Gao Yueyao, Selee Bradley, Schnabel Elise L, Poehlman William L, Chavan Suchitra A, Frugoli Julia A, Feltus Frank Alex
Department of Genetics and Biochemistry, Clemson University, Clemson, SC, United States.
Department of Electrical and Computer Engineering, Clemson University, Clemson, SC, United States.
Front Plant Sci. 2022 Apr 7;13:861639. doi: 10.3389/fpls.2022.861639. eCollection 2022.
In response to colonization by rhizobia bacteria, legumes are able to form nitrogen-fixing nodules in their roots, allowing the plants to grow efficiently in nitrogen-depleted environments. Legumes utilize a complex, long-distance signaling pathway to regulate nodulation that involves signals in both roots and shoots. We measured the transcriptional response to treatment with rhizobia in both the shoots and roots of over a 72-h time course. To detect temporal shifts in gene expression, we developed GeneShift, a novel computational statistics and machine learning workflow that addresses the time series replicate the averaging issue for detecting gene expression pattern shifts under different conditions. We identified both known and novel genes that are regulated dynamically in both tissues during early nodulation including leginsulin, defensins, root transporters, nodulin-related, and circadian clock genes. We validated over 70% of the expression patterns that GeneShift discovered using an independent RNA-Seq study. GeneShift facilitated the discovery of condition-specific temporally differentially expressed genes in the symbiotic nodulation biological system. In principle, GeneShift should work for time-series gene expression profiling studies from other systems.
作为对根瘤菌定植的响应，豆科植物能够在其根部形成固氮根瘤，从而使植物在氮素匮乏的环境中高效生长。豆科植物利用一条复杂的长距离信号通路来调节结瘤过程，该过程涉及根和地上部分的信号。我们在72小时的时间进程中测量了豆科植物地上部分和根部对根瘤菌处理的转录反应。为了检测基因表达的时间变化，我们开发了GeneShift，这是一种新颖的计算统计和机器学习工作流程，可解决时间序列重复平均问题，以检测不同条件下的基因表达模式变化。我们鉴定出了在早期结瘤过程中在两个组织中动态调控的已知和新基因，包括豆胰岛素、防御素、根转运蛋白、结瘤素相关基因和生物钟基因。我们使用独立的RNA测序研究验证了GeneShift发现的70%以上的表达模式。GeneShift有助于在共生结瘤生物系统中发现特定条件下的时间差异表达基因。原则上，GeneShift应该适用于来自其他系统的时间序列基因表达谱研究。
