Exploring the structural variant landscape in the highly dynamic genome of a recent allopolyploid crop species

最近发现的异源多倍体作物甘蓝型油菜(油菜、油菜)具有异常活跃的基因组。利用长阅读测序，我们最近发现，在任何给定的甘蓝型油菜基因中，高达10%的基因受到功能相关的、全基因组范围的基因转换和缺失的影响，这与作物进化和育种具有很高的相关性。由于它们的主要大小范围(100bp~5kb)，在高度复制的甘蓝型油菜基因组中，绝大多数全基因组结构变异(SV)无法通过短读测序检测到，因此它们的机制和进化后果尚未被研究。基于在广泛的前期工作中开发的稳健方法，我们计划对甘蓝型油菜Pangenome中的SV景观进行详细调查，使用来自具有良好特征的全球物种集合的100个遗传多样性、纯合子材料的长阅读测序。一个甘蓝型油菜“Pangemome SV Atlas”的组装将提供一个有价值的公共工具来解决多倍体基因组中小规模SV的机制，并重新访问以前研究中的大量短读数据集。通过识别与全基因组SV断裂点相关的序列基序，并在3D基因组结构和染色质相互作用的背景下研究SV模式，我们旨在对小规模同源交换背后的机制进行新的生物学见解，作为帮助潜在地利用SV在育种中的力量的预测模型的基础。在一个实际的案例研究中，我们将使用SV图谱将开花途径基因中的SV与生态地理适应性状联系起来。这将对SV在多倍体进化和适应中的作用提供新的见解。

The recent allopolyploid crop species Brassica napus (oilseed rape, canola) has an unusually dynamic genome. Using long-read sequencing, we recently discovered that up to 10% of all genes in any given B. napus genotype are affected by functionally relevant, genome-wide gene conversions and deletions with high relevance for crop evolution and breeding. Because of their predominant size range (100bp~5kb), the great majority of genome-wide structural variants (SV) were undetectable by short-read sequencing in the highly-duplicated B. napus genome, hence their mechanisms and evolutionary consequences have not yet been studied. Based on robust methods developed in extensive preliminary work, we plan a detailed survey of the SV landscape in the B. napus pangenome, using long-read sequencing in 100 genetically diverse, homozygous accessions from a well-characterised global species collection. Assembly of a B. napus “Pangemome SV Atlas” will provide a valuable public tool to address the mechanisms of small-scale SV in polyploid genomes and re-visit extensive short-read datasets from previous studies. By identifying sequence motifs associated with genome-wide SV breakpoints and investigating SV patterns in the context of 3D genome structure and chromatin interactions, we aim for novel biological insight into the mechanisms underlying small-scale homoeologous exchanges, as a basis for predictive models that help to potentially harness the power of SV in breeding. In a practical case study, we will use the SV Atlas to associate SV in floweringpathway genes to ecogeographical adaptation traits. This will give novel insight into the role of SV in polyploid evolution and adaptation.