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Transcriptome Analysis of Spartina pectinata in Response to Freezing Stress.

Nah G, Lee M, Kim DS, Rayburn AL, Voigt T, Lee DK - PLoS ONE (2016)

Bottom Line: The follow-up and second response was of genes involved in encoding the putative anti-freezing protein and the previously known DNA and cell-damage-repair proteins.Moreover, we identified the genes involved in epigenetic regulation and circadian-clock expression.Our results indicate that freezing response in S. pectinata reflects dynamic changes in rapid-time duration, as well as in metabolic, transcriptional, post-translational, and epigenetic regulation.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Science, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, 599 Gwanangno, Gwanakgu, Seoul 08826, Republic of Korea.

ABSTRACT
Prairie cordgrass (Spartina pectinata), a perennial C4 grass native to the North American prairie, has several distinctive characteristics that potentially make it a model crop for production in stressful environments. However, little is known about the transcriptome dynamics of prairie cordgrass despite its unique freezing stress tolerance. Therefore, the purpose of this work was to explore the transcriptome dynamics of prairie cordgrass in response to freezing stress at -5°C for 5 min and 30 min. We used a RNA-sequencing method to assemble the S. pectinata leaf transcriptome and performed gene-expression profiling of the transcripts under freezing treatment. Six differentially expressed gene (DEG) groups were categorized from the profiling. In addition, two major consecutive orders of gene expression were observed in response to freezing; the first being the acute up-regulation of genes involved in plasma membrane modification, calcium-mediated signaling, proteasome-related proteins, and transcription regulators (e.g., MYB and WRKY). The follow-up and second response was of genes involved in encoding the putative anti-freezing protein and the previously known DNA and cell-damage-repair proteins. Moreover, we identified the genes involved in epigenetic regulation and circadian-clock expression. Our results indicate that freezing response in S. pectinata reflects dynamic changes in rapid-time duration, as well as in metabolic, transcriptional, post-translational, and epigenetic regulation.

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Analysis of differentially expressed genes.(A) Hierarchical clustering (Pearson correlation with average linkage method) of 322 DEGs from 0 min vs. 5 min (0–5 min), 0 min vs. 30 min (0–30 min), and 5 min vs. 30 min (5–30 min) in pair-wise comparisons. Red is up-regulation, and blue is down-regulation. The color bar indicates the range of maximum and minimum values of log2 fold change of FPKM. (B) The number of up- and down-regulated genes belonging to 322 DEGs in pair-wise comparisons of three treatments (0 min, 5 min, and 30 min).
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pone.0152294.g003: Analysis of differentially expressed genes.(A) Hierarchical clustering (Pearson correlation with average linkage method) of 322 DEGs from 0 min vs. 5 min (0–5 min), 0 min vs. 30 min (0–30 min), and 5 min vs. 30 min (5–30 min) in pair-wise comparisons. Red is up-regulation, and blue is down-regulation. The color bar indicates the range of maximum and minimum values of log2 fold change of FPKM. (B) The number of up- and down-regulated genes belonging to 322 DEGs in pair-wise comparisons of three treatments (0 min, 5 min, and 30 min).

Mentions: To investigate gene expression changes, we calculated the normalized FPKM (Fragments per kilobase per million) value and performed hierarchical clustering using Pearson's correlation. There were 322 significant DEGs (q < 0.05 and /log2 (fold change)/ > 1) in the freezing treatments (Fig 3A and S3 Table). The pair-wise comparisons among the three time courses (0–5 min; 5–30 min; 0–30 min) are shown in Fig 3B. Of these, the 0–5 min comparison showed a similar number of up- and down-regulated genes (152 up-regulated and 170 down-regulated in 5 min) compared to the 0–30 min (231 up-regulated and 91 down-regulated in 30 min) and 5–30 min (214 up-regulated and 108 down-regulated in 30 min) treatments.


Transcriptome Analysis of Spartina pectinata in Response to Freezing Stress.

Nah G, Lee M, Kim DS, Rayburn AL, Voigt T, Lee DK - PLoS ONE (2016)

Analysis of differentially expressed genes.(A) Hierarchical clustering (Pearson correlation with average linkage method) of 322 DEGs from 0 min vs. 5 min (0–5 min), 0 min vs. 30 min (0–30 min), and 5 min vs. 30 min (5–30 min) in pair-wise comparisons. Red is up-regulation, and blue is down-regulation. The color bar indicates the range of maximum and minimum values of log2 fold change of FPKM. (B) The number of up- and down-regulated genes belonging to 322 DEGs in pair-wise comparisons of three treatments (0 min, 5 min, and 30 min).
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4816275&req=5

pone.0152294.g003: Analysis of differentially expressed genes.(A) Hierarchical clustering (Pearson correlation with average linkage method) of 322 DEGs from 0 min vs. 5 min (0–5 min), 0 min vs. 30 min (0–30 min), and 5 min vs. 30 min (5–30 min) in pair-wise comparisons. Red is up-regulation, and blue is down-regulation. The color bar indicates the range of maximum and minimum values of log2 fold change of FPKM. (B) The number of up- and down-regulated genes belonging to 322 DEGs in pair-wise comparisons of three treatments (0 min, 5 min, and 30 min).
Mentions: To investigate gene expression changes, we calculated the normalized FPKM (Fragments per kilobase per million) value and performed hierarchical clustering using Pearson's correlation. There were 322 significant DEGs (q < 0.05 and /log2 (fold change)/ > 1) in the freezing treatments (Fig 3A and S3 Table). The pair-wise comparisons among the three time courses (0–5 min; 5–30 min; 0–30 min) are shown in Fig 3B. Of these, the 0–5 min comparison showed a similar number of up- and down-regulated genes (152 up-regulated and 170 down-regulated in 5 min) compared to the 0–30 min (231 up-regulated and 91 down-regulated in 30 min) and 5–30 min (214 up-regulated and 108 down-regulated in 30 min) treatments.

Bottom Line: The follow-up and second response was of genes involved in encoding the putative anti-freezing protein and the previously known DNA and cell-damage-repair proteins.Moreover, we identified the genes involved in epigenetic regulation and circadian-clock expression.Our results indicate that freezing response in S. pectinata reflects dynamic changes in rapid-time duration, as well as in metabolic, transcriptional, post-translational, and epigenetic regulation.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Science, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, 599 Gwanangno, Gwanakgu, Seoul 08826, Republic of Korea.

ABSTRACT
Prairie cordgrass (Spartina pectinata), a perennial C4 grass native to the North American prairie, has several distinctive characteristics that potentially make it a model crop for production in stressful environments. However, little is known about the transcriptome dynamics of prairie cordgrass despite its unique freezing stress tolerance. Therefore, the purpose of this work was to explore the transcriptome dynamics of prairie cordgrass in response to freezing stress at -5°C for 5 min and 30 min. We used a RNA-sequencing method to assemble the S. pectinata leaf transcriptome and performed gene-expression profiling of the transcripts under freezing treatment. Six differentially expressed gene (DEG) groups were categorized from the profiling. In addition, two major consecutive orders of gene expression were observed in response to freezing; the first being the acute up-regulation of genes involved in plasma membrane modification, calcium-mediated signaling, proteasome-related proteins, and transcription regulators (e.g., MYB and WRKY). The follow-up and second response was of genes involved in encoding the putative anti-freezing protein and the previously known DNA and cell-damage-repair proteins. Moreover, we identified the genes involved in epigenetic regulation and circadian-clock expression. Our results indicate that freezing response in S. pectinata reflects dynamic changes in rapid-time duration, as well as in metabolic, transcriptional, post-translational, and epigenetic regulation.

Show MeSH