sRNA-seq of Aspergillus fumigatus RNAi double knockouts expressing a pksP inverted-repeat transgene

The RNA interference (RNAi) pathway has evolved numerous functionalities in eukaryotes, with many on display in Kingdom Fungi. RNAi can regulate gene expression, facilitate drug resistance, or even be altogether lost to improve virulence potential in some fungal pathogens. In the WHO fungal priority pathogen, Aspergillus fumigatus, the RNAi system is known to be intact and functional. To extend our limited understanding of A. fumigatus RNAi, we performed a sRNA-seq to assess sRNAs produced in several RNAi double knockouts and a wild type strain expressing a 1200 nt inverted-repeat transgene with complementarity to the pksP gene. The transgene harbors a 500-bp inverted repeat. We included an uninduced wild type strain with no inverted-repeat transgene as a control. All conditions were performed in mycelium grown for 24 hours in liquid culture. Small RNA profiling analysis of Aspergillus fumigatus RNAi double knockouts (𝚫dclA/B, 𝚫ppdA/B, 𝚫rrpA/B) and wild type expressing a 1200 nt inverted-repeat transgene with complementarity to the pksP gene, using 24-h-mycelium. Please note that GSM8721378-GSM8721380 raw files and IRT_sRNA_processed.csv processed data file have been replaced on Aug 11, 2025.

RNA干扰（RNA interference, RNAi）通路在真核生物中演化出多种功能，其中诸多功能在真菌界中得以展现。RNAi可调控基因表达、介导耐药性，在部分真菌病原体中甚至会完全丢失以提升其毒力潜力。作为世界卫生组织（WHO）划定的真菌优先病原体，烟曲霉（Aspergillus fumigatus）的RNAi系统完整且具备功能。为拓展我们对烟曲霉RNAi机制的有限认知，本研究开展小RNA测序（sRNA-seq），以评估多种RNAi双敲除株，以及一株表达与pksP基因互补的1200 nt反向重复转基因片段的野生型菌株所产生的小RNA。该转基因片段包含一段500 bp的反向重复序列。本研究设置未携带反向重复转基因片段的未诱导野生型菌株作为对照。所有实验均采用在液体培养基中培养24小时的菌丝体进行。本数据集包含烟曲霉RNAi双敲除株（ΔdclA/B、ΔppdA/B、ΔrrpA/B）以及表达与pksP基因互补的1200 nt反向重复转基因片段的野生型菌株的小RNA谱分析数据，实验材料为培养24小时的菌丝体。请注意：GSM8721378至GSM8721380的原始数据文件与IRT_sRNA_processed.csv处理后数据文件已于2025年8月11日完成替换。