Figure 1.
Comparison of tomato differentially regulated genes during interaction with Fusarium oxysporum f. sp. lycopersici (Fol) and Tomato Mosaic Virus (ToMV) at 2 DPI post-inoculation.
A, Venn diagram of differentially expressed genes in Fol and ToMV tomato incompatible interactions. B, Histogram of up regulated and down regulate genes in tomato-Fol interaction and tomato-ToMV interaction.
Figure 2.
Heatmap of Gene Ontology enriched terms in the two interactions.
Gene Ontology terms enriched are obtained comparing a differential group (differentially regulated genes in each interaction) whit a reference group (all gene of chip) using Fisher’s Exact Test, with Multiple Testing Correction of FDR, estimated at P value of <0.05. A, The rows of heatmap represent GO-terms and the columns represent samples. Each cell is colorized based on the number of genes associated with that category GO in that particular sample. B, Subclusters composed of specific GO-terms of the tomato-pathogen interactions. The green boxes highlight specific GO terms of tomato-Fol interaction, the red boxes specific GO terms of tomato-ToMV interaction.
Figure 3.
The interactive graph-based enriched gene-ontology (A) in fungus-tomato interaction and (B) in virus-tomato interaction.
Table 1.
List of abscisic acid receptors, auxin response factors (ARFs) and auxin response genes up-regulated in the tomato-Fol interaction.
Table 2.
List of the GO-terms involved in the photosynthetic process during the tomato-ToMV interaction.
Table 3.
List of up-regulated pathogenesis-related proteins involved in tomato-ToMV interaction.
Table 4.
List of genes involved in carbon fixation differentially expressed during the tomato-ToMV interaction.
Table 5.
List of the gibberellin modulated genes, up-regulated in tomato-ToMV interaction.
Figure 4.
Physical genome locations of tomato (Solanum lycopersicum) differentially regulated genes.
A, Physical map of the tomato-Fol interaction. B, Physical map of the tomato-ToMV interaction. Tomato chromosomes are represented as black horizontal bars, the approximate location of each gene is designated with vertical lines on chromosomes. The color used for each gene indicates specificity (red: differentially regulated genes in tomato-fungus interaction, blue: differentially regulated genes in tomato-virus interaction, green: overlapping differentially regulated genes. The cyan boxes on chromosomes 9 and 11 indicates the chromosomal regions in the vicinity of the Tm2(2) and I2 genes. The violet boxes on chromosomes 8, 10 and 12 indicates the richest regions of genes.
Figure 5.
Distribution of chromosome location of under-expressed genes.
The x-axis in each panel represents the range of the corresponding chromosome. The location of each differentially regulated genes in each chromosome is represented as a vertical lines at the midpoint of the location of the corresponding base pairs. The distribution of the location of all the coding genes spotted on the microarray is used as a reference and is drawn in red. The orange line represents the distribution of under-expressed genes in tomato-ToMV interaction. The green line represents the distribution of under-expressed genes in tomato-Fol interaction.
Figure 6.
Distribution of chromosome location of over-expressed genes.
The x-axis in each panel represents the range of the corresponding chromosome. The location of each differentially regulated genes in each chromosome is represented as a vertical lines at the midpoint of the location of the corresponding base pairs. The distribution of the location of all the coding genes spotted on the microarray is used as a reference and is drawn in red. The orange line represents the distribution of under-expressed genes in tomato-ToMV interaction. The green line represents the distribution of under-expressed genes in tomato-Fol interaction.
Figure 7.
Physical map of specific differentially regulated genes in tomato-ToMV and tomato-Fol interactions.
Tomato chromosomes are represented as brown horizontal bars, the approximate location of each gene is designated with vertical lines on each chromosome. The color used for each gene indicates specificity (red: differentially regulated genes in tomato-fungus interaction blue: differentially regulated genes in tomato-virus interaction, green: overlapping expressed genes in opposite direction.
Figure 8.
Comparison of differentially regulated tomato pathogen recognition genes during interaction with Fusarium oxysporum (Fol) and Tomato Mosaic Virus (ToMV).
Histograms display the differentially regulated pathogen recognition genes for each structural class (NL: NB-ARC-LRR proteins RLP Like Proteins; RLK Receptor-Like Kinases; Unknown: genes that encode novel domain associations or single domains) during the two incompatible interactions.