Department of Genomics, Branch for Northwest & West region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, 5156915-598, Iran.
Department of Food Biotechnology, Branch for Northwest & West region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, 5156915-598, Iran.
Sci Rep. 2021 Jan 15;11(1):1607. doi: 10.1038/s41598-020-80945-3.
Despite responses to salinity stress in Dunaliella salina, a unicellular halotolerant green alga, being subject to extensive study, but the underlying molecular mechanism remains unknown. Here, Empirical Bayes method was applied to identify the common differentially expressed genes (DEGs) between hypersaline and normal conditions. Then, using weighted gene co-expression network analysis (WGCNA), which takes advantage of a graph theoretical approach, highly correlated genes were clustered as a module. Subsequently, connectivity patterns of the identified modules in two conditions were surveyed to define preserved and non-preserved modules by combining the Zsummary and medianRank measures. Finally, common and specific hub genes in non-preserved modules were determined using Eigengene-based module connectivity or module membership (k) measures and validation was performed by using leave-one-out cross-validation (LOOCV). In this study, the power of beta = 12 (scale-free R2 = 0.8) was selected as the soft-thresholding to ensure a scale-free network, which led to the identification of 15 co-expression modules. Results also indicate that green, blue, brown, and yellow modules are non-preserved in salinity stress conditions. Examples of enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in non-preserved modules are Sulfur metabolism, Oxidative phosphorylation, Porphyrin and chlorophyll metabolism, Vitamin B6 metabolism. Moreover, the systems biology approach was applied here, proposed some salinity specific hub genes, such as radical-induced cell death1 protein (RCD1), mitogen-activated protein kinase kinase kinase 13 (MAP3K13), long-chain acyl-CoA synthetase (ACSL), acetyl-CoA carboxylase, biotin carboxylase subunit (AccC), and fructose-bisphosphate aldolase (ALDO), for the development of metabolites accumulating strains in D. salina.
尽管对耐盐单细胞绿藻杜氏盐藻（Dunaliella salina）应对盐胁迫的反应进行了广泛研究，但其中的潜在分子机制仍不清楚。在这里，我们应用经验贝叶斯方法来鉴定高盐和正常条件下的常见差异表达基因（DEGs）。然后，使用加权基因共表达网络分析（WGCNA），利用图论方法，将高度相关的基因聚类为一个模块。随后，通过结合 Zsummary 和 medianRank 度量标准，调查了在两种条件下识别模块的连接模式，以定义保留和非保留模块。最后，使用基于特征基因的模块连接或模块成员（k）度量标准确定非保留模块中的常见和特定枢纽基因，并通过使用留一法交叉验证（LOOCV）进行验证。在本研究中，选择β=12（无标度 R2=0.8）作为软阈值，以确保无标度网络，从而鉴定了 15 个共表达模块。结果还表明，在盐胁迫条件下，绿色、蓝色、棕色和黄色模块是非保留的。非保留模块中富集的京都基因与基因组百科全书（KEGG）途径的例子是硫代谢、氧化磷酸化、卟啉和叶绿素代谢、维生素 B6 代谢。此外，这里应用了系统生物学方法，提出了一些盐特异的枢纽基因，如活性氧诱导细胞死亡 1 蛋白（RCD1）、丝裂原活化蛋白激酶激酶激酶 13（MAP3K13）、长链酰基辅酶 A 合成酶（ACSL）、乙酰辅酶 A 羧化酶、生物素羧化酶亚基（AccC）和果糖-1,6-二磷酸醛缩酶（ALDO），用于开发杜氏盐藻中积累代谢物的菌株。
