The nonrandom three-dimensional organization of chromatin plays an important role in the regulation of gene expression. However, it remains unclear whether this organization is conserved and whether it is involved in regulating gene expression during speciation after whole-genome duplication (WGD) in plants. In this study, high-resolution interaction maps were generated using high-throughput chromatin conformation capture (Hi-C) techniques for two poplar species, Populus euphratica and Populus alba var. pyramidalis, which diverged ~14 Mya after a common WGD. We examined the similarities and differences in the hierarchical chromatin organization between the two species, including A/B compartment regions and topologically associating domains (TADs), as well as in their DNA methylation and gene expression patterns. We found that chromatin status was strongly associated with epigenetic modifications and gene transcriptional activity, yet the conservation of hierarchical chromatin organization across the two species was low. The divergence of gene expression between WGD-derived paralogs was associated with the strength of chromatin interactions, and colocalized paralogs exhibited strong similarities in epigenetic modifications and expression levels. Thus, the spatial localization of duplicated genes is highly correlated with biased expression during the diploidization process. This study provides new insights into the evolution of chromatin organization and transcriptional regulation during the speciation process of poplars after WGD.

中文翻译：

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具有共同全基因组重复的两种杨树之间染色质组织和重复基因的偏差表达的生物信息分析

染色质的非随机三维组织在基因表达的调控中发挥着重要作用。然而，目前尚不清楚该组织是否保守，以及是否参与植物全基因组复制（WGD）后物种形成过程中基因表达的调节。在本研究中，使用高通量染色质构象捕获 (Hi-C) 技术为两种杨树生成了高分辨率相互作用图，胡杨和白杨变种金字塔形，在共同的 WGD 后分歧约 14 Mya。我们检查了两个物种之间的分层染色质组织的相似性和差异，包括 A/B 区室区域和拓扑关联域 (TAD)，以及它们的 DNA 甲基化和基因表达模式。我们发现染色质状态与表观遗传修饰和基因转录活性密切相关，但两个物种的分层染色质组织的保守性较低。WGD 衍生的旁系同源物之间基因表达的差异与染色质相互作用的强度有关，共定位的旁系同源物在表观遗传修饰和表达水平方面表现出很强的相似性。因此，重复基因的空间定位与二倍化过程中的偏向表​​达高度相关。这项研究为全基因组测序后杨树物种形成过程中染色质组织和转录调控的演变提供了新的见解。