Data_Sheet_2_Identification of the Complex Interplay Between Nematode-Related lncRNAs and Their Target Genes in Glycine max L..pdf

Soybean (Glycine max) is a major plant protein source and oilseed crop. However, plant-parasitic nematodes (PPNs) affect its annual yield. In the current study, in order to better understand the regulation of defense mechanism against PPNs in soybean, we investigated the role of long non-coding RNAs (lncRNAs) in response to two nematode species, Heterodera glycines (SCN: soybean cyst nematode) and Rotylenchulus reniformis (reniform). To this end, two publicly available RNA-seq data sets (SCN data set and RAD: reniform-associated data set) were employed to discover the lncRNAome profile of soybean under SCN and reniform infection, respectively. Upon identification of unannotated transcripts in these data sets, a seven-step pipeline was utilized to sieve these transcripts, which ended up in 384 and 283 potential lncRNAs in SCN data set and RAD, respectively. These transcripts were then used to predict cis and trans nematode-related targets in soybean genome. Computational prediction of target genes function, some of which were also among differentially expressed genes, revealed the involvement of putative nematode-responsive genes as well as enrichment of multiple stress responses in both data sets. Finally, 15 and six lncRNAs were proposed to be involved in microRNA-mediated regulation of gene expression in soybean in response to SNC and reniform infection, respectively. Collectively, this study provides a novel insight into the signaling and regulatory network of soybean-pathogen interactions and opens a new window for further research.

大豆（Glycine max）是一类重要的植物蛋白源与油料作物，然而植物寄生线虫（plant-parasitic nematodes, PPNs）会对其年度产量造成负面影响。为深入解析大豆抵御植物寄生线虫的防御调控机制，本研究探究了长链非编码RNA（long non-coding RNAs, lncRNAs）在大豆响应两种线虫——大豆孢囊线虫（Heterodera glycines，简称SCN：soybean cyst nematode）与肾形线虫（Rotylenchulus reniformis，简称reniform）——过程中的作用。为此，本研究采用两份公开的RNA测序（RNA-seq）数据集（SCN数据集与RAD：肾形线虫关联数据集），分别解析大豆在受SCN与肾形线虫侵染时的长链非编码RNA组谱。在鉴定得到上述数据集中的未注释转录本（unannotated transcripts）后，研究通过七步分析流程（seven-step pipeline）对这些转录本进行筛选，最终分别在SCN数据集与RAD中获得384个和283个潜在长链非编码RNA。随后，研究以这些转录本为基础，预测大豆基因组中与线虫相关的顺式（cis）与反式（trans）靶基因。通过对靶基因功能进行计算预测，且其中部分靶基因同时属于差异表达基因（differentially expressed genes），结果显示两类数据集均存在潜在的线虫应答基因，且多种胁迫响应通路显著富集。最终，本研究分别提出15个和6个长链非编码RNA参与大豆响应SCN与肾形线虫侵染过程中的微小RNA（microRNA）介导的基因表达调控。综上，本研究为解析大豆-病原互作的信号与调控网络提供了全新视角，也为后续相关研究开辟了新方向。