and evolution of polyploids (Baduel et al., Front. Ecol. Evol. 2018; Baduel et al., Nat. Comm., 2019).
In order to investigate the impact of WGD on the epigenetic control of TEs, we deploy third-generation long-read sequencing technologies to explore genomic and epigenomic variation in experimentally-induced polyploid A. thaliana lines and epigenetic mutants.
Funding: This project is funded in part by the ANR JCJC POLYSTRESS grant (AAPG2023) as well as of a PhD fellowship from PSL University awarded to Mounia El Messaoudi.
Research articles
Baduel P, De Oliveira L, Caillieux E, Bohl-Viallefond G, Xu C, El Messaoudi M, Barois M, Singh V, Sarazin A, Teixeira FK, Boccara M, Gilbault E, de France A, Quadrana L, Loudet O, Colot V. Transposable elements are vectors of recurrent transgenerational epigenetic inheritance in nature. Science (2025)
Raingeval M, Leduque B, Baduel P, Edera A, Roux F, Colot V, Quadrana L. Retrotransposon-driven environmental regulation of FLC leads to adaptive response to herbicide. Nature Plants (2024)
Sasaki T, Ro K, Caillieux E, Manabe R, Bohl-Viallefond G, Baduel P, Colot V, Kakutani T, Quadrana L. Fast co-evolution of anti-silencing systems shapes the invasiveness of Mu-like DNA transposons in eudicots. The EMBO Journal (2022)
Baduel P, Leduque B, Ignace A, Gy I, Gil J, Loudet O, Colot V, Quadrana L. Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana. Genome Biology (2021)
Baduel P, Quadrana L, Hunter B, Bomblies K, Colot V. Relaxed purifying selection in autopolyploids drives transposable element over-accumulation which provides variants for local adaptation. Nature Communications, (2019)
Reviews
Baduel P, Sammarco I, Barrett R, Coronado-Zamora M, Crespel A, Díez-Rodríguez B, Fox J, Galanti D, González J, Jueterbock A, Wootton E, Harney E. The evolutionary consequences of interactions between the epigenome, the genome, and the environment. Evolutionary Applications (2024)
Baduel P and Sasaki E. The genetic basis of epigenetic variation and its consequences for adaptation. Current Opinion in Plant Biology (2023)
Baduel P, Quadrana L. Jumpstarting evolution: How transposition can facilitate adaptation to rapid environmental changes. Current Opinion in Plant Biology (2021)
Baduel P, Colot V. The epiallelic potential of transposable elements and its evolutionary significance in plants. Philosophical Transactions of the Royal Society B (2021)
