Comparative Transcriptome Analysis of Different Mulberry Varieties to Reveal Candidate Genes and Small Secreted Peptides Involved in the Sclerotiniose Response

Abstract

Mulberry sclerotiniose is a devastating fungal disease of mulberry fruit and has been a limitation for the utility of mulberry fruits and the diversified development of sericulture. In the present study, we presented a workflow for screening candidate sclerotiniose-resistance genes and small secreted peptides (SSPs) based on a genome-wide annotation of SSPs and comparative transcriptome analysis of different mulberry varieties. A total of 1088 SSPs with expression evidence were identified and annotated in mulberry. A comprehensive analysis of the sclerotiniose-related RNA sequencing datasets showed that photosynthesis, plant hormone signaling, and metabolic pathways were the main pathways involved in the response to sclerotiniose. Fifty-two candidate sclerotiniose-response genes (SRGs), including 15 SSPs, were identified based on comparative transcriptome analysis. These SRGs are mainly involved in the hormone signaling pathway and cell wall biogenesis. Transient overexpression in tobacco and the knock-down of five SRGs affected the resistance against Ciboria shiraiana. MaMYB29, MaMES17, and MaSSP15 were primarily determined as negative regulators of plant resistance to C. shiraiana infection. Our results provide a foundation for controlling sclerotiniose in mulberry using genetic engineering and biological approaches such as spraying antifungal peptides.