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Genome-wide transcriptomic analysis reveals correlation between higher WRKY61 expression and reduced symptom severity in Turnip crinkle virus infected Arabidopsis thaliana.

Gao R, Liu P, Yong Y, Wong SM - Sci Rep (2016)

Bottom Line: Fifteen genes (including upregulated, unchanged and downregulated) were selected for RNA-seq data validation using quantitative real-time PCR, which showed consistencies between these two sets of data.GO enrichment analysis showed that numerous terms such as stress, immunity, defence and chemical stimulus were affected in TCV-infected plants.One putative plant defence related gene named WRKY61 was selected for further investigation.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, National University of Singapore, Singapore.

ABSTRACT
Turnip crinkle virus (TCV) is a carmovirus that infects many Arabidopsis ecotypes. Most studies mainly focused on discovery of resistance genes against TCV infection, and there is no Next Generation Sequencing based comparative genome wide transcriptome analysis reported. In this study, RNA-seq based transcriptome analysis revealed that 238 (155 up-regulated and 83 down-regulated) significant differentially expressed genes with at least 15-fold change were determined. Fifteen genes (including upregulated, unchanged and downregulated) were selected for RNA-seq data validation using quantitative real-time PCR, which showed consistencies between these two sets of data. GO enrichment analysis showed that numerous terms such as stress, immunity, defence and chemical stimulus were affected in TCV-infected plants. One putative plant defence related gene named WRKY61 was selected for further investigation. It showed that WRKY61 overexpression plants displayed reduced symptoms and less virus accumulation, as compared to wild type (WT) and WRKY61 deficient lines, suggesting that higher WRKY61 expression level reduced TCV viral accumulation. In conclusion, our transcriptome analysis showed that global gene expression was detected in TCV-infected Arabidopsis thaliana. WRKY61 gene was shown to be negatively correlated with TCV infection and viral symptoms, which may be connected to plant immunity pathways.

No MeSH data available.


Related in: MedlinePlus

Gene ontology (GO) enrichment analysis of DEGs which were significantly affected (up- and down- regulated >15 FC) by TCV infection.(a) Fraction distribution of DEGs related GO terms based on molecular function, biological process, and cellular component. (b) Interactive graph of biological process of 238 DEGs which are involved in the TCV infection. The size and red colour density of the circles are proportional to the number of genes associated with the specific term. The interactive network were summarized and plotted following published REVIGO protocol (http://revigo.irb.hr).
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f2: Gene ontology (GO) enrichment analysis of DEGs which were significantly affected (up- and down- regulated >15 FC) by TCV infection.(a) Fraction distribution of DEGs related GO terms based on molecular function, biological process, and cellular component. (b) Interactive graph of biological process of 238 DEGs which are involved in the TCV infection. The size and red colour density of the circles are proportional to the number of genes associated with the specific term. The interactive network were summarized and plotted following published REVIGO protocol (http://revigo.irb.hr).

Mentions: The differentially expressed 238 genes with at least 15-FC were used to carry out GO enrichment analysis. There are approximately 1389 GO terms were assigned, and the fraction percentages for biological process (1297), cellular component (49) and molecular function (43) were 93.38%, 3.53% and 3.10% respectively (Fig. 2a). Of 1297 terms in the biological process, there were 207 terms, such as immune system process (19), response to stress (50), defense response (47), immune response (17), innate immune response (17), response to biotic stimulus (27), systemic acquired resistance (14), regulation of immune system process and regulation of innate immune response (16) and regulation of immune response (8) were directly related to plant immunity after TCV infection. The full list of the GO terms for these three fractions (biological process, cellular component and molecular function) was shown in Supplementary Table S3. In order to display the correlations of the interesting biological process GO terms, their interactive graph was shown in Fig. 2b. It displayed some key GO terms such as stress, immune response, defence response and chemical stimulus which played critical roles in the network regulation of differentially expressed GO terms, indicating that intricate regulation relationship could be present in TCV-host interaction and plant virus infection may also simultaneously influence other abiotic stress pathways in plants.


