Core effectorome of Fusarium oxysporum f. sp. conglutinans deciphered using a multiomics method exhibits diverse roles following infection in cabbage

• The chromosome-level genome assembly of Focn race 1 strain FGL03-6 was produced. • A core set of 14 candidate effectors were identified using multiomic approaches. • 11 effectors induce distinct cell death responses in cabbages with a wide range of resistance backgrounds. • Effectors Focn-EF2 and Focn-EF7 were found to be involved in Focn virulence. Fusarium oxysporum f. sp. conglutinans ( Focn ), the causal agent of Fusarium wilt of cole crops such as cabbage, causes significant yield losses worldwide. However, the molecular mechanisms underlying Focn -mediated host susceptibility remain largely unexplored. Here, we presented the chromosome-level genome assembly of the Focn race 1 strain FGL03-6 via a single-molecule real-time sequencing platform, resequenced the genomes of 23 strains belonging to races 1 and 2, and performed genome-wide identification of Focn effectors using multiomics data generated from the Focn -cabbage interaction. In total, a core set of 14 candidate effectors were identified, among which 11 induced pronounced programmed cell death (PCD) in different cabbage lines, whereas only 1 candidate triggered partial cell death on the leaves of Nicotiana benthamiana , indicating that natural host cabbage is ideal for functional study of Focn effectors compared with N. benthamiana . In addition, we found that 8 PCD-inducing effectors can trigger cell death in highly resistant (HR) cabbage line 96-100, among which 2 can also trigger cell death in HR line BI-16 and moderately resistant line 084, separately, whereas 2 effectors induced PCD exclusively in the highly susceptible line 79-156, suggesting that different effectors might be exploited when Focn invades cabbage lines with distinct genetic backgrounds. Pathogenicity assays showed that Focn-EF7 knockout mutants exhibited enhanced virulence, whereas Focn-EF2 knockout mutants displayed reduced virulence. Our findings demonstrate that Focn invades host plants using diverse effector proteins, and the newly identified core effectorome provides a solid basis for understanding the molecular interactions between Focn and cabbage and for facilitating the development of strategies for effective disease control.