Sclerotinia sclerotiorum is a model necrotrophic pathogen causing great economic losses worldwide. Sclerotia are dormant structures that play significant biological and ecological roles in the life and disease cycles of S. sclerotiorum and other species of sclerotia-forming fungi. microRNA-like RNAs (milRNAs) as non-coding small RNAs play regulatory roles in fungal development and pathogenicity. Therefore, milRNAs associated with sclerotial development in S. sclerotiorum were investigated in this study. A total of 275 milRNAs with induced expression during sclerotia development were identified, in which 51 were differentially expressed. The target genes of all milRNAs were predicted. The putative functions of the targets regulated by milRNAs were annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. The expression levels of six selected milRNAs that coordinated with their corresponding targets were validated by qRT-PCR. Among these six milRNAs, Ssc-milR-240 was potentially associated with sclerotial development by epigenetic regulation of its target histone acetyltransferase. This study will facilitate the better understanding of the milRNA regulation associated with sclerotial development in S. sclerotiorum and even other sclerotia-forming fungi. This work will provide novel insights into the molecular regulations of fungal morphogenesis and the candidate targets of milRNAs used for the sustainable management of plant diseases caused by S. sclerotiorum.

核盘菌是一种在世界范围内造成巨大经济损失的模型坏死性病原体。菌核是休眠结构，在S. sclerotiorum和其他菌核形成真菌的生命和疾病周期中发挥着重要的生物学和生态作用。microRNA 样 RNA (milRNAs) 作为非编码小 RNA 在真菌发育和致病性中发挥调节作用。因此，与S. sclerotiorum 中的菌核发育相关的 milRNA在这项研究中进行了调查。共鉴定出 275 个在菌核发育过程中诱导表达的 milRNA，其中 51 个差异表达。预测了所有 milRNA 的靶基因。基因本体论（GO）和京都基因和基因组百科全书（KEGG）分析注释了由milRNA调控的靶标的假定功能。通过 qRT-PCR 验证了与其相应靶标相协调的六种选定 milRNA 的表达水平。在这六个 milRNA 中，Ssc-milR-240 可能通过其目标组蛋白乙酰转移酶的表观遗传调控与菌核发育相关。这项研究将有助于更好地理解与S菌核发育相关的 milRNA 调节。菌核甚至其他菌核形成真菌。这项工作将为真菌形态发生的分子调控和用于可持续管理由核盘菌引起的植物病害的 milRNA 的候选目标提供新的见解。