micro-like RNAs and their targets engage in DCL2-deleted Valsa mali

Dicer proteins are mainly responsible for generating small RNAs (sRNAs). In previous study, two DCL proteins in Valsa mali, the pathogenic fungus of apple tree Valsa canker, were found to be associated with the pathogenicity and generation of sRNAs. In this study, we constructed two milRNA libraries using the the wild-type 03-8 (MVm) and Vm-DCL2 deletion mutant (MD2) strains and the differential expression of miRNA-like RNAs (milRNAs) were analyzed based on the deep-sequencing of the wild-type and Vm-DCL2 mutant, respectively. In total, by comparing the expression difference of milRNAs between MVm and MD2, it was found that 33 milRNAs were not detected in MD2, 28 milRNAs were both detected in MVm and MD2. By statistical analysis, one and 17 milRNAs showed up-regulated and down-regulated expression in MD2 compared with MVm, respectively (p<0.05). Importantly, 10 milRNAs were not detected in MD2, and identified to be DCL2 dependent milRNAs. We also identified the target genes of these milRNAs using degradome sequencing technology and found they were associated with protein phosphatase, isocitrate dehydrogenase, phosphoglycerate mutase, etc. The study will lay a foundation for the comprehensive analysis of pathogenic mechanisms of V. mali, and enrich cognition of the generation and function of fungal sRNA. milRNAs were isolated using high-throughput sequence analysis and their corresponding target genes were identified using degradome sequencing technology.