Following whole-genome duplication (WGD), duplicate gene pairs (homoeologs) can evolve varying degrees of expression divergence. However, the determinants influencing these relative expression level differences (RFPKM) between homoeologs remain elusive. In this study, we analyzed the RFPKM between homoeologs in 3 angiosperms, Nymphaea colorata, Nelumbo nucifera, and Acorus tatarinowii, all having undergone a single WGD since the origin of angiosperms. Our results show significant positive correlations in RFPKM of homoeologs among tissues within the same species, and among orthologs across these 3 species, indicating convergent expression balance/bias between homoeologous gene copies following independent WGDs. We linked RFPKM between homoeologs to gene attributes associated with dosage-balance constraints, such as protein–protein interactions, lethal-phenotype scores in Arabidopsis (Arabidopsis thaliana) orthologs, domain numbers, and expression breadth. Notably, homoeologs with lower RFPKM often had more interactions and higher lethal-phenotype scores, indicating selective pressures favoring balanced expression. Also, homoeologs with lower RFPKM were more likely to be retained after WGDs in angiosperms. Within Nelumbo, greater RFPKM between homoeologs correlated with increased cis- and trans-regulatory differentiation between species, highlighting the ongoing escalation of gene expression divergence. We further found that expression degeneration in 1 copy of homoeologs is inclined toward nonfunctionalization. Our research highlights the importance of balanced expression, shaped by dosage-balance constraints, in the evolutionary retention of homoeologs in plants.

中文翻译：

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剂量敏感性决定了被子植物全基因组重复后同源物的平衡表达和基因寿命


在全基因组复制 （WGD） 之后，重复基因对 （同源物） 可以进化出不同程度的表达差异。然而，影响同源物之间这些相对表达水平差异 （RFPKM） 的决定因素仍然难以捉摸。在这项研究中，我们分析了 3 种被子植物 Nymphaea colorata、Nelumbo nucifera 和 Acorus tatarinowii 的同源物之间的 RFPKM，这些被子植物自被子植物起源以来都经历了单一的 WGD。我们的结果表明，同一物种内组织之间以及这 3 个物种的直系同源物之间的 RFPKM 呈显著正相关，表明独立 WGD 后同源基因拷贝之间的收敛表达平衡/偏倚。我们将同源物之间的 RFPKM 与与剂量平衡约束相关的基因属性联系起来，例如蛋白质-蛋白质相互作用、拟南芥 （Arabidopsis thaliana） 直系同源物中的致死表型评分、结构域编号和表达广度。值得注意的是，RFPKM 较低的同源物通常具有更多的相互作用和较高的致死表型评分，表明选择压力有利于平衡表达。此外，在被子植物中，具有较低 RFPKM 的同源物更有可能在 WGD 后保留。在 Nelumbo 中，同源物之间更大的 RFPKM 与物种间顺式和反式调节分化的增加相关，突出了基因表达分歧的持续升级。我们进一步发现，1 个拷贝同源物中的表达变性倾向于非功能化。我们的研究强调了由剂量平衡约束塑造的平衡表达在植物中同源物进化保留中的重要性。