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

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.

Acknowledgements

This work was supported by the Hunan Province Science and Technology Innovation Plan Project (grant number 2021NK1004), the Changsha Natural Science Foundation (grant number kq2208157), and China Agriculture Research System of MOF and MAR (grant number CARS_12). The authors thank Wuhan Benagen Tech Solutions Co., Ltd for assistance with bioinformatics analysis.

Author contributions

B.L. performed the research and wrote the paper. L.Q., L.F., L.D., and R.H. participated in discussions and provided valuable advice. L.Y., Y.G., D.G., X.L., X.Z., and Q.Y. analyzed the data. M.L., T.W., and M.Y. designed and led this project.

Data availability

The genome and RNA-seq data for X5A have been deposited in the National Center for Biotechnology Information (https://www.ncbi.nlm.nih.gov/) under the BioProject accession number PRJNA950196. Additional material generated during this study can be obtained from the corresponding author upon reasonable request.

Conflict of interest

The authors declare no conflict of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

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