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Transcriptome analysis of symptomatic and recovered leaves of geminivirus-infected pepper (Capsicum annuum)

Elsa Góngora-Castillo1, Enrique Ibarra-Laclette2, Diana L Trejo-Saavedra1 and Rafael F Rivera-Bustamante1*

Author Affiliations

1 Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del I.P.N (Cinvestav)-Unidad Irapuato, Km 9.6 Libramiento Norte, Carretera Irapuato-León, Irapuato, Gto., 36821, México

2 Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Cinvestav-Irapuato, Km 9.6 Libramiento Norte, Carretera Irapuato-León, Irapuato, Gto., 36821, México

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Virology Journal 2012, 9:295  doi:10.1186/1743-422X-9-295

Published: 27 November 2012

Additional files

Additional file 1:

Correlation of aligned 454-reads to the Capsicum annuum Reference Transcriptome (CaRT) between different 454-runs from the recovered leaf cDNA library. The best fitting linear correlations for each pair-wise comparison was calculated (p < 2.26e-16): run1 vs. run2 (r2 = 0.9666), run1 vs. run3 (r2 = 0.9698) and run2 vs. run3 (r2 = 0.9703).

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Additional file 2:

Correlation of aligned 454-reads to the Capsicum annuum Reference Transcriptome (CaRT) between different runs derived from the symptomatic leaf cDNA library. The best fitting linear correlations for each pair-wise comparison was calculated (p < 2.2e-16): run1 vs. run2 (r2 = 0.9657), run1 vs. run3 (r2 = 0.9644), run1 vs. run4 (r2 = 0.9705), run2 vs. run 3 (r2 = 0.9658), run2 vs. run5 (r2 = 0.9667), run3 vs. run5 (r2 = 0.9663). Low quality was observed on run4 and therefore it was discarded from the downstream analysis (data not shown).

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Additional file 3:

Table of differentially expressed genes with Fisher’s exact test p-values and fold-changes of pair-wise comparisons.

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Additional file 4:

Hierarchical clustering of differentially expressed genes identified in PepGMV-infected pepper plants. A total of 309 genes were identified (fold change of at least ± 2 and p-value ≤ 1.57e-06) and the ratio for each comparison (Symptomatic (S) vs. Mock (M); Recovered (R) vs. Mock; Recovered vs. Symptomatic) was used for the analysis. Clustering was performed using the Smooth correlation and average linkage clustering in GeneSpring GX 7.3.1 software (Agilent Technologies®). Green indicates down-regulated, red up-regulated and black unchanged values, as shown on the color scale at the side of the figure.

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Additional file 5:

Pearson’s coefficient of determination was obtained by log2 transformation of the computational predictions and qRT-PCR expression values.

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Additional file 6:

Table S1. Clusters of orthologous and paralogous genes families in S. lycopersicum, S. tuberosum and C. annuum species. Table S2. Clusters of orthologous and paralogous of differentially expressed genes in S. lycopersicum, S. tuberosum and C. annuum species. Predicted peptides from S. lycopersicum, S. tuberosum transcripts were clustered using OrthoMCL [55].

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Additional file 7:

List of primers used in qRT-PCR assays.

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