The expression of transcription factors (TF) was also differentially affected by TEV and TEV-At17. Table S5 shows the list of differentially up-and down-regulated TF in plants infected with each type of virus. Fifty-one TFs, belonging to 20 families, were upregulated whereas 84 TFs, from 27 families, were down-regulated, including 13 ethylene-responsive binding factors (ERF), after infection with TEV-At. ERFs are linked to stress responses [31] and delays in ERF induction had been described in A. thaliana plants infected with virulent strains of the bacteria Pseudomonas syringae when compared with avirulent strains of the same bacteria [31] . Viral adaptation by avoidance of plant defenses Next, we examined the distribution of genes involved in related biological processes that are differentially affected by TEV and TEV-At17 (i.e., gene ontologies (GO) categories [32] ). The algorithm implemented in FatiGO [33] was applied to the nonredundant gene list grouped in each SOM (results are shown in Table S6 ). Only a significant differential category, response to salt stress, was identified for the SOM A3 of up-regulated genes shown in Figure 3A . By contrast, a large number of GO terms show significant over-and under-representation in the differentially down-regulated genes ( Figure 3B ). Table 2 shows the nonredundant functional categories that correspond to SOMs B1 plus B2 (i.e., genes over-expressed after infection by TEV but not differing from uninfected plants when infected with TEV-At17). Interestingly, significantly over-represented genes belong to functional categories which are related to plant responses to different abiotic (wounding, light intensity, temperature, salinity) and biotic stresses. Furthermore, genes involved in the SAR and in the activation of innate immune responses [29] were not expressed on plants infected with TEV-At17 while they were over-expressed on plants infected with the ancestral TEV, suggesting that the evolved virus acquired the ability to evade certain plant defense mechanisms, perhaps explaining the observed increase of viral load. Genes involved in basic cellular processes such as nucleic acid metabolism, translation and proteolysis were under-represented among down-regulated genes in SOMs B1 plus B2 ( Table 2 ), suggesting that the plant may be compensating for the consumption of these resources by an increased viral replication.