It is only recently, with the advent of long-read sequencing technologies, that we are beginning to uncover previously uncharted regions of complex and inherently recursive plant genomes. To comprehensively study and exploit the genome of the neglected oilseed Brassica nigra, we generated two high-quality nanopore de novo genome assemblies. The N50 contig lengths for the two assemblies were 17.1 Mb (12 contigs), one of the best among 324 sequenced plant genomes, and 0.29 Mb (424 contigs), respectively, reflecting recent improvements in the technology. Comparison with a de novo short-read assembly corroborated genome integrity and quantified sequence-related error rates (0.2%). The contiguity and coverage allowed unprecedented access to low-complexity regions of the genome. Pericentromeric regions and coincidence of hypomethylation enabled localization of active centromeres and identified centromere-associated ALE family retro-elements that appear to have proliferated through relatively recent nested transposition events (<1 Ma). Genomic distances calculated based on synteny relationships were used to define a post-triplication Brassica-specific ancestral genome, and to calculate the extensive rearrangements that define the evolutionary distance separating B. nigra from its diploid relatives.

直到最近，随着长读长测序技术的出现，我们才开始揭示复杂且本质上递归的植物基因组中以前未知的区域。为了全面研究和开发被忽视的油籽黑芥的基因组，我们生成了两个高质量的纳米孔从头基因组组装体。两个组件的 N50 重叠群长度分别为 17.1 Mb（12 个重叠群）和 0.29 Mb（424 个重叠群），是 324 个已测序植物基因组中最好的长度之一，反映了该技术的最新改进。与从头短读长组装的比较证实了基因组完整性和量化的序列相关错误率（0.2%）。连续性和覆盖范围允许前所未有地访问基因组的低复杂性区域。着丝粒周围区域和低甲基化的一致性使得活性着丝粒得以定位，并鉴定出着丝粒相关的 ALE 家族逆转录元件，这些逆转录元件似乎通过相对较新的嵌套转座事件 (<1 Ma) 进行了增殖。基于同线性关系计算的基因组距离用于定义三倍体后芸苔属特异性祖先基因组，并计算广泛的重排，这些重排定义了黑芥与其二倍体亲属之间的进化距离。