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Time-Course RNA-Seq Analysis Reveals Transcriptional Changes in Rice Plants Triggered by Rice stripe virus Infection.

Cho WK, Lian S, Kim SM, Seo BY, Jung JK, Kim KH - PLoS ONE (2015)

Bottom Line: The transcriptomes of RSV-infected samples were compared to those of mock-treated samples at 3, 7, and 15 days post-infection (dpi).Expression of genes associated with cell differentiation and flowering was significantly down-regulated in infected plants at 15 dpi.Taken together, we demonstrated that down-regulation of genes related to photosynthesis and flowering was strongly associated with disease symptoms caused by RSV and that up-regulation of genes involved in metabolic pathways, stress responses, and transcription was related to host defense mechanisms.

View Article: PubMed Central - PubMed

Affiliation: Department of Agricultural Biotechnology and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.

ABSTRACT
Rice stripe virus (RSV) has become a major pathogen of rice. To determine how the rice transcriptome is modified in response to RSV infection, we used RNA-Seq to perform a genome-wide gene expression analysis of a susceptible rice cultivar. The transcriptomes of RSV-infected samples were compared to those of mock-treated samples at 3, 7, and 15 days post-infection (dpi). From 8 to 11% of the genes were differentially expressed (>2-fold difference in expression) in RSV-infected vs. noninfected rice. Among them, 532 genes were differentially expressed at all three time points. Surprisingly, 37.6% of the 532 genes are related to transposons. Gene ontology enrichment analysis revealed that many chloroplast genes were down-regulated in infected plants at 3 and 15 dpi. Expression of genes associated with cell differentiation and flowering was significantly down-regulated in infected plants at 15 dpi. In contrast, most of the up-regulated genes in infected plants concern the cell wall, plasma membrane, and vacuole and are known to function in various metabolic pathways and stress responses. In addition, transcripts of diverse transcription factors gradually accumulated in infected plants with increasing infection time. We also confirmed that the expression of gene subsets (including NBS-LRR domain-containing genes, receptor-like kinase genes, and genes involving RNA silencing) was changed by RSV infection. Taken together, we demonstrated that down-regulation of genes related to photosynthesis and flowering was strongly associated with disease symptoms caused by RSV and that up-regulation of genes involved in metabolic pathways, stress responses, and transcription was related to host defense mechanisms.

No MeSH data available.


Related in: MedlinePlus

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.
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pone.0136736.g004: 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.

Mentions: Many down-regulated genes at 3 dpi were related to gene expression (GO:0010467), translation (GO:0006412), and photosynthesis (GO:0015979) (Fig 4). In the case of photosynthesis, 43 genes and 30 genes were down-regulated at 3 dpi and 15 dpi, respectively. Furthermore, GO terms for metabolic process (GO:0008152) and secondary metabolic process (GO:0019748) were overrepresented. In the case of metabolic process at 3 dpi and 15 dpi, 1,153 genes and 1,068 genes, respectively, were up-regulated whereas 739 genes and 685 genes, respectively, were down-regulated. It seems that transcripts for two distinct groups of metabolic genes were differently regulated by RSV infection. The number of up-regulated genes for secondary metabolic process was gradually reduced with increasing infection time. At 15 dpi, GO terms for cell communication (GO:0007154), cell differentiation (GO:0030154), pollination (GO:0009856), and flower development (GO:0009908) were significantly enriched (S1 Fig and S3–S6 Tables). Except for genes related to cell communication, genes belonging to the other three GO terms were strongly down-regulated at 15 dpi. Several stress-associated GO terms such as response to external stimulus (GO:0009605), response to abiotic stimulus (GO:0009628), response to biotic stimulus (GO:0009607), and response to endogenous stimulus (GO:0009719) were enriched both in up- and down-regulated genes (S2 Fig). In the case of the GO term for response to abiotic stimulus, 245 genes were up-regulated at 3 dpi whereas 126 genes and 124 genes were down-regulated at 7 dpi and 15 dpi, respectively. At all three time points, expression of genes required for response to biotic stimulus was strongly affected. For instance, 107 genes were highly up-regulated while 65 genes were down-regulated at 15 dpi. The number of up-regulated genes for various stress responses was always higher than that of down-regulated genes at each time point. In addition, 132 genes associated with transport (GO:0006810) were down-regulated specifically at 15 dpi.


