RNAseq-based transcriptome analysis of lettuce infected by the necrotrophic fungus Sclerotinia Sclerotiorum

Sclerotinia stem rot, caused by the necrotrophic fungal pathogen Sclerotinia sclerotiorum , is a serious constraint to lettuce production worldwide. To understand the molecular mechanisms underlying the plant’s response to S. sclerotiorum infection, next-generation sequencing was used to analyze the transcriptional alterations in lettuce post-infection in a time course of a compatible interaction. A total of 28,485, 28,777 and 29,018 unigenes were obtained at 6 hours post-inoculation (hpi), 12 hpi and 24 hpi, respectively. Among these, 4104, 4316 and 4980 genes were up-regulated while 3977, 3818 and 3802 genes were down-regulated at 6 hpi, 12 hpi and 24 hpi, respectively. Functional classification of the differentially expressed genes (DEGs) indicated that 21, 24 and 30 metabolic pathways were affected at 6 hpi, 12 hpi and 24 hpi, respectively. Some pathways were related to the plant immune response, such as ‘oxidative phosphorylation’, ‘plant hormone signal transduction’ and the ‘MAPK signaling pathway’. Real time quantitative PCR (RT-qPCR) analysis of six selected DEGs further validated the RNA-seq results. In addition, some novel potential disease responsive genes, including superoxide dismutase, WRKY transcription factors, pectinesterase inhibitor and ethylene-responsive transcription factors were identified. Our results suggest that lettuce adopts multiple strategies in regulating plant immunity to S. sclerotiorum infection. Collectively, the study provides new insights in the interaction of the plant - S. sclerotiorum pathosystem and provides information for further characterization of genes involved in plant resistance against S. sclerotiorum .