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Background   Sclerotinia sclerotiorum , the cause of Sclerotinia stem rot (SSR), is a host generalist necrotrophic fungus that can cause major yield losses in chickpea ( Cicer arietinum ) production. This study used RNA sequencing to conduct a time course transcriptional analysis of  S. sclerotiorum  gene expression during chickpea infection. It explores pathogenicity and developmental factors employed by  S. sclerotiorum  during interaction with chickpea.    Results  During infection of moderately resistant (PBA HatTrick) and highly susceptible chickpea (Kyabra) lines, 9491 and 10,487  S. sclerotiorum  genes, respectively, were significantly differentially expressed relative to in vitro. Analysis of the upregulated genes revealed enrichment of Gene Ontology biological processes, such as oxidation-reduction process, metabolic process, carbohydrate metabolic process, response to stimulus, and signal transduction. Several gene functional categories were upregulated  in planta , including carbohydrate-active enzymes, secondary metabolite biosynthesis clusters, transcription factors and candidate secreted effectors. Differences in expression of four  S. sclerotiorum  genes on varieties with different levels of susceptibility were also observed.    Conclusion  These findings provide a framework for a better understanding of  S. sclerotiorum  interactions with hosts of varying susceptibility levels. Here, we report for the first time on the  S. sclerotiorum  transcriptome during chickpea infection, which could be important for further studies on this pathogen’s molecular biology.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07655-6.

bmc genomics

Analysis of differentially expressed Sclerotinia sclerotiorum genes during the interaction with moderately resistant and highly susceptible chickpea lines