Limits...
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.

Show MeSH
Gene Ontology (GO) analysis of Spartina pectinata leaf transcriptome under freezing treatment.The contigs from the S. pectinata leaf transcriptome were assigned to three GO categories with 16 GO terms of cellular component, 15 GO terms of molecular function, and 14 GO terms of biological process. The x-axis indicates GO terms belonging to three GO categories and the y-axis represents the percentage of contig number in S. pectinata leaf transcriptome.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4816275&req=5

pone.0152294.g002: Gene Ontology (GO) analysis of Spartina pectinata leaf transcriptome under freezing treatment.The contigs from the S. pectinata leaf transcriptome were assigned to three GO categories with 16 GO terms of cellular component, 15 GO terms of molecular function, and 14 GO terms of biological process. The x-axis indicates GO terms belonging to three GO categories and the y-axis represents the percentage of contig number in S. pectinata leaf transcriptome.

Mentions: To investigate the transcriptome composition, the annotated contigs were subjected to gene ontology (GO) for three categories (cellular process, molecular process, and biological process) (Fig 2). The top six GO terms in the cellular process were ‘nucleus’ (16.83%), ‘other cytoplasmic components’ (15.85%), ‘other intracellular components’ (13.98%), ‘other membranes’ (9.45%), ‘chloroplast’ (9.28%), and ‘plasma membrane’ (6.70%). Next, the top six GO terms in the molecular process were ‘other binding’ (17.29%), ‘unknown molecular functions’ (12.11%), ‘protein binding’ (10.04%), ‘transferase activity’ (9.74%), ‘hydrolase activity’ (9.27%), and ‘DNA or RNA binding’ (8.85%). Finally, the top six GO terms in the biological process were ‘other cellular processes’ (22.22%), ‘other metabolic processes’ (21.02%), ‘unknown biological processes’ (8.99%), ‘protein metabolism’ (7.35%), ‘response to stress’ (5.86%), and ‘developmental processes’ (5.44%).


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)

Gene Ontology (GO) analysis of Spartina pectinata leaf transcriptome under freezing treatment.The contigs from the S. pectinata leaf transcriptome were assigned to three GO categories with 16 GO terms of cellular component, 15 GO terms of molecular function, and 14 GO terms of biological process. The x-axis indicates GO terms belonging to three GO categories and the y-axis represents the percentage of contig number in S. pectinata leaf transcriptome.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0152294.g002: Gene Ontology (GO) analysis of Spartina pectinata leaf transcriptome under freezing treatment.The contigs from the S. pectinata leaf transcriptome were assigned to three GO categories with 16 GO terms of cellular component, 15 GO terms of molecular function, and 14 GO terms of biological process. The x-axis indicates GO terms belonging to three GO categories and the y-axis represents the percentage of contig number in S. pectinata leaf transcriptome.
Mentions: To investigate the transcriptome composition, the annotated contigs were subjected to gene ontology (GO) for three categories (cellular process, molecular process, and biological process) (Fig 2). The top six GO terms in the cellular process were ‘nucleus’ (16.83%), ‘other cytoplasmic components’ (15.85%), ‘other intracellular components’ (13.98%), ‘other membranes’ (9.45%), ‘chloroplast’ (9.28%), and ‘plasma membrane’ (6.70%). Next, the top six GO terms in the molecular process were ‘other binding’ (17.29%), ‘unknown molecular functions’ (12.11%), ‘protein binding’ (10.04%), ‘transferase activity’ (9.74%), ‘hydrolase activity’ (9.27%), and ‘DNA or RNA binding’ (8.85%). Finally, the top six GO terms in the biological process were ‘other cellular processes’ (22.22%), ‘other metabolic processes’ (21.02%), ‘unknown biological processes’ (8.99%), ‘protein metabolism’ (7.35%), ‘response to stress’ (5.86%), and ‘developmental processes’ (5.44%).

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