Supporting data for "Long-reads assembly of the <i>Brassica napus</i> reference genome, Darmor-bzh"

The combination of long-reads and long-range information to produce genome assemblies is now accepted as a common standard. This strategy not only allows access to the gene catalogue of a given species but also reveals the architecture and organisation of chromosomes, including complex regions like telomeres and centromeres. The <i>Brassica</i> genus is not exempt and many assemblies based on long reads are now available. The reference genome for <i>Brassica napus</i>, Darmor-bzh, which was published in 2014, has been produced using short-reads and its contiguity was extremely low if compared to current assemblies of the <i>Brassica</i> genus.<br>Here, we report the new long-reads assembly of Darmor-bzh genome (<i>Brassica napus</i>) generated by combining long-reads sequencing data, optical and genetic maps. Using the PromethION device and six flowcells, we generated about 16M long-reads representing 93X coverage and more importantly 6X with reads longer than 100Kb. This ultralong-reads dataset allows us to generate one of the most contiguous and complete assembly of a <i>Brassica</i> genome to date (contigs N50 &gt; 10Mb). In addition, we exploited all the advantages of the nanopore technology to detect modified bases and sequence transcriptomic data using direct RNA to annotate the genome and focus on resistance genes.<br>Using these cutting edge technologies, and in particular by relying on all the advantages of the nanopore technology, we provide the most contiguous <i>Brassica napus</i> assembly, a resource that will be valuable for the <i>Brassica</i> community for crop improvement and will facilitate the rapid selection of agronomically important traits.

利用长读长测序（long-reads）与长程信息开展基因组组装，现已成为学界公认的通用标准。该策略不仅可获取特定物种的完整基因目录，还能揭示染色体的结构与组织特征，涵盖端粒、着丝粒等复杂区域。芸苔属（Brassica）亦不例外，目前已有众多基于长读长测序的基因组组装结果发布。2014年发布的甘蓝型油菜（Brassica napus）参考基因组Darmor-bzh，采用短读长测序技术构建，相较当前芸苔属的其他基因组组装结果，其序列连续性极低。
本研究报道了结合长读长测序数据、光学图谱与遗传图谱构建的甘蓝型油菜Darmor-bzh基因组全新长读长组装结果。本研究使用PromethION测序仪与6张流动槽，共生成约1600万条长读长序列，总测序覆盖度达93×；尤为重要的是，长度超过100千碱基对（Kb）的读长对应的覆盖度达6×。该超长读长测序数据集助力本研究构建出截至目前连续性与完整性最优的芸苔属基因组组装结果之一，其重叠群N50超过10兆碱基对（Mb）。此外，本研究充分利用纳米孔测序技术的优势，实现碱基修饰检测，并通过直接RNA测序获取转录组数据，用于基因组注释并重点聚焦抗病基因的研究。
依托上述前沿技术，尤其是纳米孔测序技术的全部优势，本研究构建了目前连续性最优的甘蓝型油菜基因组组装结果。该资源将对芸苔属研究群体开展作物遗传改良工作具有重要价值，同时将助力重要农艺性状的快速筛选。