Analysis of responsive genes to nitrogen-fixing symbiotic bacteria: a systematic vs. evolutionary preview

Background and Aim: The basic molecular mechanisms of the plant in response to biological stress have not been exactly understood. The current study was undertaken to decipher the hub genes in Medicago truncatula in response to nitrogen-fixing bacterium (Sinorhizobium meliloti) using systematic and evolutionary perspective. For this purpose, the Genomic Spatial Event database (GSE۱۲۶۸۳۳) was downloaded from Gene Expression Omnibus (GEO). Genes with differential expression (DEG) with adjusted P-value <۰.۰۵ and log fold change (FC) > |± ۳| by GEO۲R and R software were analyzed. The ۴۷۳ DEGs were obtained that ۴۰۱ of which were showed up- and down-regulations, respectively. After visualization of hub genes by Cytoscape, gene network was generated and protein-protein interaction network (PPI) was established.For functional enrichment analysis of the DEGs, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were searched to further confirm the likelihood of the coexpression. The results of GO analysis showed that the identified DEGs were mainly involved in metabolic process, catalytic activity and binding pathways. Identification of the genes with the ability of responding to biological stresses is a key tool for selecting suitable genes to regulate the genes and increase tolerance against stresses in plants.Methods: The basic molecular mechanisms of the plant in response to biological stress have not been exactly understood. The current study was undertaken to decipher the hub genes in Medicago truncatula in response to nitrogen-fixing bacterium (Sinorhizobium meliloti) using systematic and evolutionary perspective. For this purpose, the Genomic Spatial Event database (GSE۱۲۶۸۳۳) was downloaded from Gene Expression Omnibus (GEO). Genes with differential expression (DEG) with adjusted P-value <۰.۰۵ and log fold change (FC) > |± ۳| by GEO۲R and R software were analyzed. The ۴۷۳ DEGs were obtained that ۴۰۱ of which were showed up- and down-regulations, respectively. After visualization of hub genes by Cytoscape, gene network was generated and protein-protein interaction network (PPI) was established.For functional enrichment analysis of the DEGs, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were searched to further confirm the likelihood of the coexpression.Results: The results of GO analysis showed that the identified DEGs were mainly involved in metabolic process, catalytic activity and binding pathways. Identification of the genes with the ability of responding to biological stresses is a key tool for selecting suitable genes to regulate the genes and increase tolerance against stresses in plants Conclusion: The results of GO analysis showed that the identified DEGs were mainly involved in metabolic process, catalytic activity and binding pathways. Identification of the genes with the ability of responding to biological stresses is a key tool for selecting suitable genes to regulate the genes and increase tolerance against stresses in plants

کلیدواژه ها:

Medicago truncatula ، DEG ، PPI Network ، Hub genes network ، Functional enrichment analysis ، GO & KEGG pathway