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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

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.
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pone.0136736.g007: 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.

Mentions: In total, 17,271 genes were related to transposon elements (TEs) in the rice genome. We determined the number of TE-associated genes that were differentially expressed at each time point. Most TEs (54.6 to 59.9%) were not differentially expressed in response to RSV infection (Fig 7A). About 12.7 to 13.5% of TEs showed significant changes in gene expression in response to RSV. The number of down-regulated TEs was much higher than that of up-regulated genes. Amazingly, the number of down-regulated TEs gradually decreased (from 1818 to 1257 genes) while the number of up-regulated TEs increased (from 518 to 1017 genes) with increasing time after RSV inoculation.


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)

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.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4549299&req=5

pone.0136736.g007: 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.
Mentions: In total, 17,271 genes were related to transposon elements (TEs) in the rice genome. We determined the number of TE-associated genes that were differentially expressed at each time point. Most TEs (54.6 to 59.9%) were not differentially expressed in response to RSV infection (Fig 7A). About 12.7 to 13.5% of TEs showed significant changes in gene expression in response to RSV. The number of down-regulated TEs was much higher than that of up-regulated genes. Amazingly, the number of down-regulated TEs gradually decreased (from 1818 to 1257 genes) while the number of up-regulated TEs increased (from 518 to 1017 genes) with increasing time after RSV inoculation.

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