Chromosome-level genome assembly and comprehensive multi-omics analysis uncovers a group of genes reject the integration of alien fragments through modulating the transmission rate, recombination rate and growth vigor

Cabbage, a significant Brassica vegetable crop of Cruciferae, is extensively cultivated and consumed globally. The Ogura cytoplasmic male sterility (CMS) system, in conjunction with the presence of a fertility restorer, is a primary approach for exploiting heterosis and achieving the innovation and reutilization of cabbage CMS materials. However, despite its crucial significance, the genomic data and genetic impacts of the Ogura CMS fertility restorer line (cabbage-radish introgression line) remain restricted. Here, we report a chromosome-level genome assembly of Ogura CMS fertility restorer line, which consists of 591.8 Mb in 9 chromosomes with a contig N50 of 32.3 Mb. To elucidate the mechanism of the integration of alien radish fragments and the rejection of cabbage receptor genome, we generated and analyzed a dataset encompassing genomes, transcriptomes, ATAC-seq and BS-seq. The conjoint analysis results reveal that the integration of alien radish fragments causes transcriptional activation of cabbage receptor genome and this kind of transcriptional activation is associated with increasing chromatin accessibility. DNA methylation is not an effective cause of gene expression level change, but the integration of alien fragments can lead to the clustered of differentially methylated loci at chromosome C09, affecting gene expression level change correlated with p53 and MAPK signaling pathway. In addition, the receptor genome rejects the integration of alien fragments mainly by reducing the TR of alien fragments and leading to homologous recombination supression, which ultimately shows that multiple agronomic traits of the cabbage-radish introgression lines showed significant weakness. This multiomics research provides molecular insight into the mechanism underlying integration of alien fragments and rejection of receptor genome in Ogura CMS fertility restorer line.