甘蓝型油菜与二倍体亲本(白菜和甘蓝)的3D基因组结构特征比较与分析

Brassica napus is one of the most important model for studying plant polyploidization due to the short history of its polyploid origin and formation. However, a majority of researches mainly focus on the genome variation on the one dimension, and the knowledge of three-dimensional (3D) genome structure and its dynamics during polyploidization remain poorly understand. High-throughput chromatin conformation capture (Hi-C) technology was recently developed in the field of three dimensional (3D) genome, which has been used to study the genome-wide 3D chromatin conformation in the nucleus. Here, to directly examine whole-genome chromatin interactions, we will perform Hi-C experiment and analysis on Brassica napus (AACC) and its diploid parents (Brassica rapa (AA) and Brassica oleracea (CC)). Then, we will characterize 3D genome architectures and find differences of the existence of A/B compartments, topologically associated domains (TADs) and chromatin loops between Brassica napus and its diploid parents (Brassica rapa and Brassica oleracea). Furthermore, we will also investigate the spatial proximity of homologs between inter-subgenomic in Brassica napus. This project will explore the evolutionary dynamics of 3D genome architecture following polyploidization in Brassica napus, which provides an important source for our understanding of evolutionary pattern of plant polyploid formation.

甘蓝型油菜起源和形成的历史较短，是植物多倍化研究的优选模型。现有报道大多是从一维基因组的角度研究多倍体化基因组变异，关于多倍体植物的三维基因组结构和多倍体化过程中三维基因组的结构变化的研究鲜有报道。高通量染色质构象捕获（Hi-C）是3D基因组领域近年来发展起来的一类技术，用于研究细胞核内染色质的三维空间构象。本项目将利用Hi-C技术测定甘蓝型油菜（AACC）与其二倍体亲本白菜（AA）和甘蓝（CC）的染色质交互数据，鉴定与比较甘蓝型油菜与白菜和甘蓝中的A/B区室（compartments）、拓扑结构域（TADs）和染色质环（loops）等三维结构基本特征，并研究甘蓝型油菜亚基因组间的同源基因的共定位作用，以此阐述甘蓝型油菜多倍化过程中三维结构的变化。本项目将解析多倍体物种形成中染色质三维结构的演化机制，为探讨多倍体植物基因组的进化规律提供重要的理论证据。

芸薹属植物是研究基因组进化的理想模型。白菜和甘蓝由共同的六倍体祖先分化而来，两者基因组序列非常保守，其保留下来的同源基因具有明显偏好性。探明同源基因的偏好性机制对于研究芸薹属物种基因组进化具有重要意义。高通量染色质构象捕获（Hi-C）是3D基因组领域近年来发展起来的一类技术，用于研究细胞核内染色质的三维空间构象。基因组的转录调控与生物功能与其三维结构密切相关。该项目构建了白菜和甘蓝三维基因组精细图谱和甘蓝型油菜三维基因组普通图谱。通过鉴定比较白菜和甘蓝的不同层次的染色质三维结构，发现两者的包括A/B区室,拓扑结构域在内的染色质结构非常保守。还发现两者的基因组三维结构与基因表达和表观修饰存在密切联系。此外。研究发现，在白菜和甘蓝中拥有基因数量更多的亚基因组的染色质交互更强，更易保留下来的同源基因对之间的染色质交互频率更高，表明进化中保留下来的同源基因具有空间邻近的特征。该项成果首次研究了芸薹属三维基因组结构特征，并研究了其与芸薹属进化过程的联系，为芸薹属基因组进化研究提供了新思路。