The WRKY gene family plays a very diverse role in plant growth and development. These genes contained an evolutionarily conserved WRKY DNA binding domain, which shows functional diversity and extensive expansion of the gene family. In this study, we conducted a genome-wide comparative analysis to investigate the evolutionary aspects of the WRKY gene family across various plant species and revealed significant expansion and diversification ranging from aquatic green algae to terrestrial plants. Phylogeny reconstruction of WRKY genes was performed using the Maximum Likelihood (ML) method; the genes were grouped into seven different clades and further classified into algae, bryophytes, pteridophytes, dicotyledons, and monocotyledons subgroups. Furthermore, duplication analysis showed that the increase in the number of WRKY genes in higher plant species was primarily due to tandem and segmental duplication under purifying selection. In addition, the selection pressures of different subfamilies of the WRKY gene were investigated using different strategies (classical and Bayesian maximum likelihood methods (Data monkey/PAML)). The average dN/dS for each group are less than one, indicating purifying selection. Our comparative genomic analysis provides the basis for future functional analysis, understanding the role of gene duplication in gene family expansion, and selection pressure analysis.

In higher eukaryotes, the genes’ architecture has become an essential determinant of the variation in the number of transcripts (expression level) and the specificity of gene expression in plant tissue under stress conditions. The modern rise in genome-wide analysis accounts for summarizing the essential factors through the translocation of gene networks in a regulatory manner. Stress tolerance genes are in two groups: structural genes, which code for proteins and enzymes that directly protect cells from stress (such as genes for transporters, osmo-protectants, detoxifying enzymes, etc.), and the genes expressed in regulation and signal transduction (such as transcriptional factors (TFs) and protein kinases). The genetic regulation and protein activity arising from plants’ interaction with minerals and abiotic and biotic stresses utilize high-efficiency molecular profiling. Collecting gene expression data concerning gene regulation in plants towards focus predicts an acceptable model for efficient genomic tools. Thus, this review brings insights into modifying the expression study, providing a valuable source for assisting the involvement of genes in plant growth and metabolism-generating gene databases. The manuscript significantly contributes to understanding gene expression and regulation in plants, particularly under stress conditions. Its insights into stress tolerance mechanisms have substantial implications for crop improvement, making it highly relevant and valuable to the field.