Table 1.
Summary of Illumina sequencing and transcriptome assemblies for RNA-Seq libraries.
Fig 1.
Correlation between qRT-PCR and RNA-Seq.
The X-axis represents the log2 fold change of RNA-Seq. The Y-axis indicates the log2 value of fold change from qRT-PCR. Different colors represent different time points. The size of each point is proportional to the log2 (FPKM) in 0 DPI.
Fig 2.
Validation of 24 randomly selected genes through qRT-PCR.
Fold changes of the transcript levels at different time points are shown. The average expression level at 0 DPI was set to 1. Error bars represent standard error from three independent experimental replicates.
Fig 3.
Most represented patterns of time-course data for DEGs.
Unigene expression profiles are clustered using the Short Time-series Expression Minor program. The y-axes represent expression level and the x-axes represent different stages after C. destructans infection. A) Expression increased at 0.25 DPI relative to the 0 DPI. In the middle stage, the expression of part genes decreased and then slightly increased at 7 DPI. B) The expression pattern of most of the unigenes rapidly increased at 0.5 DPI relative to the 0 and 0.25 DPI, and then decreased at 4 DPI. At 7 DPI there were slightly increased. C) The expression of part down-regulated unigenes decreased at 0.25 DPI and then remained at low level from 0.5 DPI to 4 DPI. At last two stages the unigenes sharply increased at 7 DPI and sharply decreased at 12 DPI. D) The expression of the down-regulated unigenes sharply decreased at 0.5 DPI relative to the 0 DPI, then other stage maintained relative stable expression.
Fig 4.
Significant enrichment functional groups of DEGs.
The most significant GO terms (P < 0.05) of differentially expressed unigenes are graphically presented by comparing with total transcripts. The x-axis represents log10 of the enrichment P value. The y-axis indicates the number of unigenes in log2 value. The size of each point is proportional to the percentage (DEG associated with GO terms/All unigenes associated with GO terms).
Table 2.
The number of up- and down-regulated DEGs based on pair-wise comparison with control (fold change > 3; P < 0.001).
Fig 5.
Most represented patterns of time-course data for other comparisions.
The y-axes represent Z-score and the x-axes represent different stages after C. destructans infection.
Table 3.
Summary of comparisions among all the time points (fold change > 3; P < 0.001).
Fig 6.
Expression profiles of six randomly selected RGs through qRT-PCR.
Fold changes of the transcript levels at different time points are shown. The average expression level at 0 DPI was set to 1. Error bars represent standard error.
Fig 7.
Heatmap showing the FPKM values of up-regulated RGs.
The FPKM for the RGs in the control and six infected stages was used for hierarchical analysis. The heatmap shows the expression abundance of the RGs. The colors correspond to the value of FPKM, ranging from green (low expression) to red (high expression).
Fig 8.
Heatmap showing the FPKM values of uniquely expressed unigenes upon infection.
The FPKM for the uniquely expressed unigenes upon infection in the control and six infected stages was used for hierarchical analysis. The colors correspond to the value of FPKM, ranging from green (low expression) to red (high expression).
Fig 9.
Model of C. destructans infection in the effector-triggered immunity, phytohormones, reactive oxygen species and ginsenoside biosynthetic pathway.