Department of Biology, Colorado State University, Fort Collins, CO, USA.
Department of Biology, New Mexico Institute of Mining and Technology, Socorro, NM, USA.
Mol Biol Evol. 2022 Apr 10;39(4). doi: 10.1093/molbev/msac074.
Whole-genome duplications (WGDs) are a prominent process of diversification in eukaryotes. The genetic and evolutionary forces that WGD imposes on cytoplasmic genomes are not well understood, despite the central role that cytonuclear interactions play in eukaryotic function and fitness. Cellular respiration and photosynthesis depend on successful interaction between the 3,000+ nuclear-encoded proteins destined for the mitochondria or plastids and the gene products of cytoplasmic genomes in multi-subunit complexes such as OXPHOS, organellar ribosomes, Photosystems I and II, and Rubisco. Allopolyploids are thus faced with the critical task of coordinating interactions between the nuclear and cytoplasmic genes that were inherited from different species. Because the cytoplasmic genomes share a more recent history of common descent with the maternal nuclear subgenome than the paternal subgenome, evolutionary "mismatches" between the paternal subgenome and the cytoplasmic genomes in allopolyploids might lead to the accelerated rates of evolution in the paternal homoeologs of allopolyploids, either through relaxed purifying selection or strong directional selection to rectify these mismatches. We report evidence from six independently formed allotetraploids that the subgenomes exhibit unequal rates of protein-sequence evolution, but we found no evidence that cytonuclear incompatibilities result in altered evolutionary trajectories of the paternal homoeologs of organelle-targeted genes. The analyses of gene content revealed mixed evidence for whether the organelle-targeted genes are lost more rapidly than the non-organelle-targeted genes. Together, these global analyses provide insights into the complex evolutionary dynamics of allopolyploids, showing that the allopolyploid subgenomes have separate evolutionary trajectories despite sharing the same nucleus, generation time, and ecological context.
全基因组加倍（Whole-genome duplications，WGDs）是真核生物多样化的一个突出过程。尽管细胞质基因组与核质相互作用在真核生物功能和适应性中起着核心作用，但 WGD 对细胞质基因组施加的遗传和进化力量仍未得到很好的理解。细胞呼吸和光合作用依赖于核编码蛋白与线粒体或质体的成功相互作用，这些核编码蛋白的数量超过 3000 个，并且依赖于多亚基复合物中的细胞质基因组的基因产物，如 OXPHOS、细胞器核糖体、光合作用系统 I 和 II 以及 Rubisco。因此，异源多倍体面临着协调来自不同物种的核基因和细胞质基因相互作用的关键任务。由于细胞质基因组与母核亚基因组的共同起源史比父核亚基因组更为接近，因此异源多倍体中父核亚基因组与细胞质基因组之间的进化“不匹配”可能导致异源多倍体的父源同源基因的进化速度加快，这可能是通过放松净化选择或强烈的定向选择来纠正这些不匹配。我们从六个独立形成的异源四倍体中报告了证据，表明亚基因组表现出不同的蛋白质序列进化率，但我们没有发现细胞质核不兼容导致细胞器靶向基因的父源同源基因进化轨迹发生改变的证据。对基因含量的分析提供了混合证据，表明细胞器靶向基因是否比非细胞器靶向基因更快地丢失。总的来说，这些全局分析提供了对异源多倍体复杂进化动态的深入了解，表明尽管共享相同的核、世代时间和生态背景，但异源多倍体的亚基因组具有独立的进化轨迹。
