Chromosome-level genome assembly of Chinese cabbage J405 reveals underlying high resistance to Alternaria brassicicola-induced black spot disease

• A chromosome-level genome assembly of Chinese cabbage J405 was established. • Overexpression of BraBIK1 enhances resistance. • Silencing BraBIK1 compromises resistance in J405 Chinese cabbage. • BraBIK1 integrates defense pathways and hormone signaling in Chinese cabbage. Through germplasm screening, we previously identified Chinese cabbage line J405, which displays strong resistance to black spot disease caused by Alternaria brassicicola . To elucidate the molecular basis of this resistance, we generated a chromosome-level genome assembly of J405 and compared it with other Brassica species. We further characterized BraBIK1 , a receptor-like cytoplasmic kinase family gene, and analyzed its promoter activity. The J405 genome is 440 Mb in size and encodes 49,923 protein-coding genes, with transposable elements comprising 57.65% of the genome. The 10 assembled chromosomes harbor abundant secondary metabolite biosynthetic clusters and R-gene clusters, many of which exhibit pathogen-responsive expression. Each chromosome also contains numerous SSR loci, with A/T and AT/TA motifs predominating. Expansion of gene families related to oxidoreductases, transferases, and basal metabolism was observed in J405. Functional assays demonstrated that BraBIK1 overexpression enhances resistance to A. brassicicola , whereas silencing reduces resistance. BraBIK1 activates genes associated with both PTI and ETI immune responses, as well as multiple hormone signaling pathways. Subcellular localization confirmed BraBIK1 at the plasma membrane. GUS reporter assays showed broad expression throughout Arabidopsis thaliana and induction by various phytohormones. Taken together, the expression of secondary metabolite genes and R genes, along with the functional contribution of BraBIK1 and expansion of related families, likely underpins the exceptional disease resistance of J405. In this study, we established a chromosome-level genome assembly of Chinese cabbage J405, developed 127,343 genome-wide SSR markers, and functionally validated BraBIK1 . These results provide valuable resources for genetic improvement of vegetable crop resilience and quality.