Table_3_Comprehensive Time-Course Transcriptome and Co-expression Network Analyses Identify Salt Stress Responding Mechanisms in Chlamydomonas reinhardtii Strain GY-D55.XLSX

It is highly necessary to understand the molecular mechanism underlying the salt stress response in green algae, which may contribute to finding the evolutionary cues of abiotic stress response in plants. Here, we reported a comprehensive temporal investigation of transcriptomes using data at eight different time points, from an early stage (2 h) to a late stage (up to 96 h) in Chlamydomonas reinhardtii GY-D55 cells. The principal component analysis (PCA) of transcriptome profiles showed that the samples of the early and late stages were well separated. A total of 12,445 genes were detected as differentially expressed genes. There were 1,861/2,270 common upregulated/downregulated genes for each time point compared with control samples. Samples treated with salt for 2, 8, and 24 h had a relatively large number of characteristic upregulated/downregulated genes. The functional enrichment analysis highlighted the timing of candidate regulatory mechanisms for salt stress responses in GY-D55 cells. Short time exposure to salt stress impaired oxidation-reduction, protein synthesis and modification, and photosynthesis. The algal cells promoted transcriptional regulation and protein folding to deal with protein synthesis/modification impairments and rapidly accumulated glycerol in the early stage (2–4 h) to cope with osmotic stress. At 12 and 24 h, GY-D55 cells showed increased expressions of signaling and photosynthetic genes to deal with the damage of photosynthesis. The co-expression module blue was predicted to regulate endoplasmic reticulum (ER) stress at early time points. In addition, we identified a total of 113 transcription factors (TFs) and predicted the potential roles of Alfin, C2C2, and the MYB family TFs in algal salt stress response.

解析绿藻盐胁迫响应的分子机制，可为探寻植物非生物胁迫响应的演化线索提供重要参考。本研究以莱茵衣藻(Chlamydomonas reinhardtii) GY-D55细胞为材料，对其从早期（2小时）至晚期（最长96小时）的8个不同时间点样本开展了全面的时序转录组分析。转录组特征的主成分分析(PCA)结果显示，早期与晚期处理样本呈现良好的分离效果。本研究共鉴定得到12445个差异表达基因；相较于对照样本，每个时间点均存在1861个共同上调基因与2270个共同下调基因。经盐处理2、8、24小时的样本，其特征性上调/下调基因数量相对较多。功能富集分析揭示了莱茵衣藻GY-D55细胞盐胁迫响应候选调控机制的时序性特征。短期盐胁迫暴露会破坏氧化还原稳态、蛋白质合成与修饰过程以及光合作用功能；藻细胞会启动转录调控与蛋白质折叠途径以应对蛋白质合成与修饰损伤，并在胁迫早期（2-4小时）快速积累甘油以抵御渗透胁迫。在处理12与24小时时，GY-D55细胞的信号传导与光合相关基因表达量上调，以修复光合作用所受损伤。共表达模块blue（蓝色）被预测可在早期时间点调控内质网(ER)应激过程。此外，本研究共鉴定得到113个转录因子(TFs)，并预测了Alfin、C2C2以及MYB家族转录因子在藻盐胁迫响应中的潜在功能。