结构变异是指一个区域的DNA序列在重复次数，方向和染色体的位置上的变化，通常其长度大于50碱基。相较于单核苷酸位点多态性，结构变异影响的序列更长，通常会导致更大的表型变异，已有研究发现结构变异在植物中广泛存在，对植物的适应和分化具有重要的意义。但是由于受限于结构变异识别的困难和理论模型的缺失，结构变异一直缺乏系统性的研究。胡桃属物种因其种子富含油脂具有食用价值，木质坚硬也是重要的木材，是一种分布广泛的经济作物，人们对其进行了广泛的研究，而对胡桃属的结构变异研究一直比较匮乏。胡桃属中存在两个特殊的生物学现象。首先，胡桃属存在三支物种，分别是黑核桃组，白核桃组和核桃组，而这三支物种的系统发育一直存在一些争议，不同的基因标记物构建的系统发育关系存在一些偏差，后被证明这是由于核桃组的杂交起源。其次，在胡桃属中存在着麻核桃，而所有的麻核桃均为不育的杂交一代，表明麻核桃中存在着生殖隔离现象。但到目前为止，对胡桃属的结构变异的研究存在空白。基于此，本研究以胡桃属为例，对其在染色体水平上的7个已测序的物种，通过全基因组比对进行结构变异的识别，并进一步探究结构变异对胡桃属核桃组杂交起源和麻核桃生殖隔离的作用。具体完成如下工作：

    （1）我们对胡桃属7个染色体水平测序的物种分别与其外类群枫杨进行了全基因组比对，基于全基因组比对的结果，我们识别了其与外类群之间的结构变异，回答结构变异是否包含胡桃属中的一支核桃组为黑核桃组和白核桃组的杂交种的信号。首先，利用MUMMER4进行全基因组比对，并且识别到胡桃属各物种与外类群枫杨之间共458个倒位、1879个易位和1974个复制，大部分倒位长度介于10³到10⁵之间，复制和易位则集中在10³到10⁴之间。通过对不同物种不同类型结构变异的特征分析，我们发现倒位在长度显著高于复制和易位的长度；长末端重复序列和长散在重复序列等重复序列会降低结构变异的出现，而短散在重复序列会提高倒位的出现。其次，通过对结构变异的聚类，我们获得了胡桃属结构变异的聚类结果；基于此聚类结果并利用距离法和基于PhyloNet的杂交网络构建两种方法分别构建了系统发育关系，我们得到核桃组为黑白两支核桃的杂交结果。接着，通过将结构变异定位在其产生的系统发育时期，我们发现约90%的结构变异符合核桃组杂交起源的系统发育关系；并且定位到了核桃组中8个结构变异来自于白核桃，3个结构变异来自于黑核桃。通过以结构变异为研究对象的分析，我们也发现了核桃组为黑核桃组与白核桃组的杂交支的证据，进一步验证了之前基于单核苷酸位点多态性数据计算的结果，进而说明通过全基因组比对识别到的一部分结构变异也可以作为系统发育和杂交事件识别的标记。进一步，我们构建了胡桃属各支的祖先核型。最后，通过GO富集分析，我们分析了结构变异影响的基因功能，包括从白核桃组继承的DNA损伤检查点与从黑核桃继承的泛素依赖的蛋白降解，核小体组装和酸酐水解等相关基因。

    （2）我们对麻核桃两个亲本Juglans cathayensis和Juglans mandshurica的基因组比对到另外的亲本Juglans regia上，识别了麻核桃中潜在的结构变异，并探讨了麻核桃作为一个杂一代其亲本生殖隔离的原因。首先，我们基于全基因组比对和结构变异的识别，得到了两组亲本的结构变异。其次，通过对这些结构变异的聚类，我们确定了麻核桃基因组中潜在的结构变异。接着，我们经过验证进一步得到准确的35个倒位，其中有6个大片段倒位超多10kb，很可能会导致麻核桃的生殖隔离。最后，通过GO富集分析，我们发现这6个大片段的倒位涉及花粉管萌发等相关基因，进而说明了结构变异对麻核桃生殖隔离的作用。

       通过对核桃组的杂交起源和麻核桃的生殖隔离这两个问题的研究，我们发现了结构变异对杂交的检测和物种分化的作用。同时，同时随着测序技术和结构变异算法的发展，结构变变异的应用及其重要性将会更广泛地体现。