Genome-wide transcriptomic analysis reveals correlation between higher WRKY61 expression and reduced symptom severity in Turnip crinkle virus infected Arabidopsis thaliana.

Gao R, Liu P, Yong Y, Wong SM - Sci Rep (2016)

Gene ontology (GO) enrichment analysis of DEGs which were significantly affected (up- and down- regulated >15 FC) by TCV infection.(a) Fraction distribution of DEGs related GO terms based on molecular function, biological process, and cellular component. (b) Interactive graph of biological process of 238 DEGs which are involved in the TCV infection. The size and red colour density of the circles are proportional to the number of genes associated with the specific term. The interactive network were summarized and plotted following published REVIGO protocol (http://revigo.irb.hr).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4834565&req=5

f2: Gene ontology (GO) enrichment analysis of DEGs which were significantly affected (up- and down- regulated >15 FC) by TCV infection.(a) Fraction distribution of DEGs related GO terms based on molecular function, biological process, and cellular component. (b) Interactive graph of biological process of 238 DEGs which are involved in the TCV infection. The size and red colour density of the circles are proportional to the number of genes associated with the specific term. The interactive network were summarized and plotted following published REVIGO protocol (http://revigo.irb.hr).
Mentions: The differentially expressed 238 genes with at least 15-FC were used to carry out GO enrichment analysis. There are approximately 1389 GO terms were assigned, and the fraction percentages for biological process (1297), cellular component (49) and molecular function (43) were 93.38%, 3.53% and 3.10% respectively (Fig. 2a). Of 1297 terms in the biological process, there were 207 terms, such as immune system process (19), response to stress (50), defense response (47), immune response (17), innate immune response (17), response to biotic stimulus (27), systemic acquired resistance (14), regulation of immune system process and regulation of innate immune response (16) and regulation of immune response (8) were directly related to plant immunity after TCV infection. The full list of the GO terms for these three fractions (biological process, cellular component and molecular function) was shown in Supplementary Table S3. In order to display the correlations of the interesting biological process GO terms, their interactive graph was shown in Fig. 2b. It displayed some key GO terms such as stress, immune response, defence response and chemical stimulus which played critical roles in the network regulation of differentially expressed GO terms, indicating that intricate regulation relationship could be present in TCV-host interaction and plant virus infection may also simultaneously influence other abiotic stress pathways in plants.

Bottom Line: Fifteen genes (including upregulated, unchanged and downregulated) were selected for RNA-seq data validation using quantitative real-time PCR, which showed consistencies between these two sets of data.GO enrichment analysis showed that numerous terms such as stress, immunity, defence and chemical stimulus were affected in TCV-infected plants.One putative plant defence related gene named WRKY61 was selected for further investigation.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, National University of Singapore, Singapore.

ABSTRACT
Turnip crinkle virus (TCV) is a carmovirus that infects many Arabidopsis ecotypes. Most studies mainly focused on discovery of resistance genes against TCV infection, and there is no Next Generation Sequencing based comparative genome wide transcriptome analysis reported. In this study, RNA-seq based transcriptome analysis revealed that 238 (155 up-regulated and 83 down-regulated) significant differentially expressed genes with at least 15-fold change were determined. Fifteen genes (including upregulated, unchanged and downregulated) were selected for RNA-seq data validation using quantitative real-time PCR, which showed consistencies between these two sets of data. GO enrichment analysis showed that numerous terms such as stress, immunity, defence and chemical stimulus were affected in TCV-infected plants. One putative plant defence related gene named WRKY61 was selected for further investigation. It showed that WRKY61 overexpression plants displayed reduced symptoms and less virus accumulation, as compared to wild type (WT) and WRKY61 deficient lines, suggesting that higher WRKY61 expression level reduced TCV viral accumulation. In conclusion, our transcriptome analysis showed that global gene expression was detected in TCV-infected Arabidopsis thaliana. WRKY61 gene was shown to be negatively correlated with TCV infection and viral symptoms, which may be connected to plant immunity pathways.

No MeSH data available.


Related in: MedlinePlus