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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

Validation of RNA-seq data using qRT-PCR.Two internal controls (a) CBP20 and (b) tubulin genes were used to validate the RNA-Seq data. Fold changes of gene expression detected by RNA-seq were plotted against the data of qRT-PCR. The reference line indicates the linear relationship between the results of RNA-seq and qRT-PCR analyses.
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f3: Validation of RNA-seq data using qRT-PCR.Two internal controls (a) CBP20 and (b) tubulin genes were used to validate the RNA-Seq data. Fold changes of gene expression detected by RNA-seq were plotted against the data of qRT-PCR. The reference line indicates the linear relationship between the results of RNA-seq and qRT-PCR analyses.

Mentions: In order to validate the data from RNA-seq analysis, among all the 238 DEGs, five genes were randomly selected from the top 20 most significantly upregulated or downregulated genes, respectively (Supplementary Table S2). Five genes were randomly selected from the non-significant changed gene category (Supplementary Table S1). In total, fifteen genes (five upregulated, five with no significant changes and five down-regulated) were randomly selected for expression analysis by qRT-PCR. The expression data for these selected genes between RNA-seq and qRT-PCR data were shown in Supplementary Table S4. In general, there is a strong correlation between these two sets of data, which was shown by a linear relationship for the gene expression (both CBP20 and tubulin were used as internal controls) (Fig. 3), suggesting the qRT-PCR and RNA-seq data exhibited decent agreement in all of the randomly selected upregulated, normal expression and downregulated genes.


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)

Validation of RNA-seq data using qRT-PCR.Two internal controls (a) CBP20 and (b) tubulin genes were used to validate the RNA-Seq data. Fold changes of gene expression detected by RNA-seq were plotted against the data of qRT-PCR. The reference line indicates the linear relationship between the results of RNA-seq and qRT-PCR analyses.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f3: Validation of RNA-seq data using qRT-PCR.Two internal controls (a) CBP20 and (b) tubulin genes were used to validate the RNA-Seq data. Fold changes of gene expression detected by RNA-seq were plotted against the data of qRT-PCR. The reference line indicates the linear relationship between the results of RNA-seq and qRT-PCR analyses.
Mentions: In order to validate the data from RNA-seq analysis, among all the 238 DEGs, five genes were randomly selected from the top 20 most significantly upregulated or downregulated genes, respectively (Supplementary Table S2). Five genes were randomly selected from the non-significant changed gene category (Supplementary Table S1). In total, fifteen genes (five upregulated, five with no significant changes and five down-regulated) were randomly selected for expression analysis by qRT-PCR. The expression data for these selected genes between RNA-seq and qRT-PCR data were shown in Supplementary Table S4. In general, there is a strong correlation between these two sets of data, which was shown by a linear relationship for the gene expression (both CBP20 and tubulin were used as internal controls) (Fig. 3), suggesting the qRT-PCR and RNA-seq data exhibited decent agreement in all of the randomly selected upregulated, normal expression and downregulated genes.

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