Pathogenic fungi secrete numerous effectors into host cells to manipulate plants’ defense mechanisms. Valsa mali, a necrotrophic fungus, severely impacts apple production in China due to the occurrence of Valsa canker. Here, we predicted 210 candidate effector protein (CEP)-encoding genes from V. mali. The transcriptome analysis revealed that 146 CEP-encoding genes were differentially expressed during the infection of the host, Malus sieversii. Proteome analysis showed that 27 CEPs were differentially regulated during the infection stages. Overall, 25 of the 146 differentially expressed CEP-encoding genes were randomly selected to be transiently expressed in Nicotiana benthamiana. Pathogenicity analysis showed that the transient expression of VM1G-05058 suppressed BAX-triggered cell death while the expression of VM1G-10148 and VM1G-00140 caused cell death in N. benthamiana. In conclusion, by using multi-omics analysis, we identified potential effector candidates for further evaluation in vivo. Our results will provide new insights into the investigation of virulent mechanisms of V. mali.
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