Table 1.
Differentially expressed ESTs identified in both libraries based on their enzyme codes.
Figure 1.
Gene Ontology categories uniquely identified in either EST collections using the AgriGO Singular Enrichment Analysis (SEA).
Processes identified only in fungus-inoculated tissue are considered up-regulated by fungal infection (grey bars) and processes identified only in mock-inoculated tissue are considered down-regulated (black bars). Statistical significance was detected with the Fisher’s exact test (p-value ≤0.05) and data points are indicated as Log10 of the p-value. (A) GO terms in the cellular component category. (B) GO terms in the cellular function category. GO terms in the biological processes category are indicated in Fig. S1.
Figure 2.
Gene Ontology categories identified in both EST collections using the AgriGO Singular Enrichment Analysis (SEA).
Data points represent the number of ESTs in each collection that was placed in each GO category. Statistical significance of the relative abundance of ESTs in each collection was detected with the Fisher’s exact test (* = p≤0.1, **p≤0.05).
Table 2.
Differentially expressed transcripts represented by ESTs identified in both libraries.
Figure 3.
Patterns of expression of differentially expressed genes in fungus-inoculated tissue (p≤0.05).
Expression of these genes in response to several other stresses was assessed through the publicly available microarray database, TAIR. Putative Arabidopsis orthologs of those bean genes were used to create a heat map obtained with the clustering tool of Genevestigator. Gene numbers in green and red colors indicate their down- or up-regulation in our study, respectively.
Figure 4.
Cellular function overview of proteins encoded by photosynthesis-related genes differentially expressed upon fungus attack.
Putative Arabidopsis orthologs of these genes (p≤0.05, Table 2) were used as input for Mapman analysis.
Figure 5.
Expression level of selected gene used to validate the bioinformatic analysis of the bean EST collection.
(A) Percentage of ESTs encoding the indicated protein in each EST collection obtained from mock- or fungus-inoculated tissue. Numbers on top of the bars indicate the p-value calculated with Fisher’s exact test. (B) Relative expression of the same genes assessed by RT-qPCR. Statistical significance was detected with the Student’s t-test in (*** = p<0.001).
Figure 6.
A model of the bean innate immune system.
The proposed model represents key molecular components and metabolic processes known to be involved in plant-pathogen interactions based on KEGG, for which bean orthologs have been identified in our EST collection with significant statistical support (p≤0.05). Gene Ontology (GO) categories and Enzyme Codes (EC) inside boxes are differentially represented in the bean EST libraries (arrowheads pointing down represent down-regulation and arrowheads pointing up represent up-regulation). Continuous arrows represent established relationship between components of the pathway and intermittent arrows represent undirected relationship. Components of PAMP-triggered immunity (PTI) are depicted to the right of the diagram.