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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

Transcriptome analysis of RNA-seq data of mock and Turnip crinkle virus (TCV)-infected Arabidopsis thaliana.(a) Numbers of all the detected genes and differentially expressed genes (DEG) with at least 15-fold change (FC) in mock and TCV-infected Arabidopsis plants. (b) Plot for the distribution and comparison of Fragments per kilobase of transcript per million fragments mapped (FPKM) values for genes expressed in the mock and TCV-infected plants. (c) Volcano plot to inspect DEGs under different conditions between mock and TCV-infected plants. For instance, the genes which are located above the red line represent the DEGs under conditions of log2 (FC) >4 and p < 0.00005.
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f1: Transcriptome analysis of RNA-seq data of mock and Turnip crinkle virus (TCV)-infected Arabidopsis thaliana.(a) Numbers of all the detected genes and differentially expressed genes (DEG) with at least 15-fold change (FC) in mock and TCV-infected Arabidopsis plants. (b) Plot for the distribution and comparison of Fragments per kilobase of transcript per million fragments mapped (FPKM) values for genes expressed in the mock and TCV-infected plants. (c) Volcano plot to inspect DEGs under different conditions between mock and TCV-infected plants. For instance, the genes which are located above the red line represent the DEGs under conditions of log2 (FC) >4 and p < 0.00005.

Mentions: The mapping output generated by TopHat was processed by Cufflinks toolkits for transcript assembly and differential gene expression analysis. In general, a total of 39,747 expressed genes were detected from the mock and TCV-infected samples (Fig. 1a, Supplementary Table S1). In addition to the well-known 27,677 protein coding genes in Arabidopsis, this 39,747 discovered gene transcripts also included non-coding RNA genes, such as miRNA genes, siRNA genes and long non-coding RNA genes. In order to narrow down the DEG list, the genes with at least 15-fold change (FC) were selected for further investigation. There were 238 genes in total and the numbers of up- and down-regulated genes in TCV-infected samples were 155 and 83, respectively (Fig. 1 and Supplementary Table S2). Many functional classes of genes, such as ATNADP-ME1 (NADP-malic enzyme 1), ALPHA-DOX1 (peroxidase superfamily protein), ALD1 (AGD2-like defense response protein 1), stress response protein (stress responsive A/B barrel domain) as well as a few WRKY family proteins, were found to be significantly affected in TCV-infected plants compared to that of the mock control plants (Supplementary Table S2).


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)

Transcriptome analysis of RNA-seq data of mock and Turnip crinkle virus (TCV)-infected Arabidopsis thaliana.(a) Numbers of all the detected genes and differentially expressed genes (DEG) with at least 15-fold change (FC) in mock and TCV-infected Arabidopsis plants. (b) Plot for the distribution and comparison of Fragments per kilobase of transcript per million fragments mapped (FPKM) values for genes expressed in the mock and TCV-infected plants. (c) Volcano plot to inspect DEGs under different conditions between mock and TCV-infected plants. For instance, the genes which are located above the red line represent the DEGs under conditions of log2 (FC) >4 and p < 0.00005.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: Transcriptome analysis of RNA-seq data of mock and Turnip crinkle virus (TCV)-infected Arabidopsis thaliana.(a) Numbers of all the detected genes and differentially expressed genes (DEG) with at least 15-fold change (FC) in mock and TCV-infected Arabidopsis plants. (b) Plot for the distribution and comparison of Fragments per kilobase of transcript per million fragments mapped (FPKM) values for genes expressed in the mock and TCV-infected plants. (c) Volcano plot to inspect DEGs under different conditions between mock and TCV-infected plants. For instance, the genes which are located above the red line represent the DEGs under conditions of log2 (FC) >4 and p < 0.00005.
Mentions: The mapping output generated by TopHat was processed by Cufflinks toolkits for transcript assembly and differential gene expression analysis. In general, a total of 39,747 expressed genes were detected from the mock and TCV-infected samples (Fig. 1a, Supplementary Table S1). In addition to the well-known 27,677 protein coding genes in Arabidopsis, this 39,747 discovered gene transcripts also included non-coding RNA genes, such as miRNA genes, siRNA genes and long non-coding RNA genes. In order to narrow down the DEG list, the genes with at least 15-fold change (FC) were selected for further investigation. There were 238 genes in total and the numbers of up- and down-regulated genes in TCV-infected samples were 155 and 83, respectively (Fig. 1 and Supplementary Table S2). Many functional classes of genes, such as ATNADP-ME1 (NADP-malic enzyme 1), ALPHA-DOX1 (peroxidase superfamily protein), ALD1 (AGD2-like defense response protein 1), stress response protein (stress responsive A/B barrel domain) as well as a few WRKY family proteins, were found to be significantly affected in TCV-infected plants compared to that of the mock control plants (Supplementary Table S2).

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