Table_1_Chromosome-Scale Assembly of Winter Oilseed Rape Brassica napus.DOCX

Rapeseed (Brassica napus), the second most important oilseed crop globally, originated from an interspecific hybridization between B. rapa and B. oleracea. After this genome collision, B. napus underwent extensive genome restructuring, via homoeologous chromosome exchanges, resulting in widespread segmental deletions and duplications. Illicit pairing among genetically similar homoeologous chromosomes during meiosis is common in recent allopolyploids like B. napus, and post-polyploidization restructuring compounds the difficulties of assembling a complex polyploid plant genome. Specifically, genomic rearrangements between highly similar chromosomes are challenging to detect due to the limitation of sequencing read length and ambiguous alignment of reads. Recent advances in long read sequencing technologies provide promising new opportunities to unravel the genome complexities of B. napus by encompassing breakpoints of genomic rearrangements with high specificity. Moreover, recent evidence revealed ongoing genomic exchanges in natural B. napus, highlighting the need for multiple reference genomes to capture structural variants between accessions. Here we report the first long-read genome assembly of a winter B. napus cultivar. We sequenced the German winter oilseed rape accession ‘Express 617’ using 54.5x of long reads. Short reads, linked reads, optical map data and high-density genetic maps were used to further correct and scaffold the assembly to form pseudochromosomes. The assembled Express 617 genome provides another valuable resource for Brassica genomics in understanding the genetic consequences of polyploidization, crop domestication, and breeding of recently-formed crop species.

油菜（学名：Brassica napus），作为全球第二大重要的油料作物，起源于萝卜（B. rapa）与芜菁（B. oleracea）之间的种间杂交。此后，油菜经历了广泛的基因组重构，通过同源染色体交换，导致了广泛的片段性缺失与重复。在近期的异源多倍体，如油菜中，同源染色体在减数分裂期间的非规范配对现象较为普遍，而多倍体化后的基因组重构进一步加剧了组装复杂多倍体植物基因组时的困难。特别是，由于测序读长限制和读段对齐的模糊性，检测高度相似的染色体之间的基因组重排极具挑战。近期长读长测序技术的进步为通过高特异性地涵盖基因组重排的断点，解析油菜基因组复杂性提供了新的有利机遇。此外，近期证据揭示了自然油菜中的持续基因组交换，凸显了需要多个参考基因组来捕捉不同品种之间的结构变异。在此，我们报告了首个冬季油菜品种的长读长基因组组装。我们使用54.5倍长读长对德国冬季油菜品种‘Express 617’进行了测序。短读段、连锁读段、光学图谱数据和高密度遗传图谱被用于进一步校正和构建组装，形成伪染色体。组装的Express 617基因组为理解多倍体化、作物驯化和新形成作物物种的育种提供了另一项宝贵的资源。