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

文献类型： 外文期刊

作者： Li, Bao 1 ; Yang, Qian 1 ; Yang, Lulu 3 ; Zhou, Xing 1 ; Deng, Lichao 1 ; Qu, Liang 1 ; Guo, Dengli 3 ; Hui, Rongkui 1 ; Guo, Yiming 1 ; Liu, Xinhong 1 ; Wang, Tonghua 1 ; Fan, Lianyi 1 ; Li, Mei 1 ; Yan, Mingli 1 ;

作者机构： 1.Hunan Acad Agr Sci, Crop Res Inst, Changsha 410125, Hunan, Peoples R China

2.Hunan Hybrid Rapeseed Engn & Technol Res Ctr, Changsha 410125, Hunan, Peoples R China

3.Wuhan Benagen Tech Solut Co Ltd, Dept Cell Biol & Genet, Wuhan 430021, Hubei, Peoples R China

期刊名称：HORTICULTURE RESEARCH （ 影响因子：8.7； 五年影响因子：9.0 ）

ISSN： 2662-6810

年卷期： 2023 年 10 卷 10 期

页码：

收录情况： SCI

摘要： 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.

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