Integrated transcriptomic and metabolomic analyses provide insights into defense against Colletotrichum fructicola in octoploid strawberries.

Background: The Colletotrichum fructicola (C. fructicola) is a hemibiotrophic fungus, which causes devastating anthracnose in strawberry. At present, the resistance mechanism to C. fructicola remains poorly understood.

Results: Here, we used RNA-sequencing and liquid chromatography-mass spectrometry (LC-MS) metabolomics to excavate the molecular mechanism of strawberry resistance to C. fructicola. The differentially accumulated metabolites (DAMs) and differentially expressed genes (DEGs) were screened at different stages after C. fructicola infection in the susceptible 'Benihoppe' and resistant cultivar 'Sweet Charlie'. The core common DEGs with high association of common DAMs were identified by multi-omics integration analysis, and showed convergence and divergence in the two strawberry cultivars. Strikingly, the phenylpropanoids biosynthesis was simultaneously enriched in a multi-level omics at different stages after C. fructicola infection in the resistant (R) and susceptible (S) strawberries. Furthermore, we constructed the DEGs-DAMs map of phenylpropanoid biosynthesis. More importantly, we showed that chloroplasts and starch and sugar metabolism related genes, such as chlorophyII A-B binding genes, glycosyl hydrolase (GH) family genes and so on, were differentially expressed.

Conclusions: Taken together, our study revealed major changes in genes and metabolites expression associated with C. fructicola resistance, and identified the multi-level regulatory network based on phenylpropanoid biosynthesis, useful for further mechanistic excavation of resistance to C. fructicola in strawberries.