Distinct Expression and Methylation Patterns for Genes with Different Fates following a Single Whole-Genome Duplication in Flowering Plants
Distinct Expression and Methylation Patterns for Genes with Different Fates following a Single Whole-Genome Duplication in Flowering Plants
复制标题
开花植物中单次全基因组复制后具有不同命运的基因的不同表达和甲基化模式
DOI：
10.1093/molbev/msaa105
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发表时间：
2020-08-01
影响因子：
10.7
通讯作者：
Chen, Jinming
中科院分区：
文献类型：
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作者：
Shi, Tao;Rahmani, Razgar Seyed;Chen, Jinming
摘要在大多数已测序的开花植物中，都发现了多个全基因组重复(WGD)。WGD后复制的基因通常有不同的命运，可能会再次迅速消失，保留很长时间(呃)，或者随后经历小规模的复制。然而，由于被子植物中连续的WGD使基因轨迹复杂化，不同的表达、表观遗传调控和功能约束如何与WGD后这些不同的基因命运相关仍然需要进一步的研究。在这项研究中，我们研究了莲花(Nelumbo Nucifera)，一种在K-PG边界具有单一WGD的被子植物。在通过染色体水平组装、转录组和亚硫酸氢盐测序改进的种内同源鉴定的基础上，我们不仅探索了WGD后不同命运的基因在基因组特征、表达和甲基化模式上的根本差异，而且还探讨了形成WGD后表达差异和重复之间表达偏差的因素。我们发现，在WGD之后，恢复为单拷贝的基因表现出最高的表达水平和广度、基因体甲基化和内含子数量，而长期保留的重复基因表现出最高的蛋白质-蛋白质相互作用程度和蛋白质长度，而在基因侧翼区域的甲基化程度最低。对于那些长期保留的重复对，表达差异的程度与它们的序列差异、蛋白质-蛋白质相互作用的程度和表达水平有关，而它们在表达水平上反映亚基因组优势的偏向与亚基因组分裂的偏向有关。总体而言，我们对莲花的古多倍体性质的研究突出了不同的功能限制因素对植物单一WGD后基因命运和重复差异的影响。
Abstract 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.