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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 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.
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pone.0136736.g005: 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.

Mentions: Many up-regulated genes were involved in the cell wall (GO:0005618), plasma membrane (GO:0005886), and vacuole (GO:0005773) (Fig 5). The 276 genes related to the plasma membrane were up-regulated only at 3 dpi, while transcripts of 121 vacuolar genes accumulated only at 15 dpi. Furthermore, transcripts for 130 cell wall-related genes accumulated at 3 dpi and those for 111 cell wall-related genes accumulated at 15 dpi. In contrast, GO terms associated with thylakoids (GO:0009579), ribosomes (GO:0005840), and plastids (GO:0009536) were enriched with down-regulated genes. Plastid- and ribosome-associated genes were specifically up-regulated at 3 dpi while thylakoid-associated genes were down-regulated at 3 dpi and 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 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.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0136736.g005: 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.
Mentions: Many up-regulated genes were involved in the cell wall (GO:0005618), plasma membrane (GO:0005886), and vacuole (GO:0005773) (Fig 5). The 276 genes related to the plasma membrane were up-regulated only at 3 dpi, while transcripts of 121 vacuolar genes accumulated only at 15 dpi. Furthermore, transcripts for 130 cell wall-related genes accumulated at 3 dpi and those for 111 cell wall-related genes accumulated at 15 dpi. In contrast, GO terms associated with thylakoids (GO:0009579), ribosomes (GO:0005840), and plastids (GO:0009536) were enriched with down-regulated genes. Plastid- and ribosome-associated genes were specifically up-regulated at 3 dpi while thylakoid-associated genes were down-regulated at 3 dpi and 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