The transcriptomics of an experimentally evolved plant-virus interaction.
Models of plant-virus interaction assume that the ability of a virus to infect a host genotype depends on the matching between virulence and resistance genes. Recently, we evolved tobacco etch potyvirus (TEV) lineages on different ecotypes of Arabidopsis thaliana, and found that some ecotypes selected for specialist viruses whereas others selected for generalists. Here we sought to evaluate the transcriptomic basis of such relationships. We have characterized the transcriptomic responses of five ecotypes infected with the ancestral and evolved viruses. Genes and functional categories differentially expressed by plants infected with local TEV isolates were identified, showing heterogeneous responses among ecotypes, although significant parallelism existed among lineages evolved in the same ecotype. Although genes involved in immune responses were altered upon infection, other functional groups were also pervasively over-represented, suggesting that plant resistance genes were not the only drivers of viral adaptation. Finally, the transcriptomic consequences of infection with the generalist and specialist lineages were compared. Whilst the generalist induced very similar perturbations in the transcriptomes of the different ecotypes, the perturbations induced by the specialist were divergent. Plant defense mechanisms were activated when the infecting virus was specialist but they were down-regulated when infecting with generalist.
Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022 València, Spain.
Julia
J
Hillung
Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Eduardo Primo Yúfera 3, 46012 València, Spain.
Francisco
F
García-García
Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Eduardo Primo Yúfera 3, 46012 València, Spain.|Bioinformatics of Rare Diseases (BIER), CIBER de Enfermedades Raras (CIBERER), 46012 València, Spain.|Functional Genomics Node, INB at CIPF, 46012 València, Spain.
Joaquín
J
Dopazo
Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022 València, Spain.
José M
JM
Cuevas
Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022 València, Spain.|The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe NM 87501, USA.
Santiago F
SF
Elena
D017360:Arabidopsis / Q000235:genetics / Q000276:immunology* / Q000821:virology*; D060146:Ecotype; D020869:Gene Expression Profiling; D054884:Host-Pathogen Interactions; D017800:Potyvirus / Q000235:genetics / Q000276:immunology* / Q000472:pathogenicity*