Genome assembly and genomic architecture of a prominent cold-resistant rapeseed germplasm

Cold stress is one of the most limiting factors affecting crop production. Winter rapeseed, as an important oilseed crop, is often subjected to low temperature stress and consequent yield loss at high latitudes. Therefore, identification of highly cold-resistant winter type rapeseed and elucidation of the genomic architecture are crucial for genetic improvement of the trait. Here, we report a chromosome-level reference genome of a prominent cold-resistant winter rapeseed cultivar, NTS57. Phylogenetic analysis revealed that the A subgenome was more closely related to that of other semi-winter rapeseed accessions, while the C subgenome was in a clade with that of winter rapeseed accessions. Comparative genomic analyses revealed extensive structural variation between the NTS57 and other public rapeseed accessions, some of which are involved in plant temperature sensing or vernalization. Gene expression profiling under cold stress identified more than ten thousand differentially expressed genes which are enriched in the regulation of circadian rhythms, photosynthesis, cold response, etc. Gene co-expression analysis was performed and identified three functional modules which is associated with cold response in NTS57 rapeseed. DNA methylation profiling revealed that the methylation levels were significantly decreased at both protein-coding genes and repetitive elements, suggesting that demethylation is required for cold stress response. Overall, this research provided a basis for genetic dissection and improvement of cold tolerance in rapeseed. ### Competing Interest Statement The authors have declared no competing interest.