Microarrays derived from Solanum tuberosum expressed sequence tags were used to test the hypothesis that genetically distinct enveloped viruses elicit unique changes in Nicotiana benthamiana gene expression. The results of our study, which included Sonchus yellow net virus (SYNV), a plant rhabdovirus that replicates in the nucleus of infected cells, and Impatiens necrotic spot virus (INSV), a plant bunyavirus that replicates in the cytoplasm, were consistent with this hypothesis. Statistically significant changes (P< or =0.01) in the expression of 275, 2646 and 4165 genes were detected in response to INSV at 2, 4 and 5 days post-inoculation (d.p.i.), respectively. In contrast, 35, 665 and 1458 genes were expressed differentially in response to SYNV at 5, 11 and 14 d.p.i., respectively. The microarray results were verified by Northern hybridization using a subset of these genes as probes. Notably, INSV, but not SYNV, induced expression of small heat-shock protein genes to high levels. In contrast to SYNV, infection by INSV resulted in downregulation of all histone genes, of which the downregulation of histone 2b expression to very low levels was confirmed by Northern hybridization. The expression of a putative WRKY transcription factor at 11 d.p.i., but not at 5 or 14 d.p.i., in SYNV-infected tissue suggested that the temporal response to virus infection was identified readily using our experimental design. Overall, infection by INSV resulted in larger fold changes in host gene expression relative to infection by SYNV. Taken together, the present data demonstrate differential responses of a common host to two genetically distinct viruses.