Rapeseed (Brassica napus L.) is a recent allotetraploid crop, which is well known for its high oil production. Here, we report a high‐quality genome assembly of a typical semi‐winter rapeseed cultivar, 'Zhongshuang11' (hereafter 'ZS11'), using a combination of single‐molecule sequencing and chromosome conformation capture (Hi‐C) techniques. Most of the high‐confidence sequences (93.1%) were anchored to the individual chromosomes with a total of 19 centromeres identified, matching the exact chromosome count of B. napus. The repeat sequences in the A and C subgenomes in B. napus expanded significantly from 500 000 years ago, especially over the last 100 000 years. These young and recently amplified LTR‐RTs showed dispersed chromosomal distribution but significantly preferentially clustered into centromeric regions. We exhaustively annotated the nucleotide‐binding leucine‐rich repeat (NLR) gene repertoire, yielding a total of 597 NLR genes in B. napus genome and 17.4% of which are paired (head‐to‐head arrangement). Based on the resequencing data of 991 B. napus accessions, we have identified 18 759 245 single nucleotide polymorphisms (SNPs) and detected a large number of genomic regions under selective sweep among the three major ecotype groups (winter, semi‐winter and spring) in B. napus. We found 49 NLR genes and five NLR gene pairs colocated in selective sweep regions with different ecotypes, suggesting a rapid diversification of NLR genes during the domestication of B. napus. The high quality of our B. napus 'ZS11' genome assembly could serve as an important resource for the study of rapeseed genomics and reveal the genetic variations associated with important agronomic traits.

中文翻译：

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高质量的甘蓝型油菜基因组揭示了转座因子的扩展，亚基因组进化和抗病性

油菜籽（甘蓝型油菜）是近来的一种四倍体作物，以其高产油而闻名。在这里，我们结合了单分子测序和染色体构象捕获（Hi-C）技术，报道了典型的半冬季油菜品种“ Zhongshuang11”（以下简称“ ZS11”）的高质量基因组装配。大多数高可信度序列（93.1％）锚定在单个染色体上，共鉴定出19个着丝粒，与油菜双歧杆菌的确切染色体数匹配。甘蓝型油菜A和C亚基因组的重复序列从50万年前开始显着增长，尤其是在过去的10万年中。这些年轻的和最近扩增的LTR-RTs表现出分散的染色体分布，但明显优先聚集在着丝粒区域。我们详尽地注释了核苷酸结合的富含亮氨酸的重复序列（NLR）基因，在甘蓝型油菜的基因组中总共产生597个NLR基因，其中有17.4％是配对的（头对头排列）。根据991个甘蓝型油菜种质的重测序数据，我们鉴定出18 759 245个单核苷酸多态性（SNPs），并在选择性扫描下检测到三个主要生态类型组（冬季，半冬季和春季）中的大量基因组区域。在那不勒斯。我们发现49个NLR基因和5个NLR基因对共处在具有不同生态类型的选择性扫描区域中，这表明在油菜的驯化过程中NLR基因快速多样化。我们的甘蓝型油菜“ ZS11”基因组装配的高质量可以作为研究油菜基因组的重要资源，并揭示与重要农艺性状相关的遗传变异。