Chromosome-level assemblies of seven A. thaliana accessions using PacBio long-read sequencing.

We report chromosome-level, reference-quality assemblies of seven Arabidopsis thaliana accessions selected across the geographic range of this model plant. Each genome assembly revealed between 13-17 Mb of rearranged and 5-6 Mb of novel sequence introducing copy-number changes in ~5000 genes, including ~1,900 genes which are not part of the current reference annotation. By analyzing the collinearity between the genomes, we identified nearly 600 hotspots of rearrangements covering ~8% of the genome. Hotspots of rearrangements are characterized by accession-specific accumulation of tandem duplications and are enriched for genes implicated in disease resistance and secondary metabolite biosynthesis. Concomitant loss of meiotic recombination in hybrids within these regions is consistent with the accumulation of rare and deleterious alleles and incompatibility loci. Together this suggests that hotspots of rearrangements are governed by different evolutionary dynamics as compared to the rest of the genome and facilitate rapid response to the ever-evolving challenges of biotic stress.