Using a time-course RNA-seq analysis we identified transcriptomic changes during formation of nodule-like structures (NLS) in rice and compared rice RNA-seq dataset with a nodule transcriptome dataset in Medicago truncatula. Plant hormones can induce the formation of nodule-like structures (NLS) in plant roots even in the absence of bacteria. These structures can be induced in roots of both legumes and non-legumes. Moreover, nitrogen-fixing bacteria can recognize and colonize these root structures. Therefore, identifying the genetic switches controlling the NLS organogenesis program in crops, especially cereals, can have important agricultural implications. Our recent study evaluated the transcriptomic response occurring in rice roots during NLS formation, 7 days post-treatment (dpt) with auxin, 2,4-D. In this current study, we investigated the regulation of gene expression occurring in rice roots at different stages of NLS formation: early (1-dpt) and late (14-dpt). At 1-dpt and 14-dpt, we identified 1662 and 1986 differentially expressed genes (DEGs), respectively. Gene ontology enrichment analysis revealed that the dataset was enriched with genes involved in auxin response and signaling; and in anatomical structure development and morphogenesis. Next, we compared the gene expression profiles across the three time points (1-, 7-, and 14-dpt) and identified genes that were uniquely or commonly differentially expressed at all three time points. We compared our rice RNA-seq dataset with a nodule transcriptome dataset in Medicago truncatula. This analysis revealed there is some amount of overlap between the molecular mechanisms governing nodulation and NLS formation. We also identified that some key nodulation genes were not expressed in rice roots during NLS formation. We validated the expression pattern of several genes via reverse transcriptase polymerase chain reaction (RT-PCR). The DEGs identified in this dataset may serve as a useful resource for future studies to characterize the genetic pathways controlling NLS formation in cereals.

中文翻译：

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时程 RNA-seq 分析提供了对水稻结节样结构形成过程中基因调控的更好理解。

使用时程 RNA-seq 分析，我们确定了水稻结节样结构 (NLS) 形成过程中的转录组变化，并将水稻 RNA-seq 数据集与蒺藜苜蓿中的结节转录组数据集进行了比较。即使在没有细菌的情况下，植物激素也可以诱导植物根部形成结节样结构 (NLS)。这些结构可以在豆科植物和非豆科植物的根中诱导。此外，固氮细菌可以识别和定殖这些根结构。因此，识别控制农作物（尤其是谷物）中 NLS 器官发生程序的遗传开关可能具有重要的农业意义。我们最近的研究评估了 NLS 形成过程中水稻根部发生的转录组反应，即用生长素 2,4-D 处理后 7 天 (dpt)。在目前的这项研究中，我们研究了在 NLS 形成的不同阶段发生在水稻根中的基因表达调控：早期 (1-dpt) 和晚期 (14-dpt)。在 1-dpt 和 14-dpt，我们分别鉴定了 1662 和 1986 个差异表达基因 (DEG)。基因本体富集分析表明，该数据集富含与生长素反应和信号传导有关的基因；以及解剖结构发育和形态发生。接下来，我们比较了三个时间点（1-、7-和 14-dpt）的基因表达谱，并确定了在所有三个时间点独特或普遍差异表达的基因。我们将我们的水稻 RNA-seq 数据集与蒺藜苜蓿中的结节转录组数据集进行了比较。该分析表明，控制结瘤和 NLS 形成的分子机制之间存在一定程度的重叠。我们还发现，在 NLS 形成过程中，一些关键的结瘤基因在水稻根部中没有表达。我们通过逆转录酶聚合酶链反应 (RT-PCR) 验证了几个基因的表达模式。该数据集中确定的 DEG 可作为未来研究表征控制谷物 NLS 形成的遗传途径的有用资源。