Most diploid organisms have polyploid ancestors. The evolutionary process of polyploidization is poorly understood but has frequently been conjectured to involve some form of ‘genome shock’, such as genome reorganization and subgenome expression dominance. Here we study polyploidization in Arabidopsis suecica, a post-glacial allopolyploid species formed via hybridization of Arabidopsis thaliana and Arabidopsis arenosa. We generated a chromosome-level genome assembly of A. suecica and complemented it with polymorphism and transcriptome data from all species. Despite a divergence around 6 million years ago (Ma) between the ancestral species and differences in their genome composition, we see no evidence of a genome shock: the A. suecica genome is colinear with the ancestral genomes; there is no subgenome dominance in expression; and transposon dynamics appear stable. However, we find changes suggesting gradual adaptation to polyploidy. In particular, the A. thaliana subgenome shows upregulation of meiosis-related genes, possibly to prevent aneuploidy and undesirable homeologous exchanges that are observed in synthetic A. suecica, and the A. arenosa subgenome shows upregulation of cyto-nuclear processes, possibly in response to the new cytoplasmic environment of A. suecica, with plastids maternally inherited from A. thaliana. These changes are not seen in synthetic hybrids, and thus are likely to represent subsequent evolution.

大多数二倍体生物都有多倍体祖先。多倍体化的进化过程知之甚少，但经常被推测涉及某种形式的“基因组休克”，例如基因组重组和亚基因组表达优势。在这里，我们研究拟南芥中的多倍体化，这是一种通过拟南芥和拟南芥杂交形成的冰期后异源多倍体物种。我们生成了A. suecica的染色体水平基因组组装，并用来自所有物种的多态性和转录组数据对其进行了补充。尽管大约 600 万年前 (Ma) 祖先物种之间存在差异并且它们的基因组组成存在差异，但我们没有看到基因组休克的证据：A. suecica基因组与祖先基因组共线；表达中没有亚基因组优势；和转座子动力学显得稳定。然而，我们发现变化表明逐渐适应多倍体。特别是，A. thaliana亚基因组显示减数分裂相关基因的上调，可能是为了防止在合成的A. suecica 中观察到的非整倍体和不良同源交换，而A. arenosa亚基因组显示细胞核过程的上调，可能是为了响应到A. suecica的新细胞质环境，质体从A. thaliana母系遗传. 这些变化在合成杂交种中是看不到的，因此很可能代表随后的进化。