A gap-free reference genome reveals structural variations associated with flowering time in rapeseed (<i>Brassica napus</i>)

Abstract

Allopolyploid oilseed rape (<i>Brassica napus</i>) is an important oil crop and vegetable. However, the latest version of its reference genome, with collapsed duplications, gaps, and other issues, prevents comprehensive genomic analysis. Herein, we report a gap-free assembly of the rapeseed cv. Xiang5A genome using a combination of ONT (Oxford Nanopore Technologies) ultra-long reads, PacBio high-fidelity reads, and Hi-C datasets. It includes gap-free assemblies of all 19 chromosomes and telomere-to-telomere assemblies of eight chromosomes. Compared with previously published genomes of <i>B. napus</i>, our gap-free genome, with a contig N50 length of 50.70 Mb, has complete assemblies of 9 of 19 chromosomes without manual intervention, and greatly improves contiguity and completeness, thereby representing the highest quality genome assembly to date. Our results revealed that <i>B. napus</i> Xiang5A underwent nearly complete triplication and allotetraploidy relative to <i>Arabidopsis thaliana</i>. Using the gap-free assembly, we found that 917 flowering-related genes were affected by structural variation, including <i>BnaA03.VERNALIZATION INSENSITIVE 3</i> and <i>BnaC04.HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 1</i>. These genes may play crucial roles in regulating flowering time and facilitating the adaptation of Xiang5A in the Yangtze River Basin of China. This reference genome provides a valuable genetic resource for rapeseed functional genomic studies and breeding.