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

Bao Li; Qian Yang; Lulu Yang; Xing Zhou; Lichao Deng; Liang Qu; Dengli Guo; Rongkui Hui; Yiming Guo; Xinhong Liu; Tonghua Wang; Lianyi Fan; Mei Li; Mingli Yan

doi:10.1093/hr/uhad171

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

Hortic Res. 2023 Aug 29;10(10):uhad171. doi: 10.1093/hr/uhad171. eCollection 2023 Oct.

Authors

Bao Li^{1

2}, Qian Yang^{1

2}, Lulu Yang³, Xing Zhou^{1

2}, Lichao Deng^{1

2}, Liang Qu^{1

2}, Dengli Guo³, Rongkui Hui^{1

2}, Yiming Guo^{1

2}, Xinhong Liu^{1

2}, Tonghua Wang^{1

2}, Lianyi Fan^{1

2}, Mei Li^{1

2}, Mingli Yan^{1

2}

Affiliations

¹ Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, China.
² Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, Hunan 410125, China.
³ Department of Cell Biology and Genetics, Wuhan Benagen Tech Solutions Company Limited, Wuhan, Hubei 430021, China.

Abstract

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.