A pan-genome of 72 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range

Abstract Although originally primarily a model for functional biology, the thale cress Arabidopsis thaliana has, owing to its broad geographical distribution and adaptation to diverse abiotic and biotic environments, developed into a powerful model in population genomics. Here, we present chromosome-level genome assemblies of 72 diverse accessions located across the global species range. We found that genomic co-linearity is remarkably 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. Pan-genome analyses of the gene space uncovered 40,382 distinct genes, 52% being present in all accessions and 48% appearing to be dispensable, including 23% private to a single accession, indicating a vast unexplored genic diversity. The availability of 72 new Arabidopsis thaliana genome assemblies will empower future genetic research.