SignificanceDespite widespread reports on deciphering the sequences of all kinds of genomes, most of these reconstructed genomes rely on a comparison of short DNA sequencing reads to a reference sequence, rather than being independently reconstructed. This method limits the insights on genomic differences to local, mostly small-scale variation, because large rearrangements are likely overlooked by current methods. We have de novo assembled the genome of a common strain ofArabidopsis thalianaLandsbergerectaand revealed hundreds of rearranged regions. Some of these differences suppress meiotic recombination, impacting the haplotypes of a worldwide population ofA. thaliana. In addition to sequence changes, this work, which, to our knowledge is the first comparison of an independent, chromosome-level assembledA. thalianagenome, revealed hundreds of unknown, accession-specific genes.