Table_1_Identifying Temporally Regulated Root Nodulation Biomarkers Using Time Series Gene Co-Expression Network Analysis.xlsx

Root nodulation results from a symbiotic relationship between a plant host and Rhizobium bacteria. Synchronized gene expression patterns over the course of rhizobial infection result in activation of pathways that are unique but overlapping with the highly conserved pathways that enable mycorrhizal symbiosis. We performed RNA sequencing of 30 Medicago truncatula root maturation zone samples at five distinct time points. These samples included plants inoculated with Sinorhizobium medicae and control plants that did not receive any Rhizobium. Following gene expression quantification, we identified 1,758 differentially expressed genes at various time points. We constructed a gene co-expression network (GCN) from the same data and identified link community modules (LCMs) that were comprised entirely of differentially expressed genes at specific time points post-inoculation. One LCM included genes that were up-regulated at 24 h following inoculation, suggesting an activation of allergen family genes and carbohydrate-binding gene products in response to Rhizobium. We also identified two LCMs that were comprised entirely of genes that were down regulated at 24 and 48 h post-inoculation. The identity of the genes in these modules suggest that down-regulating specific genes at 24 h may result in decreased jasmonic acid production with an increase in cytokinin production. At 48 h, coordinated down-regulation of a specific set of genes involved in lipid biosynthesis may play a role in nodulation. We show that GCN-LCM analysis is an effective method to preliminarily identify polygenic candidate biomarkers of root nodulation and develop hypotheses for future discovery.

根结瘤的形成源自植物宿主与根瘤菌之间的共生关系。在根瘤菌感染过程中同步的基因表达模式导致了一系列独特但又与高度保守的促进菌根共生的途径存在部分重叠的通路被激活。本研究对30个拟南芥根成熟区样本在五个不同时间点进行了RNA测序。这些样本包括接种了Sinorhizobium medicae的植物和未接种任何根瘤菌的对照植物。在基因表达量化后，我们识别出在各个时间点有1,758个差异表达基因。基于相同数据，我们构建了基因共表达网络（GCN），并确定了由特定接种时间点差异表达基因组成的链接社区模块（LCMs）。其中一个LCM包含在接种后24小时上调的基因，这表明过敏原家族基因和碳水化合物结合基因产物在响应根瘤菌时被激活。我们还识别出两个完全由接种后24小时和48小时下调的基因组成的LCMs。这些模块中基因的身份表明，在24小时内下调特定基因可能导致茉莉酸酸产量减少，细胞分裂素产量增加。在48小时时，参与脂质生物合成的一组特定基因的协调下调可能在结瘤过程中发挥作用。我们展示GCN-LCM分析是一种有效的初步识别多基因候选生物标志物和为未来的发现发展假设的方法。