For most sequenced flowering plants, multiple whole-genome duplications (WGDs) are found. Duplicated genes following WGD often have different fates that can quickly disappear again, be retained for long(er) periods, or subsequently undergo small-scale duplications. However, how different expression, epigenetic regulation, and functional constraints are associated with these different gene fates following a WGD still requires further investigation due to successive WGDs in angiosperms complicating the gene trajectories. In this study, we investigate lotus (Nelumbo nucifera), an angiosperm with a single WGD during the K–pg boundary. Based on improved intraspecific-synteny identification by a chromosome-level assembly, transcriptome, and bisulfite sequencing, we explore not only the fundamental distinctions in genomic features, expression, and methylation patterns of genes with different fates after a WGD but also the factors that shape post-WGD expression divergence and expression bias between duplicates. We found that after a WGD genes that returned to single copies show the highest levels and breadth of expression, gene body methylation, and intron numbers, whereas the long-retained duplicates exhibit the highest degrees of protein–protein interactions and protein lengths and the lowest methylation in gene flanking regions. For those long-retained duplicate pairs, the degree of expression divergence correlates with their sequence divergence, degree in protein–protein interactions, and expression level, whereas their biases in expression level reflecting subgenome dominance are associated with the bias of subgenome fractionation. Overall, our study on the paleopolyploid nature of lotus highlights the impact of different functional constraints on gene fate and duplicate divergence following a single WGD in plant.

中文翻译：

---

一个单一的全基因组重复在开花植物中具有不同命运的基因的不同表达和甲基化模式。

对于大多数测序的开花植物，发现了多个全基因组重复（WGD）。WGD之后的重复基因通常具有不同的命运，可以很快再次消失，保留更长的时间或随后进行小规模的重复。但是，由于被子植物中连续的WGD使基因轨迹复杂化，因此在WGD之后如何将不同的表达，表观遗传调控和功能限制与这些不同的基因命运相关联。在这项研究中，我们调查了荷花（Nelumbo nucifera），在K–pg边界内有单个WGD的被子植物。基于染色体级装配，转录组和亚硫酸氢盐测序，提高了种内同义性鉴定的基础，我们不仅探索了基因组特征，表达和甲基化模式在WGD后不同命运的基本区别，还探讨了影响基因形成的因素。 WGD之后的表达差异和重复之间的表达偏差。我们发现，在WGD之后，返回单拷贝的基因显示出最高的表达水平和广度，基因体甲基化和内含子数量，而长期保留的重复则显示出最高程度的蛋白质-蛋白质相互作用和蛋白质长度，而最低基因侧翼区域的甲基化。对于那些长期保留的重复对，表达差异的程度与其序列差异，蛋白间相互作用程度和表达水平相关，而它们在表达水平上反映亚基因组优势的偏差与亚基因组分级分离的偏差相关。总体而言，我们对莲花的古多倍体性质的研究突出了植物中单一WGD后不同功能限制对基因命运和重复发散的影响。