Structural variation (SV) is generally defined as a region of DNA that shows a change in copy number (deletions, insertions and duplications), orientation (inversions) or chromosomal location (translocations) between individuals. Usually, its length is greater than 50 bps. Compared with single nucleotide polymorphism, structural variation affects longer sequences and may usually lead to greater phenotypic variation. It has been found that structural variation exists widely in plants, which is of great significance to plant adaptation and differentiation. However, limited by the difficulty of structural variation identification and the lack of theoretical model, structural variation has been short of systematic research in a long time. Because of the species in Juglans whose seeds are rich in oil and have edible value and hard wood makes it useful of furniture, is a world-widely distributed cash crop. Therefore, the study of Juglans is of great significance, but the structure variation in Juglans is still not clear. There are two main problems in Juglans. Firstly, there are three sections of Juglans, Section. Juglans, Section. Cardiocaryon and Section. Rhysocaryon, and the phylogeny of these three species has been controversial. There were some deviations in the phylogenetic relationship constructed by different gene markers, which was later proved to be due to the hybridization origin of Section. Juglans. Secondly, all of Juglans hopeiensis was found first generation hybrids, indicating that there is reproductive isolation in Juglans hopeiensis. So far, there has been gap in the study of structural variation of Juglans for a long time. According to the background, taking Juglans as an example, this study identified the structural variation genomes assembly of 7 species at the chromosome level through whole genome alignment, and further explored the role of structural variation on the hybridization origin of Section. Juglans and the reproductive isolation of Juglans hopeiensis. The specific work is as follows:

(1) In order to figure out whether structure variation could be new evidence of the hybridization origin of Section. Juglans, we aligned the whole genome of seven species of Juglans with their outer group Pterocarya stenoptera. Firstly, we identified the structural variation between them and the outer group according to the results of the whole genome alignment. We found 458 inversions, 1879 translocations and 1974 duplications between 7 species in Juglans and Pterocarya stenoptera in total. Most of inversions range from 1000bp to 100,000bp in length while most of duplications and translocations range from 1000bp to 10,000bp in length. And then we statistically analyzed the characteristics of different structural variation of different species, We found that the length distribution of inversion is significantly higher than duplication and translocation. Secondly, We found that long terminal repeated, long interspersed nuclear elements repeats will reduce the occurrence of structural variation, while short interspersed nuclear elements will increase the occurrence of inversion. Then, through the cluster analysis of structural variation, we obtained the structural variation among Juglans. Phylogeny was constructed by distance method and PhyloNet. We found that the Section. Juglans was a hybrid of Section. Cardiocaryon and Section. Rhysocaryon. Using HyDe to detect hybridization events, we also detected the hybridization origin of Section. Juglans based on translocation structure variation. Then, by locating the structural variation in the phylogenetic period, we found that about 90% of the structural variation are consist with the phylogenetic relationship of the hybridization origin of Section. Juglans, of which 8 structural variations in Section. Juglans inherited from Section. Cardiocaryon and 3 structural variations inherited from Section. Rhysocaryon. Through the analysis of structural variation, we also found the evidence that Section. Juglans is the hybrid branch of Section. Cardiocaryon and Section. Rhysocaryon, which further verified the previous calculation results based on single nucleotide polymorphism data and suggested that structural variation can also be used as a marker for the study of phylogeny. Furthermore, we constructed the ancestral karyotypes of each Section of Juglans. Finally, through GO enrichment analysis, we analyzed the gene functions affected by structural variation, including DNA damage checkpoint from Section. Cardiocaryon and ubiquitin dependent protein degradation, nucleosome assembly and acid anhydride from Section. Rhysocaryon.

(2)In order to explore the reproductive isolation of parents of Juglans hopeiensis, we used whole genome alignment to compare the two parents Juglans cathayensis and Juglans mandshurica to Juglans regia, and identified the structural variation in the parent of Juglans hopeiensis. By cluster analysis, we identified the potential structural variation in the genome of Juglans hopeiensis. After verification, we identified the 35 inversions, of which 6 large inversions are more than 10kb. These large inversions is likely to lead to reproductive isolation. Through GO enrichment analysis, we found that the inversion of six large fragments involved genes related to pollen tube germination, which further explained the effect of structural variation on reproductive isolation of parents of Juglans hopeiensis.

By analyzing the hybridization origin of Section. Juglans and reproductive isolation of Juglans hopeiensis, we found the role of structural variation in hybridization detection and species differentiation. With the development of sequencing technology and structural variation algorithm, the application and importance of structural variation will be more widely reflected.