Transcription profiling analysis of genes and pathomechanisms underlying the defense response against Tobacco Etch Virus infection in Arabidopsis thaliana

The aim of this study was to identify potential genes and mechanisms in Arabidopsis thaliana (L.) Heynh. in response to Tobacco Etch Virus (TEV) infection by bioinformatics methods. The transcription profile GSE37269 containing 28 TEV-At17b infected and 25 non-infected samples of A. thaliana was downloaded and used. Limma software in R language was used to identify differentially expressed genes (DEGs) between mock and infected samples, and Gene Ontology and pathway enrichment analysis of DEGs were performed. Protein-protein interaction (PPI) network was constructed by STRING database. Moreover, a weighted gene co-expression network of closely co-expressed DEGs was constructed. Total 1781 DEGs including 873 up-regulated and 908 down-regulated genes were obtained. Up-regulated DEGs were mainly enriched in response to reactive oxygen species, and phenylalanine metabolism as well as biosynthesis of phenylpropanoids, while down-regulated DEGs were mainly enriched in external encapsulating structure organization. Up-regulated genes of AT2G18690 and AT1G19020, down-regulated gene of LAC11 (laccase 11) and IRX12 (iroquois homeobox 12) were hub nodes in PPI network. A significant co-expressed module containing AT5G37485, AT4G36430 and ATH8 (thioredoxin H-type 8) was identified and genes of it were significantly enriched in cellular response to reactive oxygen species and oxidative stress. AT4G36430 and ATH8 in the response to hydrogen peroxide and oxidative stress, and some peroxidase-like genes in the secondary metabolic and phenylpropanoid biosynthesis, may be responsible for the antiviral response to TEV-At17b infection in A. thaliana.