Table_14_Integrated miRNAome and Transcriptome Analysis Reveals Argonaute 2-Mediated Defense Responses Against the Devastating Phytopathogen Sclerotinia sclerotiorum.XLSX

Argonaute 2 (AGO2)-mediated role in plant defense against fungal pathogens remains largely unknown. In this study, integrated miRNAome and transcriptome analysis employing ago2 mutant was performed to reveal AGO2-associated miRNAs and defense responses against the devastating necrotrophic phytopathogen Sclerotinia sclerotiorum. Both miRNAome and transcriptomes of S. sclerotiorum-inoculated ago2-1 mutant (ago2-Ss) and wild-type (WT-Ss) as well as mock-inoculated ago2-1 mutant (ago2) and wild-type (WT) Arabidopsis plants, were analyzed by sRNA and mRNA deep sequencing. Differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) of the comparisons WT-Ss/WT, ago2/WT, ago2-Ss/WT-Ss, and ago2-Ss/ago2 were identified. Furthermore, integration analysis for the DEMs and DEGs identified over 40 potential AGO2-dependent Sclerotinia sclerotiorum-responsive (ATSR) DEM-DEG pairs involving modulation of immune recognition, calcium flux, redox homeostasis, hormone accumulation and signaling, cell wall modification and metal ion homeostasis. Data-mining result indicated that most of the DEMs were bound with AGO2. Moreover, Arabidopsis mutant analysis demonstrated that three ROS and redox homeostatasis related DEGs of identified DEM-DEG pairs, GSTU2, GSTU5, and RBOHF contributed to the AGO2-mediated defense against S. sclerotiorum. This work provides genome-wide prediction of miRNA–target gene pairs that are potentially associated with the AGO2-dependent resistance against S. sclerotiorum.

Argonaute 2（AGO2）介导的植物抗真菌病原体防御机制目前仍未得到充分阐明。本研究利用ago2突变体开展整合miRNA组学与转录组学分析，以揭示AGO2相关miRNA以及针对毁灭性死养营养型植物病原菌核盘菌（Sclerotinia sclerotiorum）的防御反应。研究通过小RNA（sRNA）与mRNA深度测序，对四类拟南芥样本的miRNA组与转录组进行分析：接种核盘菌的ago2-1突变体（ago2-Ss）、野生型拟南芥（WT-Ss）、空白接种的ago2-1突变体（ago2）以及野生型拟南芥（WT）。针对四组比较组合——WT-Ss/WT、ago2/WT、ago2-Ss/WT-Ss及ago2-Ss/ago2，分别鉴定得到差异表达基因（differentially expressed genes, DEGs）与差异表达miRNA（differentially expressed miRNAs, DEMs）。进一步对DEMs与DEGs开展整合分析，共筛选得到40余组潜在的AGO2依赖型核盘菌响应（ATSR）DEM-DEG对，其涉及免疫识别、钙信号流、氧化还原稳态、激素积累与信号传导、细胞壁修饰以及金属离子稳态的调控。数据挖掘结果显示，绝大多数DEMs均能与AGO2结合。此外，拟南芥突变体分析证实，所鉴定DEM-DEG对中3个与活性氧（ROS）及氧化还原稳态相关的差异表达基因GSTU2、GSTU5与RBOHF，参与了AGO2介导的抗核盘菌防御过程。本研究实现了全基因组范围内与AGO2依赖型抗核盘菌抗性潜在相关的miRNA-靶基因对的预测。