Structural variations (SVs) are recognized to have an important role in transcriptional regulation, especially in the light of resolved 3D genome structure using high-throughput chromosome conformation capture (Hi-C) technology in mammals. However, the effect of SVs on 3D genome organization in plants remains rarely understood. In this study, we identified 295,496 SVs and 5251 topologically associating domains (TADs) in two diploid and two tetraploid cottons. We observed that approximately 16% of SVs occurred in TAD boundary regions that were called boundary affecting-structural variations (BA-SVs), and had a large effect on disrupting TAD organization. Nevertheless, SVs preferred occurring in TAD interior instead of TAD boundary, probably associated with the relaxed evolutionary selection pressure. We noticed the biased evolution of the At and Dt subgenomes of tetraploid cottons, in terms of SV-mediated disruption of 3D genome structure relative to diploids. In addition, we provide evidence showing that both SVs and TAD disruption could lead to expression difference of orthologous genes. This study advances our understanding of the effect of SVs on 3D genome organization and gene expression regulation in plants.

结构变异 (SV) 被认为在转录调控中具有重要作用，特别是考虑到哺乳动物中使用高通量染色体构象捕获 (Hi-C) 技术解析的 3D 基因组结构。然而，SVs 对植物 3D 基因组组织的影响仍然鲜为人知。在这项研究中，我们在两个二倍体和两个四倍体棉花。我们观察到大约 16% 的 SV 发生在被称为边界影响结构变化 (BA-SV) 的 TAD 边界区域，并且对破坏 TAD 组织有很大影响。尽管如此，SV 更喜欢发生在 TAD 内部而不是 TAD 边界，这可能与宽松的进化选择压力有关。我们注意到四倍体棉花的 At 和 Dt 亚基因组在 SV 介导的 3D 基因组结构相对于二倍体的破坏方面存在偏差。此外，我们提供的证据表明 SVs 和 TAD 破坏都可能导致直系同源基因的表达差异。这项研究加深了我们对 SVs 对植物 3D 基因组组织和基因表达调控的影响的理解。