Time-Course RNA-Seq Analysis Reveals Transcriptional Changes in Rice Plants Triggered by Rice stripe virus Infection.

Cho WK, Lian S, Kim SM, Seo BY, Jung JK, Kim KH - PLoS ONE (2015)

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.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4549299&req=5

pone.0136736.g004: 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.
Mentions: Many down-regulated genes at 3 dpi were related to gene expression (GO:0010467), translation (GO:0006412), and photosynthesis (GO:0015979) (Fig 4). In the case of photosynthesis, 43 genes and 30 genes were down-regulated at 3 dpi and 15 dpi, respectively. Furthermore, GO terms for metabolic process (GO:0008152) and secondary metabolic process (GO:0019748) were overrepresented. In the case of metabolic process at 3 dpi and 15 dpi, 1,153 genes and 1,068 genes, respectively, were up-regulated whereas 739 genes and 685 genes, respectively, were down-regulated. It seems that transcripts for two distinct groups of metabolic genes were differently regulated by RSV infection. The number of up-regulated genes for secondary metabolic process was gradually reduced with increasing infection time. At 15 dpi, GO terms for cell communication (GO:0007154), cell differentiation (GO:0030154), pollination (GO:0009856), and flower development (GO:0009908) were significantly enriched (S1 Fig and S3–S6 Tables). Except for genes related to cell communication, genes belonging to the other three GO terms were strongly down-regulated at 15 dpi. Several stress-associated GO terms such as response to external stimulus (GO:0009605), response to abiotic stimulus (GO:0009628), response to biotic stimulus (GO:0009607), and response to endogenous stimulus (GO:0009719) were enriched both in up- and down-regulated genes (S2 Fig). In the case of the GO term for response to abiotic stimulus, 245 genes were up-regulated at 3 dpi whereas 126 genes and 124 genes were down-regulated at 7 dpi and 15 dpi, respectively. At all three time points, expression of genes required for response to biotic stimulus was strongly affected. For instance, 107 genes were highly up-regulated while 65 genes were down-regulated at 15 dpi. The number of up-regulated genes for various stress responses was always higher than that of down-regulated genes at each time point. In addition, 132 genes associated with transport (GO:0006810) were down-regulated specifically at 15 dpi.

Bottom Line: The transcriptomes of RSV-infected samples were compared to those of mock-treated samples at 3, 7, and 15 days post-infection (dpi).Expression of genes associated with cell differentiation and flowering was significantly down-regulated in infected plants at 15 dpi.Taken together, we demonstrated that down-regulation of genes related to photosynthesis and flowering was strongly associated with disease symptoms caused by RSV and that up-regulation of genes involved in metabolic pathways, stress responses, and transcription was related to host defense mechanisms.

View Article: PubMed Central - PubMed

Affiliation: Department of Agricultural Biotechnology and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.

ABSTRACT
Rice stripe virus (RSV) has become a major pathogen of rice. To determine how the rice transcriptome is modified in response to RSV infection, we used RNA-Seq to perform a genome-wide gene expression analysis of a susceptible rice cultivar. The transcriptomes of RSV-infected samples were compared to those of mock-treated samples at 3, 7, and 15 days post-infection (dpi). From 8 to 11% of the genes were differentially expressed (>2-fold difference in expression) in RSV-infected vs. noninfected rice. Among them, 532 genes were differentially expressed at all three time points. Surprisingly, 37.6% of the 532 genes are related to transposons. Gene ontology enrichment analysis revealed that many chloroplast genes were down-regulated in infected plants at 3 and 15 dpi. Expression of genes associated with cell differentiation and flowering was significantly down-regulated in infected plants at 15 dpi. In contrast, most of the up-regulated genes in infected plants concern the cell wall, plasma membrane, and vacuole and are known to function in various metabolic pathways and stress responses. In addition, transcripts of diverse transcription factors gradually accumulated in infected plants with increasing infection time. We also confirmed that the expression of gene subsets (including NBS-LRR domain-containing genes, receptor-like kinase genes, and genes involving RNA silencing) was changed by RSV infection. Taken together, we demonstrated that down-regulation of genes related to photosynthesis and flowering was strongly associated with disease symptoms caused by RSV and that up-regulation of genes involved in metabolic pathways, stress responses, and transcription was related to host defense mechanisms.

No MeSH data available.


Related in: MedlinePlus