Abstract
Identification of genes that are coexpressed across various tissues and environmental stresses is biologically interesting, since they may play coordinated role in similar biological processes. Genes with correlated expression patterns can be best identified by using coexpression network analysis of transcriptome data. In the present study, we analyzed the temporal-spatial coordination of gene expression in root, leaf and panicle of rice under drought stress and constructed network using WGCNA and Cytoscape. Total of 2199 differentially expressed genes (DEGs) were identified in at least three or more tissues, wherein 88 genes have coordinated expression profile among all the six tissues under drought stress. These 88 highly coordinated genes were further subjected to module identification in the coexpression network. Based on chief topological properties we identified 18 hub genes such as ABC transporter, ATP-binding protein, dehydrin, protein phosphatase 2C, LTPL153 - Protease inhibitor, phosphatidylethanolaminebinding protein, lactose permease-related, NADP-dependent malic enzyme, etc. Motif enrichment analysis showed the presence of ABRE cis-elements in the promoters of > 62% of the coordinately expressed genes. Our results suggest that drought stress mediated upregulated gene expression was coordinated through an ABA-dependent signaling pathway across tissues, at least for the subset of genes identified in this study, while down regulation appears to be regulated by tissue specific pathways in rice.
Highlights
It is well documented that transcriptionally coexpressed genes tend to be functionally related and may interact with each other at physiological or molecular level
Clusters II grouped two genes with tissue specific opposite regulation; LOC_Os03g20680 (LEA) was repressed in leaf at tillering stage, while LOC_Os01g39020 (HSF protein) was repressed in roots at both tillering and panicle elongation stage, where as these genes were induced in other stages. These results suggest that drought stress mediated upregulated gene expression is coordinated through a common signaling pathway across tissues, at least for the subset of genes identified in this study, while downregulation in general appears to be tissue specific in rice
The commonly upregulated genes consisted of several dehydrins, late embryogenesis abundant proteins (LEAs) proteins and heat shock proteins, suggesting that protection of cellular machinery is a common theme across tissues and development under drought stress
Summary
It is well documented that transcriptionally coexpressed genes tend to be functionally related and may interact with each other at physiological or molecular level. Number of comprehensive method have been developed and applied to construct networks from diverse high-throughput data sources such as microarray, generation sequencing (NGS), chromatin immunoprecipitation (ChIP) and protein-protein interaction assays [1]. These high-throughput techniques have made it possible to analyze thousands of genes in one shot. Gene networks are the basis of biological complexity and have become the core area of research in systems biology These networks are modeled as graph where, node represents the functional unit such as gene, protein, metabolite, etc., and edges are dependencies or interaction between the nodes. In case of the expression data of transcripts, the interaction may be the expression co-relation between the paired genes that is generally measured in terms of Pearson co-relation coefficient
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