We report a public resource for examining the spatiotemporal RNA expression of 54,893 M. truncatula genes during the first 72 hours of response to rhizobial inoculation. Using a methodology that allows synchronous inoculation and growth of over 100 plants in a single media container, we harvested the same segment of each root responding to rhizobia in the initial inoculation over a time course, collected individual tissues from these segments with laser capture microdissection, and created and sequenced RNA libraries generated from these tissues. We demonstrate the utility of the resource by examining the expression patterns of a set of genes induced very early in nodule signaling, as well as two gene families (CLE peptides and nodule specific PLAT-domain proteins) and show that despite similar whole root expression patterns, there are tissue differences in expression between the genes. Using a rhizobial response data set generated from transcriptomics on intact root segments, we also examined differential temporal expression patterns and determined that, after nodule tissue, the epidermis and cortical cells contained the most temporally patterned genes. We circumscribed gene lists for each time and tissue examined and developed an expression pattern visualization tool. Finally, we explored transcriptomic differences between the inner cortical cells that become nodules and those that do not, confirming that the expression of ACC synthases distinguishes inner cortical cells that become nodules and provide and describe potential downstream genes involved in early nodule cell division.

中文翻译：

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激光捕获显微切割转录组揭示了蒺藜根对根瘤菌响应的时空组织基因表达模式。

我们报告了一个公共资源，用于检查根瘤菌接种反应的前 72 小时内 54,893 个 M. truncatula 基因的时空 RNA 表达。使用允许在单个培养基容器中同步接种和生长超过 100 株植物的方法，我们在一段时间内收获了初始接种中对根瘤菌有反应的每个根的相同部分，并通过激光捕获显微切割从这些部分收集了单个组织，创建并测序从这些组织中生成的 RNA 文库。我们通过检查根瘤信号传导早期诱导的一组基因以及两个基因家族（CLE 肽和根瘤特异性 PLAT 结构域蛋白）的表达模式来证明该资源的实用性，并表明尽管全根表达模式相似，基因之间的表达存在组织差异。使用从完整根段转录组学生成的根瘤菌反应数据集，我们还检查了差异时间表达模式，并确定在根瘤组织之后，表皮和皮质细胞包含最具时间模式的基因。我们限制了每次检查的基因列表和组织，并开发了表达模式可视化工具。最后，我们探索了成为结节的内皮层细胞和那些没有成为结节的内皮层细胞之间的转录组差异，证实了 ACC 合酶的表达区分了成为结节的内皮层细胞，并提供和描述了参与早期结节细胞分裂的潜在下游基因。