BACKGROUND Maize experienced a whole-genome duplication event approximately 5 to 12 million years ago. Because this event occurred after speciation from sorghum, the pre-duplication subgenomes can be partially reconstructed by mapping syntenic regions to the sorghum chromosomes. During evolution, maize has had uneven gene loss between each ancient subgenome. Fractionation and divergence between these genomes continue today, constantly changing genetic make-up and phenotypes and influencing agronomic traits. RESULTS Here we regenerate the subgenome reconstructions for the most recent maize reference genome assembly. Based on both expression and abundance data for homeologous gene pairs across multiple tissues, we observed functional divergence of genes across subgenomes. Although the genes in the larger maize subgenome are often expressing more highly than their homeologs in the smaller subgenome, we observed cases where homeolog expression dominance switches in different tissues. We demonstrate for the first time that protein abundances are higher in the larger subgenome, but they also show tissue-specific dominance, a pattern similar to RNA expression dominance. We also find that pollen expression is uniquely decoupled from protein abundance. CONCLUSION Our study shows that the larger subgenome has a greater range of functional assignments and that there is a relative lack of overlap between the subgenomes in terms of gene functions than would be suggested by similar patterns of gene expression and protein abundance. Our study also revealed that some reactions are catalyzed uniquely by the larger and smaller subgenomes. The tissue-specific, nonequivalent expression-level dominance pattern observed here implies a change in regulatory control which favors differentiated selective pressure on the retained duplicates leading to eventual change in gene functions.

中文翻译：

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组织特异性基因表达和蛋白质丰度模式与玉米中的分级偏差相关。

背景技术玉米经历了大约5到1200万年前的全基因组复制事件。因为此事件发生在高粱物种形成之后，所以可以通过将同义区域映射到高粱染色体上来部分复制前亚基因组。在进化过程中，每个古代亚基因组之间的玉米基因丢失均不均匀。这些基因组之间的分离和分化一直持续到今天，不断改变遗传组成和表型，并影响农艺性状。结果在这里，我们为最新的玉米参考基因组装配再生了亚基因组重建。基于跨多个组织的同源基因对的表达和丰度数据，我们观察到了跨亚基因组的基因的功能差异。尽管较大的玉米亚基因组中的基因通常比较小的亚基因组中的同源基因表达更高，但我们观察到同源基因表达优势在不同组织中切换的情况。我们首次证明在较大的亚基因组中蛋白质丰度更高，但它们也显示出组织特异性优势，这种模式类似于RNA表达优势。我们还发现花粉表达与蛋白质丰度是唯一脱钩的。结论我们的研究表明，较大的亚基因组具有更大的功能分配范围，并且与基因表达和蛋白质丰度的相似模式相比，亚基因组之间在基因功能方面相对缺乏重叠。我们的研究还表明，某些反应被更大和更小的亚基因组独特地催化。在此观察到的组织特异性，非等价的表达水平优势模式意味着调节控制的改变，这有利于对保留的重复序列进行差异化的选择性压力，最终导致基因功能的改变。