The transcriptomics of an evolved plant-virus gene-for-gene interaction

We performed threefold evolution experiment with tobacco etch potyvirus isolate At17b (TEV-At17b) in five different ecotypes of Arabidopsis thaliana L. (Di-2, Ei-2, Ler-0, St-0, and Wt-1,), that are heterogeneous in their susceptibility to TEV-At17b infection. After the evolution phase, (i) we characterized the fitness and virulence of the evolved lineages across all host ecotypes, (ii) the molecular changes fixed in the viral genomes. Next, we analyzed the transcriptoma of the plants using Agilent Microarray tecnology (i)plants infected with local adapted viral lineage, (ii)plants infected with evolved virus vs. ancestal virus, (iii) virus evolved in new host and infecting its original host, (iv) transcriptoma of most specialized and most generalized viruses infecting all five ecotypes. We used at least 3 biological replicates for each sample category and as control we used mock inoculated plants. Plants of none sample category were mixed, but mantained as independent biological replicate. The data from ancestral viral strain TEV-At17b infecting A. thaliana ecotypes were taken at diferent time point (block 1) as data for evolved virus. Both sets of arrays were normalized on the whole.