During evolution successful allopolyploids must overcome ‘genome shock’ between hybridizing species but the underlying process remains elusive. Here, we report concerted genomic and epigenomic changes in resynthesized and natural Arabidopsis suecica (TTAA) allotetraploids derived from Arabidopsis thaliana (TT) and Arabidopsis arenosa (AA). A. suecica shows conserved gene synteny and content with more gene family gain and loss in the A and T subgenomes than respective progenitors, although A. arenosa-derived subgenome has more structural variation and transposon distributions than A. thaliana-derived subgenome. These balanced genomic variations are accompanied by pervasive convergent and concerted changes in DNA methylation and gene expression among allotetraploids. The A subgenome is hypomethylated rapidly from F₁ to resynthesized allotetraploids and convergently to the T-subgenome level in natural A. suecica, despite many other methylated loci being inherited from F₁ to all allotetraploids. These changes in DNA methylation, including small RNAs, in allotetraploids may affect gene expression and phenotypic variation, including flowering, silencing of self-incompatibility and upregulation of meiosis- and mitosis-related genes. In conclusion, concerted genomic and epigenomic changes may improve stability and adaptation during polyploid evolution.

在进化过程中，成功的异源多倍体必须克服杂交物种之间的“基因组休克”，但潜在的过程仍然难以捉摸。在这里，我们报告了源自拟南芥( TT) 和拟南芥(AA)的再合成和天然拟南芥 (TTAA) 异源四倍体的一致基因组和表观基因组变化。尽管来自A. arenosa的亚基因组比来自A. thaliana的亚基因组具有更多的结构变异和转座子分布，但A. suecica表现出保守的基因同线性和内容，在A和T亚基因组中比各自的祖先有更多的基因家族获得和丢失。这些平衡的基因组变异伴随着异源四倍体中 DNA 甲基化和基因表达的普遍趋同和协调变化。A 亚基因组从 F _{1迅速低甲基化到重新合成的异源四倍体，并收敛到天然}A. suecica中的 T 亚基因组水平，尽管许多其他甲基化位点从 F ₁遗传到所有异源四倍体。异源四倍体中DNA甲基化（包括小RNA）的这些变化可能会影响基因表达和表型变异，包括开花、自交不亲和性的沉默以及减数分裂和有丝分裂相关基因的上调。总之，协调一致的基因组和表观基因组变化可能会提高多倍体进化过程中的稳定性和适应性。