| Summary: | <i>Sclerotinia sclerotiorum</i> is a necrotrophic phytopathogenic fungus that produces sclerotia. Sclerotia are essential components of the survival and disease cycle of this devastating pathogen. In this study, we analyzed comparative transcriptomics of hyphae and sclerotia. A total of 1959 differentially expressed genes, 919 down-regulated and 1040 up-regulated, were identified. Transcriptomes data provide the possibility to precisely comprehend the sclerotia development. We further analyzed the differentially expressed genes (DEGs) in sclerotia to explore the molecular mechanism of sclerotia development, which include ribosome biogenesis and translation, melanin biosynthesis, autophagy and reactivate oxygen metabolism. Among these, the autophagy-related gene <i>SsAtg1</i> was up-regulated in sclerotia. Atg1 homologs play critical roles in autophagy, a ubiquitous and evolutionarily highly conserved cellular mechanism for turnover of intracellular materials in eukaryotes. Therefore, we investigated the function of <i>SsAtg1</i> to explore the function of the autophagy pathway in <i>S. sclerotiorum</i>. Deficiency of <i>SsAtg1</i> inhibited autophagosome accumulation in the vacuoles of nitrogen-starved cells. Notably, Δ<i>SsAtg1</i> was unable to form sclerotia and displayed defects in vegetative growth under conditions of nutrient restriction. Furthermore, the development and penetration of the compound appressoria in Δ<i>SsAtg1</i> was abnormal. Pathogenicity analysis showed that <i>SsAtg1</i> was required for full virulence of <i>S. sclerotiorum</i>. Taken together, these results indicate that <i>SsAtg1</i> is a core autophagy-related gene that has vital functions in nutrient utilization, sclerotia development and pathogenicity in <i>S. sclerotiorum</i>.
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