Abstract

Chalkbrood disease, caused by the lethal fungal pathogen Ascosphaera apis , poses a severe threat to honeybees and the global beekeeping industry. Pathogens often utilize specific molecules like long non-coding RNAs (lncRNAs) to boost their infectivity and bypass host defenses. Here, we performed an in-depth investigation of the lncRNAs produced by A. apis invading the Asian honeybee ( Apis cerana ) worker larvae. We identified 1379 fungal lncRNAs and observed significant changes in their expression across different stages of infection. Comprehensive analyses revealed that these lncRNAs may act as critical regulators to promote fungal growth and disease progression via a diverse array of regulatory mechanisms, including antisense lncRNA-mediated modulation, cis - and trans -acting regulatory effects, and competing endogenous RNA (ceRNA) network activity. Our data elucidate whether and how lncRNAs modulate the A. apis infection of A. cerana worker larvae, laying a basis for clarifying the underlying mechanisms. Ascosphaera apis , an obligate lethal fungal pathogen that infects bee larvae, and causes chalkbrood disease, poses a significant threat to the global beekeeping industry. Long non-coding RNAs (lncRNAs) are employed by pathogens to enhance infectivity and evade host immunity. Here, lncRNAs in A. apis spores (AaCK group) and the guts of 4-, 5-, and 6-day-old Apis cerana cerana worker larvae inoculated with A. apis spores (AaT1, AaT2, and AaT3 groups) were identified, characterized, and validated. Additionally, the expression pattern of fungal lncRNAs during infection was analyzed, followed by an investigation of the regulatory manners and roles of differentially expressed lncRNAs (DElncRNAs). A total of 1379 lncRNAs were identified in AaCK, AaT1, AaT2, and AaT3 groups using bioinformatics, involving various types such as sense lncRNAs, antisense lncRNAs, bidirectional lncRNAs, intergenic lncRNAs, and intronic lncRNAs. Additionally, 4, 9, and 75