idopNetwork Analysis of Salt-Responsive Transcriptomes Reveals Hub Regulatory Modules and Genes in Populus euphratica

Abstract

Euphrates poplar (Populus euphratica) is known as a system model to study the genomic mechanisms underlying the salt resistance of woody species. To characterize how dynamic gene regulatory networks (GRNs) drive the defense response of this species to salt stress, we performed mRNA sequencing of P. euphratica roots under short-term (ST) and long-term (LT) salt stress treatments across multiple time points. Comparisons of these transcriptomes revealed the diverged gene expression patterns between the ST and LT treated samples. Based on the informative, dynamic, omnidirectional, and personalized networks model (idopNetwork), inter- and intra-module networks were constructed across different time points for both the ST and LT groups. Through the analysis of the inter-module network, we identified module 4 as the hub, containing the largest number of genes. Further analysis of the gene network within module 4 revealed that gene XM_011048240.1 had the most prominent interactions with other genes. Under short-term salt stress, gene interactions within the network were predominantly promoted, whereas under long-term stress, these interactions shifted towards inhibition. As for the gene ontology (GO) annotation of differentially expressed genes, the results suggest that P. euphratica may employ distinct response mechanisms during the early and late stages of salt stress. Taking together, these results offer valuable insights into the regulatory mechanism involved in P. euphratica’s stress response, advancing our understanding of complex biological processes.