The interaction and co-evolution between nuclear and cytoplasmic genomes are one of the fundamental hallmarks of eukaryotic genome evolution and, two billion years later, are still major contributors to the formation of new species. Although many studies have investigated the role of cytonuclear interactions following allopolyploidization, the relative magnitude of the effect of subgenome dominance vs. cytonuclear interaction on genome evolution remains unclear. The Brassica triangle of U features three diploid species that together have formed three separate allotetraploid species on similar evolutionary timescales, providing an ideal system for understanding the contribution of the cytoplasmic donor to hybrid polyploid. Here, we investigated the evolutionary pattern of organelle-targeted genes in B. carinata (BBCC) and two varieties of B. juncea (AABB) at the whole-genome level, with particular focus on cytonuclear enzyme complexes. We found partial evidence that plastid-targeted genes experience selection to match plastid genomes, but no obvious corresponding signal in mitochondria-targeted genes from these two separately formed allopolyploids. Interestingly, selection acting on plastid genomes always reduced the retention rate of plastid-targeted genes encoded by the B subgenome, regardless of whether the B. nigra (BB) subgenome was contributed by the paternal or maternal progenitor. More broadly, this study illustrates the distinct selective pressures experienced by plastid- and mitochondria-targeted genes, despite a shared pattern of inheritance and natural history. Our study also highlights an important role for subgenome dominance in allopolyploid genome evolution, even in genes whose function depends on separately inherited molecules.

中文翻译：

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细胞核相互作用和亚基因组优势塑造了U芸苔三角中细胞器靶向基因的进化

核基因组和细胞质基因组之间的相互作用和共同进化是真核基因组进化的基本标志之一，并且在20亿年后仍然是新物种形成的主要贡献者。尽管许多研究已经研究了异源多倍化后细胞核相互作用的作用，但亚基因组优势与细胞核相互作用对基因组进化的影响的相对程度仍不清楚。U 的芸苔三角具有三个二倍体物种，它们在相似的进化时间尺度上共同形成了三个独立的异源四倍体物种，为理解细胞质供体对杂种多倍体的贡献提供了一个理想的系统。在这里，我们在全基因组水平上研究了 B. carinata (BBCC) 和两个芥菜品种 (AABB) 中细胞器靶向基因的进化模式，特别关注细胞核酶复合物。我们发现部分证据表明质体靶向基因经历了选择以匹配质体基因组，但来自这两个单独形成的异源多倍体的线粒体靶向基因没有明显的相应信号。有趣的是，作用于质体基因组的选择总是降低 B 亚基因组编码的质体靶向基因的保留率，无论 B. nigra (BB) 亚基因组是由父系还是母系祖细胞贡献。更广泛地说，这项研究说明了质体和线粒体靶向基因所经历的不同选择压力，尽管它们具有共同的遗传和自然史模式。我们的研究还强调了亚基因组优势在异源多倍体基因组进化中的重要作用，甚至在功能依赖于单独遗传分子的基因中也是如此。