Fig 1.
Symptoms on inoculated leaves of C. annuum following CaCV infection 4 days after mechanical inoculation.
CaCV-resistant line showing coalescing necrotic lesions (A) and susceptible line without visible symptoms (B).
Fig 2.
Gene ontology categories of differentially expressed genes in C. annuum in response to CaCV infection.
The number and percentage of up- or down-regulated genes in CaCV resistant line classified into three major domains were plotted using WEGO tool. Significant relationship (p< 0.05) between up- and down-regulated genes indicated with ‘*’.
Table 1.
List of most highly up-regulated DE (log2-fold > 3.0, FPKM >300) putative defense-related genes in CaCV-resistant C. annuum x C. chinense in comparison to CaCV-susceptible C. annuum.
Fig 3.
Validation of RNA-Seq gene expression by real-time quantitative PCR (qPCR).
FPKM (fragments per kilobase of exon per million fragments mapped) values obtained by RNA-Seq analysis and relative expression levels obtained by qPCR for 15 selected genes in CaCV resistant (R) and susceptible (S) Capsicum annuum plants inoculated with capsicum chlorosis virus are shown. Error bars represent the standard error for three biological replicates. Putative resistance genes are consecutively numbered 1–12; PR, pathogenesis-related.
Table 2.
Comparison of transcript fold change as detected by RNA-Seq and qPCR.