Table_2_Integration of the Pokeweed miRNA and mRNA Transcriptomes Reveals Targeting of Jasmonic Acid-Responsive Genes.XLSX

The American pokeweed plant, Phytolacca americana, displays broad-spectrum resistance to plant viruses and is a heavy metal hyperaccumulator. However, little is known about the regulation of biotic and abiotic stress responses in this non-model plant. To investigate the control of miRNAs in gene expression, we sequenced the small RNA transcriptome of pokeweed treated with jasmonic acid (JA), a hormone that mediates pathogen defense and stress tolerance. We predicted 145 miRNAs responsive to JA, most of which were unique to pokeweed. These miRNAs were low in abundance and condition-specific, with discrete expression change. Integration of paired mRNA-Seq expression data enabled us to identify correlated, novel JA-responsive targets that mediate hormone biosynthesis, signal transduction, and pathogen defense. The expression of approximately half the pairs was positively correlated, an uncommon finding that we functionally validated by mRNA cleavage. Importantly, we report that a pokeweed-specific miRNA targets the transcript of OPR3, novel evidence that a miRNA regulates a JA biosynthesis enzyme. This first large-scale small RNA study of a Phytolaccaceae family member shows that miRNA-mediated control is a significant component of the JA response, associated with widespread changes in expression of genes required for stress adaptation.

美洲商陆（Phytolacca americana）对植物病毒具有广谱抗性，同时亦是一种重金属超富集植物。然而，目前对于这类非模式植物的生物与非生物胁迫响应调控机制仍缺乏深入认知。为探究microRNAs（miRNAs）在基因表达调控中的作用，我们对经茉莉酸（jasmonic acid, JA）处理的商陆样本开展了小RNA转录组测序——茉莉酸是一类介导病原体防御与胁迫耐受性的植物激素。本研究共预测得到145个响应茉莉酸的miRNAs，其中绝大多数为商陆所特有。这类miRNAs表达丰度偏低，且具有处理条件特异性，其表达变化模式清晰可辨。通过整合配对的mRNA-Seq表达数据，我们成功鉴定出具有表达相关性的新型茉莉酸响应靶基因，这些靶基因参与激素生物合成、信号转导及病原体防御过程。约半数靶基因与对应miRNAs的表达呈正相关，这一现象较为罕见，我们通过mRNA剪切实验对该相关性进行了功能验证。尤为重要的是，本研究发现一种商陆特有的miRNA靶向OPR3基因的转录本，这为miRNA调控茉莉酸生物合成酶的表达提供了全新证据。此项针对商陆科（Phytolaccaceae）植物的首次大规模小RNA研究表明，miRNA介导的调控是茉莉酸响应过程中的关键组成部分，与胁迫适应所需基因的广泛表达变化紧密关联。