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Open Access Highly Accessed Research article

Altered gene expression changes in Arabidopsis leaf tissues and protoplasts in response to Plum pox virus infection

Mohan Babu13, Jonathan S Griffiths124, Tyng-Shyan Huang12 and Aiming Wang12*

Author Affiliations

1 Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, 1391 Sandford St., London, Ontario, N5V 4T3, Canada

2 Department of Biology, The University of Western Ontario, Biological & Geological Building, 1151 Richmond St., London, Ontario, N6A 5B7, Canada

3 Department of Molecular Genetics, The University of Toronto, M5S 1A8, Canada

4 Department of Botany, The University of British Columbia, Vancouver, V6T 1Z4, Canada

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BMC Genomics 2008, 9:325  doi:10.1186/1471-2164-9-325

Published: 9 July 2008

Additional files

Additional file 1:

Supplemental Table 1. Expression levels of genes induced in PPV-infected Arabidopsis leaf tissues 17 days post inoculation.

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Additional file 2:

Supplemental Table 2. Expression levels of genes repressed in PPV-infected Arabidopsis leaf tissues 17 days post inoculation.

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Additional file 3:

Supplemental Table 3. Expression levels of differentially regulated genes in PPV-infected Arabidopsis protoplasts.

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Additional file 4:

Supplemental Table 4. Expression levels of common genes induced in PPV-infected Arabidopsis protoplasts and in infected leaf tissues.

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Additional file 5:

Supplemental Table 5. Expression levels of common genes repressed in PPV-infected Arabidopsis protoplasts and in infected leaf tissues.

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Additional file 6:

Supplemental Figure 1. Hierarchical clustering of common genes that were significantly differentially regulated by PPV in infected leaf tissues and in transfected protoplast cells. Expression levels are color-coded with red indicating upregulation by pPPV-SK68; green indicating downregulation by pPPV-SK68 and black indicating no change in expression. The intensity of color represents the degree of gene expression levels. The putative function of each gene is shown on the right side of the cluster.

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Additional file 7:

Supplemental Figure 2. K-means profiling of gene expression using 411 Arabidopsis genes differentially regulated by PPV in transfected protoplasts at three different time points. The expression profiles were grouped into twelve distinct cluster groups. The AGI locus identifier of each gene differentially regulated by PPV in the transfected protoplasts at different time points in each cluster group is shown on the right side of the cluster. Values on the y-axis indicate the relative expression level of the gene, while the x-axis represents hours post transfection. Number of genes belonging to each cluster is shown in the cluster inset.

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Additional file 8:

Supplemental Table 6. Gene expression profiles of Arabidopsis genes differentially regulated by PPV infectious clone in transfected protoplasts belonging to twelve distinct cluster groups.

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Additional file 9:

Supplemental Table 7. Identification of Prunus persica orthologs to Arabidopsis genes induced by PPV infection in the leaf tissues at 17 days post inoculation.

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Additional file 10:

Supplemental Table 8. Cross comparison of genes significantly differentially regulated by PPV (≥ 2.5- or ≤ -2.5-fold) in this study with the Arabidopsis genes regulated by other positive sense RNA viruses.

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Additional file 11:

Supplemental Figure 3. Confirmation of microarray data by sqRT-PCR and Northern hybridizations. Panel A shows confirmation of microarray data using sqRT-PCR for genes induced in PPV-infected Arabidopsis protoplasts. Panel B shows confirmation of microarray data using sqRT-PCR (left panel) and Northern hybridizations (right panel) for Arabidopsis genes differentially regulated in PPV-infected protoplasts and in PPV-infected leaves. Probes for sqRT-PCR and Northern hybridizations were generated by PCR amplification of Arabidopsis cDNA using gene specific primers shown in Table 3. sqRT-PCR of the constitutively expressed Actin 2 gene (At3g18780) was used as a loading control. pPPV-SK68, a PPV infectious cDNA clone used to transfect protoplasts; pPPV-SK68Δ, a mutant non-infectious clone of pPPV-SK68 was used as a control; hpt, hours post transfection.

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