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Article|29 Aug 2023|OPEN
A gap-free reference genome reveals structural variations associated with flowering time in rapeseed (Brassica napus)
Bao Li1,2 , Qian Yang1,2 , Lulu Yang3 , Xing Zhou1,2 , Lichao Deng1,2 , Liang Qu1,2 , Dengli Guo3 , Rongkui Hui1,2 , Yiming Guo1,2 , Xinhong Liu1,2 , Tonghua Wang1,2 , Lianyi Fan1,2 , Mei Li1,2 , , Mingli Yan,1,2 ,
1Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, China
2Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, Hunan 410125, China
3Department of Cell Biology and Genetics, Wuhan Benagen Tech Solutions Company Limited, Wuhan, Hubei 430021, China
*Corresponding author. E-mail:,

Horticulture Research 10,
Article number: uhad171 (2023)
Views: 51

Received: 28 Mar 2023
Accepted: 20 Aug 2023
Published online: 29 Aug 2023


Allopolyploid oilseed rape (Brassica napus) 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 B. napus, 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 B. napus Xiang5A underwent nearly complete triplication and allotetraploidy relative to Arabidopsis thaliana. Using the gap-free assembly, we found that 917 flowering-related genes were affected by structural variation, including BnaA03.VERNALIZATION INSENSITIVE 3 and BnaC04.HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 1. 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.