A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range

Here, we present chromosome-level genome assemblies of 69 diverse accessions located across the global species range. We found that genomic co-linearity is very conserved, even among geographically and genetically distant accessions.

Along chromosome arms, megabase-scale rearrangements are rare, typically present only in a single accession. This indicates that the highly re-arranged karyotype of Arabidopsis thaliana (as compared to other Brassicaceae species), is quasi-fixed and that rearrangements in chromosome arms are counter-selected. In contrast, centromeric regions show much higher structural dynamics, and divergences in core centromeres account for most of the variation in genome size.