Although originally primarily a system for functional biology, Arabidopsis thaliana has, owing to its broad geographical distribution and adaptation to diverse environments, developed into a powerful model in population genomics. Here we present chromosome-level genome assemblies of 69 accessions from a global species range. We found that genomic colinearity is very conserved, even among geographically and genetically distant accessions. Along chromosome arms, megabase-scale rearrangements are rare and typically present only in a single accession. This indicates that the karyotype is quasi-fixed and that rearrangements in chromosome arms are counter-selected. Centromeric regions display higher structural dynamics, and divergences in core centromeres account for most of the genome size variations. Pan-genome analyses uncovered 32,986 distinct gene families, 60% being present in all accessions and 40% appearing to be dispensable, including 18% private to a single accession, indicating unexplored genic diversity. These 69 new Arabidopsis thaliana genome assemblies will empower future genetic research.

虽然拟南芥最初主要是一个功能生物学系统，但由于其广泛的地理分布和对不同环境的适应，已发展成为群体基因组学的强大模型。在这里，我们展示了来自全球物种范围的 69 个种质的染色体水平基因组组装。我们发现基因组共线性非常保守，即使在地理和遗传上相距较远的种质中也是如此。沿着染色体臂，兆碱基规模的重排很少见，并且通常仅存在于单个种质中。这表明核型是准固定的并且染色体臂中的重排是反选择的。着丝粒区域表现出更高的结构动态，核心着丝粒的差异解释了大部分基因组大小的变化。泛基因组分析发现了 32,986 个不同的基因家族，其中 60% 存在于所有种质中，40% 似乎是可有可无的，其中 18% 是单个种质独有的，表明尚未探索的基因多样性。这 69 个新的拟南芥基因组组合将为未来的基因研究提供支持。