Understanding the interplay between environmental cues and genome evolution
TEs are well known to be exquisitely sensitive to the environment. We are thus investigating the impact of climate on TE activity using the genome sequences publicly available for over one thousand A. thaliana accessions taken from across the globe. By combining population genomic approaches and mathematical modelling we are forecasting the impact of environmentally-induced transposition in response to ongoing global warming. We believe that these results are an important step to understand how environmental changes can affect the evolution of genomes and provide a new framework to forecast the impact of ongoing global warming on species’ survival and biodiversity. Find more here!
Contribution of TE mobilization to crop diversity
Tomatoes come in a multitude of shapes and flavors despite a narrow genetic pool. In this project we aim to use whole-genome resequencing data available for 602 cultivated and wild accessions to determine the contribution of TEs to tomato diversity. preliminary analysis revealed extensive transposition in tomato. Furthermore, genome-wide association studies (GWAS) revealed hundreds of TE insertions associated with extreme variations in major agronomic traits or secondary metabolites. Importantly, these associations cannot be detected by SNPs, suggesting a unique and important role for TE mobilization in tomato diversification. If you want to know more about how TEs can impact phenotypic variation in tomato, follow this link!
Transcriptional regulation of TEs
We are generating ATAC-seq, HiC and long-read sequencing (ONT) to characterise the transcriptomic and diversity of TEs using a comprehensive panel of A. thaliana and tomato mutant plants defective in the epigenetic silencing of TEs. In addition, we are constructing the a comprehensive TE expression atlas using publicly available RNAseq for hundreds of tissues and growing conditions. This atlas will enable us to determine when and where TEs are expressed in nature.
Transposon accumulation lines
We are also exploiting the epiRIL population in A. thaliana developed in the V. Colot team to investigate experimentally the transgenerational dynamics of TE mobilization when this was kick-started using genetic tricks. Following de novo transposition, we are able to measure precisely the transposition rate, landscape and how new insertions impact the expression of the nearby genes. Moreover, we can compare their transcriptomic impact before and after TE insertions become epigenetically silenced! These results will provide a first experimental assessment of the fitness landscape of active transposition. You can find more here.