The majority of diploid organisms have polyploid ancestors. The evolutionary process of polyploidization (and subsequent re-diploidization) is poorly understood, but has frequently been conjectured to involve some form of "genome shock" --- partly inspired by studies in crops, where polyploidy has been linked to major genomic changes such as genome reorganization and subgenome expression dominance. It is unclear, however, whether such dramatic changes would be characteristic of natural polyploidization, or whether they are a product of domestication. Here, we study polyploidization in Arabidopsis suecica (n = 13), a post-glacial allopolyploid species formed via hybridization of A. thaliana (n = 5) and A. arenosa (n = 8). We generated a chromosome-level genome assembly of A. suecica and complemented it with polymorphism and transcriptome data from multiple individuals of all species. Despite a divergence of ~6 Mya between the two ancestral species and appreciable differences in their genome composition, we see no evidence of a genome shock: the A. suecica genome is highly colinear with the ancestral genomes, there is no subgenome dominance in expression, and transposable element dynamics appear to be stable. We do, however, find strong evidence for changes suggesting gradual adaptation to polyploidy. In particular, the A. thaliana subgenome shows upregulation of meiosis-related genes, possibly in order to prevent aneuploidy and undesirable homeologous exchanges that are frequently observed in experimentally generated A. suecica, and the A. arenosa subgenome shows upregulation of cyto-nuclear related processes, possibly in response to the new cytoplasmic environment of A. suecica, with plastids maternally inherited from A. thaliana.

中文翻译：

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拟南芥异源多倍体的逐步进化

大多数二倍体生物具有多倍体祖先。人们对多倍体化（以及随后的再二倍体化）的进化过程了解甚少，但经常被推测涉及某种形式的“基因组休克”-部分受作物研究的启发，其中多倍体与主要的基因组变化有关作为基因组重组和亚基因组表达的主导。但是，尚不清楚这种剧烈变化是否是自然多倍体化的特征，还是它们是驯化的产物。在这里，我们研究拟南芥（n = 13）中的多倍体化，这是一种通过拟南芥（n。5）和槟榔（n。arenosa）（n = 8）杂交形成的冰川后的同种多倍体物种。我们生成了A的染色体级基因组装配体。suecica，并补充了来自所有物种的多个个体的多态性和转录组数据。尽管两个祖先物种之间的〜6 Mya差异很大，并且它们的基因组组成存在明显差异，但我们看不到任何基因组震荡的迹象：酿酒酵母基因组与祖先基因组高度共线，在表达上没有亚基因组优势，转座子动力学似乎是稳定的。但是，我们确实找到了强有力的证据，表明发生了变化，表明逐渐适应多倍体。特别地，拟南芥亚基因组显示减数分裂相关基因的上调，可能是为了防止在实验产生的拟南芥中经常观察到的非整倍性和不良的同源交换，而槟榔亚种的亚基因组显示了与细胞核相关的上调。流程，