Dual RNA-seq reveals distinct families of co-regulated and structurally conserved effectors in Botrytis cinerea infection of Arabidopsis thaliana

Abstract Background Botrytis cinerea is a broad-host pathogen causing gray mold disease and significant losses in the yield of numerous crops. However, the mechanisms underlying its rapid invasion and efficient killing of plant cells remain unclear. Results In this study, we elucidated the dynamics of B. cinerea infection in Arabidopsis thaliana by live-cell imaging and dual RNA sequencing. We found extensive transcriptional reprogramming events in both the pathogen and host, which involved metabolic pathways, signaling cascades, and transcriptional regulation. For the pathogen, we identified 852 candidate effector proteins (CEPs) and comprehensively analyzed their co-expression, sequence similarity, and structural conservation. The results revealed temporal co-regulation patterns of these CEPs, indicating coordinated deployment of effectors during B. cinerea infection. Functional screening of 48 selected CEPs in Nicotiana benthamiana demonstrated that B. cinerea may predominantly depend on cell death-inducing proteins (CDIPs) for rapid host colonization. Conclusions The findings provide important insights into the transcriptional dynamics and effector biology driving B. cinerea pathogenesis. The rapid infection of this pathogen involves the temporal co-regulation of CEPs and the prominent role of CDIPs in host cell death. Overall, this work provides a valuable resource for developing novel strategies for disease control targeting this devastating pathogen.