Fig 1.
Summary of pair-end sequenced data and the number of expressed rice genes as determined by RNA-Seq for rice plants that were infected with RSV or not infected (mock).
Data were collected 3, 7, and 15 days post-infection (dpi). (A) The average coverage of pair-end sequenced RNA-Seq data obtained from each sample. Mock and RSV indicate rice plants that were exposed to non-viruliferous SBPH (green bars) and viruliferous SBPH (orange bars), respectively. (B) The distribution of fold-changes in expression at each time point by comparing RSV to Mock. Genes were divided into five groups: not expressed (gray), down-regulated with < 2-fold change (green); down-regulated with > 2- fold change (dark green); up-regulated with < 2-fold change (orange); and up-regulated with > 2-fold change (red). (C) Ratio versus intensity (R-I) scatter plot of RNA-Seq. X and Y axes represent log2-converted Mock*RSV and Mock/RSV values.
Table 1.
Number of trimmed reads, mapped reads, and mapped nucleotides obtained by an RNA-Seq analysis of rice plants that were infected or not infected (mock).
Data were collected 3, 7, and 15 days post-infection (dpi).
Fig 2.
The number of differentially expressed genes (DEGs) in rice in response to RSV infection.
Data were collected 3, 7, and 15 days post-infection (dpi). (A) Venn diagram displaying the distribution of DEGs (genes with > 2-fold change in expression) at each time point. Total indicates the total number of both up-regulated and down-regulated DEGs while Down and Up indicate the number of down-regulated and up-regulated DEGs, respectively. (B) The functional classification of DEGs commonly identified at each time point. A total of 532 genes were differentially expressed at all three time points, while 104 and 109 genes were down-regulated and up-regulated, respectively, at all three time points. The DEGs were manually assigned to 11 functional categories. (C) Hierarchical clustering according to changes in expression over time of the 532 genes that were expressed at all three time points. Cluster analysis was performed with the Genesis program [38].
Fig 3.
Number of identified GO terms at each time point by GO enrichment analysis.
(A) The number of enriched GO terms at each time point. To identify enriched GO terms at each time point, the DEGs at each time point were divided into up-regulated and down-regulated groups. Green and red bars indicate groups of down- and up-regulated genes, respectively. Venn diagrams illustrate the distribution of enriched GO terms for the down-regulated DEGs (B) and up-regulated DEGs (C) at each time point.
Fig 4.
Identified enriched GO terms associated with biological process.
GO directed acyclic hierarchical graph (DAG) shows the structural networks of identified GO terms according to biological process. Green and red colors indicate down- and up-regulation, respectively, at each time point, and the number represents the number of DEGs associated with the given GO term. The dashed rectangles represent GO terms that are not significant.
Fig 5.
Identified enriched GO terms associated with cellular component.
GO directed acyclic hierarchical graph (DAG) shows the structural networks of identified GO terms according to biological process. Green and red indicate down- and up-regulation, respectively, at each time point, and the number represents the number of DEGs associated with the given GO term. The rectangles formed with broken lines represent GO terms that were not significant.
Fig 6.
Identification of TFs that were differentially expressed in response to RSV infection.
(A) The distribution of fold-changes in expression of TFs at each time point in response to RSV infection. Genes were divided into five groups: not expressed (gray); down-regulated with < 2-fold change (green); down-regulated with > 2-fold change (dark green); up-regulated with < 2-fold change (orange); and up-regulated with > 2-fold change (red). (B) The number of differentially expressed TFs according to the 11 representative TF families at each time point. When the number of differentially up-regulated genes was greater than the number of down-regulated genes, red was used. In the opposite case, green was used.
Fig 7.
Expression of rice genes associated with transposon elements, receptor-like kinases, and NBS-LRR proteins in response to RSV infection.
(A) Expression of genes related to transposon elements (TEs). A total of 17,271 TEs were selected based on the rice genome annotation project. Genes were divided into five groups: not expressed (gray); down-regulated with < 2-fold change (green color); down-regulated with > 2-fold change (dark green color); up-regulated with < 2-fold change (orange color); and up-regulated with > 2-fold change (red color). (B) Expression of genes encoding receptor-like kinases. A total of 1,070 receptor-like kinases belonging to 50 families were selected based on a previous study [39]. (C) The number of expressed NBS-LRR genes on each rice chromosome. A total of 405 rice genes that contained an NBS-LRR domain were selected. The bar graph indicates the number of expressed NBS-LRR genes on each chromosome.
Table 2.
Comparison of DEGs between RNA-Seq and microarray studies.
We compared the number of DEGs between RNA-Seq (this study) and microarray [8]. Up, down, and common indicate up-regulated, down-regulated, and commonly identified DEGs, respectively. To identify commonly identified DEGs, DEGs at 3 dpi of RNA-Seq data was compared to those of microarray data at 3 dpi. DEGs at 7 dpi of RNA-Seq data were compared to those of microarray data at 6 dpi and 9 dpi. DEGs at 15 dpi of RNA-Seq data were compared to those of microarray data at 12 dpi.