Abstract
Transposable elements (TEs) are repetitive DNA sequences with the intrinsic ability to move and amplify in genomes. Active transposition of TEs is linked to the formation of extrachromosomal circular DNA (eccDNA). However, the complete landscape of this eccDNA compartment and its interactions with the genome were not well defined. In addition, at the beginning of my thesis, there were no bioinformatics tools available to identify eccDNAs from long-read sequencing data.To address these questions during my PhD, we first developed a tool, called ecc_finder, to automate eccDNA detection from long-read sequencing and optimized detection from short-read sequences to characterize TE mobility. By applying ecc_finder to Arabidopsis, human and wheat eccDNA-seq data (with genome sizes ranging from 120 Mb to 17 Gb), we documented the broad applicability of ecc_finder as well as optimization of computational time, sensitivity and accuracy.In the second project, we developed a meta-assembly tool called SASAR to reconcile the results of different genome assemblies from long-read sequencing data. For different plant species, SASAR obtained high quality genome assemblies in an efficient time and resolved structural variations caused by TEs.In the last project, we used SASAR-assembled genome and ecc_finder-detected eccDNA to characterize eccDNA-genome interactions. In Arabidopsis hypomethylated epigenetic mutants, we highlighted the role of the epigenome in protecting genome stability not only from TE mobility but also from genomic rearrangements and gene chimerism. Overall, our findings on eccDNA, genome assembly and their interactions, as well as the development of tools, offer new insights into the role of TEs in the adaptive evolution of plants to rapid environmental change.