Genome duplication is widespread in wild and crop plants. However, little is known about genome-wide selection in polyploids due to the complexity of duplicated genomes. In polyploids, the patterns of purifying selection and adaptive substitutions may be affected by masking owing to duplicated genes or homeologs as well as effective population size. Here, we resequence 25 accessions of the allotetraploid Arabidopsis kamchatica, which is derived from the diploid species A. halleri and A. lyrata. We observe a reduction in purifying selection compared with the parental species. Interestingly, proportions of adaptive non-synonymous substitutions are significantly positive in contrast to most plant species. A recurrent pattern observed in both frequency and divergence-diversity neutrality tests is that the genome-wide distributions of both subgenomes are similar, but the correlation between homeologous pairs is low. This may increase the opportunity of different evolutionary trajectories such as in the HMA4 gene involved in heavy metal hyperaccumulation.

中文翻译：

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异源多倍体拟南芥kamchatica的亚基因组中的多态性模式和选择。

基因组复制在野生植物和农作物中普遍存在。然而，由于重复的基因组的复杂性，对多倍体的全基因组选择知之甚少。在多倍体中，由于重复的基因或同源物以及有效种群的大小，掩蔽可能会影响纯化选择和适应性替代的模式。在这里，我们对来自二倍体A. halleri和A. lyrata的异源四倍体拟南芥kamchatica的25个序列进行重新排序。与亲本相比，我们观察到纯化选择的减少。有趣的是，与大多数植物物种相比，自适应非同义替换的比例显着为正。在频率和发散-多样性中立性测试中都观察到一种复发模式，即两个亚基因组的全基因组分布相似，但是同源对之间的相关性较低。这可能会增加不同进化轨迹的机会，例如参与重金属超富集的HMA4基因的机会。