Transcriptomic and proteomic analyses of mulberry (Morus atropurpurea) fruit response to Ciboria carunculoides

The aim of this work was to gain insights into the molecular mechanisms and dynamics of the mulberry (Morus atropurpurea) fruit response to Ciboria carunculoides infection. A transcriptomic and proteomic study was carried out based on RNA sequencing and isobaric tags for relative and absolute quantification analysis, respectively. These data were then validated using quantitative real-time PCR and multiple reaction monitoring assays. Comparative analyses revealed that 9.0% of the transcriptome and 20.8% of the proteome were differentially regulated after C. carunculoides infection at the early stage (stage 1) and middle stage (stage 2), but correlation analysis revealed that only 145 genes were differentially regulated at both the transcriptome and proteome levels. The combined transcriptome and proteome analysis showed that plant hormone signal transduction, calcium-mediated defense signaling, transcription factors, and secondary metabolites were stimulated, whereas photosynthesis and cellular growth related metabolism were suppressed after C. carunculoides infection. These finding provide theoretical foundation for disease resistance breeding of C. carunculoides. Biological significance: Ciboria carunculoides is a major fungal pathogen that infects mulberry fruit, leading to extensive damage and productivity loss. Despite this major impact, the mulberry fruit response to C. carunculoides infection has yet to be characterized. This study provides the first system-wide datasets with which to examine changes in the transcriptome and proteome after C. carunculoides infection in mulberry fruit. The results showed that plant hormone signal transduction, calcium-mediated defense signaling, and other pathways were stimulated, whereas photosynthesis and cellular growth related metabolism were suppressed by C. carunculoides. These results will lead to a better understanding of the molecular mechanisms triggered in mulberry fruit in response to C. carunculoides infection and will provide new molecular targets for regulating defense responses to fungal pathogens in berry fruits.