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Early changes in shoot transcriptome of rice in response to Rhodotorula mucilaginosa JGTA-S1.

Saha C, Seal A - Genom Data (2015)

Bottom Line: Some of the Rhodotorula species are found to exhibit plant growth promoting activities and also have been reported to protect plants against invading pathogens.Transcriptional changes were monitored in 6 h and 24 h treated rice plant shoots as compared to 0 h control.The microarray data has been submitted to the NCBI GEO repository under the accession number of GSE64321.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Dr. B.C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata700019, West Bengal, India.

ABSTRACT
Yeasts of Rhodotorula genus have been reported to show endophytic colonization in different plants. Some of the Rhodotorula species are found to exhibit plant growth promoting activities and also have been reported to protect plants against invading pathogens. A yeast strain closely related to Rhodotorula mucilaginosa was isolated from the endosphere of Typha angustifolia collected from a Uranium mine. A microarray analysis was performed to investigate the early changes in rice shoot transcripts in response to this yeast (R. mucilaginosa JGTA-S1). Transcriptional changes were monitored in 6 h and 24 h treated rice plant shoots as compared to 0 h control. The microarray data has been submitted to the NCBI GEO repository under the accession number of GSE64321.

No MeSH data available.


Related in: MedlinePlus

Differentially expressed genes were classified according to their GO ontology using agriGO via Parametric Analysis of Gene Set Enrichment (PAGE) analysis. GO abundance charts were plotted on the basis of Z-score statistical value for all three comparisons: 6 h vs 0 h (control) (A), 24 h vs 0 h (control) (B) & 24 h vs 6 h (C). Up and down-regulation terms are indicated in blue and green color respectively.
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f0010: Differentially expressed genes were classified according to their GO ontology using agriGO via Parametric Analysis of Gene Set Enrichment (PAGE) analysis. GO abundance charts were plotted on the basis of Z-score statistical value for all three comparisons: 6 h vs 0 h (control) (A), 24 h vs 0 h (control) (B) & 24 h vs 6 h (C). Up and down-regulation terms are indicated in blue and green color respectively.

Mentions: Upon R. mucilaginosa JGTA-S1 treatment, 404 genes were differentially regulated within 6 h and 209 genes within 24 h in rice shoots. The volcano plots for the data are shown in Fig. 1A, B, C. Statistically significant differentially expressed up- and down-regulated genes (p < 0.05 & FC ≥ 2.0) are shown in red and blue colored cross signs. Among the 404 genes, within 6 h of infection, 198 genes were up-regulated and 206 genes were down-regulated (Table 1). The differentially regulated genes were classified according to their GO ontology. Genes differentially expressed within 6 h were classified into 127 categories (Table S1) among which 21 most significant categories are shown in Fig. 2A. When compared to control, within 24 h, 113 genes were up-regulated and 96 genes were down-regulated (Table 1). Genes differentially regulated within this time frame were classified into 80 GO categories (Table S1) among which 16 significant categories are shown in Fig. 2B. Genes differentially regulated at 24 h and those regulated within 6 h post infection were compared, 86 genes were found to be up-regulated and 38 genes were down-regulated (Table 1). These were found to be categorized into 63 GO categories among which 7 are shown in Fig. 2C.


Early changes in shoot transcriptome of rice in response to Rhodotorula mucilaginosa JGTA-S1.

Saha C, Seal A - Genom Data (2015)

Differentially expressed genes were classified according to their GO ontology using agriGO via Parametric Analysis of Gene Set Enrichment (PAGE) analysis. GO abundance charts were plotted on the basis of Z-score statistical value for all three comparisons: 6 h vs 0 h (control) (A), 24 h vs 0 h (control) (B) & 24 h vs 6 h (C). Up and down-regulation terms are indicated in blue and green color respectively.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664776&req=5

f0010: Differentially expressed genes were classified according to their GO ontology using agriGO via Parametric Analysis of Gene Set Enrichment (PAGE) analysis. GO abundance charts were plotted on the basis of Z-score statistical value for all three comparisons: 6 h vs 0 h (control) (A), 24 h vs 0 h (control) (B) & 24 h vs 6 h (C). Up and down-regulation terms are indicated in blue and green color respectively.
Mentions: Upon R. mucilaginosa JGTA-S1 treatment, 404 genes were differentially regulated within 6 h and 209 genes within 24 h in rice shoots. The volcano plots for the data are shown in Fig. 1A, B, C. Statistically significant differentially expressed up- and down-regulated genes (p < 0.05 & FC ≥ 2.0) are shown in red and blue colored cross signs. Among the 404 genes, within 6 h of infection, 198 genes were up-regulated and 206 genes were down-regulated (Table 1). The differentially regulated genes were classified according to their GO ontology. Genes differentially expressed within 6 h were classified into 127 categories (Table S1) among which 21 most significant categories are shown in Fig. 2A. When compared to control, within 24 h, 113 genes were up-regulated and 96 genes were down-regulated (Table 1). Genes differentially regulated within this time frame were classified into 80 GO categories (Table S1) among which 16 significant categories are shown in Fig. 2B. Genes differentially regulated at 24 h and those regulated within 6 h post infection were compared, 86 genes were found to be up-regulated and 38 genes were down-regulated (Table 1). These were found to be categorized into 63 GO categories among which 7 are shown in Fig. 2C.

Bottom Line: Some of the Rhodotorula species are found to exhibit plant growth promoting activities and also have been reported to protect plants against invading pathogens.Transcriptional changes were monitored in 6 h and 24 h treated rice plant shoots as compared to 0 h control.The microarray data has been submitted to the NCBI GEO repository under the accession number of GSE64321.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Dr. B.C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata700019, West Bengal, India.

ABSTRACT
Yeasts of Rhodotorula genus have been reported to show endophytic colonization in different plants. Some of the Rhodotorula species are found to exhibit plant growth promoting activities and also have been reported to protect plants against invading pathogens. A yeast strain closely related to Rhodotorula mucilaginosa was isolated from the endosphere of Typha angustifolia collected from a Uranium mine. A microarray analysis was performed to investigate the early changes in rice shoot transcripts in response to this yeast (R. mucilaginosa JGTA-S1). Transcriptional changes were monitored in 6 h and 24 h treated rice plant shoots as compared to 0 h control. The microarray data has been submitted to the NCBI GEO repository under the accession number of GSE64321.

No MeSH data available.


Related in: MedlinePlus