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Transcriptomic Analysis of Drought Stress Responses in Ammopiptanthus mongolicus Leaves Using the RNA-Seq Technique.

Gao F, Wang J, Wei S, Li Z, Wang N, Li H, Feng J, Li H, Zhou Y, Zhang F - PLoS ONE (2015)

Bottom Line: GO and KEGG analyses revealed hormone signal transduction and phenylpropanoid biosynthesis were enriched during drought treatment.The sequence collection assembled in the present study represents one of the most comprehensive transcriptome databases for A. mongolicus currently.The differentially expressed transcripts identified in our study provide a good start for identifying the key genes in stress response and performing functional analysis to reveal their roles in stress adaptation in planta.

View Article: PubMed Central - PubMed

Affiliation: College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China.

ABSTRACT
Ammopiptanthus mongolicus (Maxim. Ex Kom.) Cheng f., a relic tree of the Tertiary period, plays a critical role in maintaining desert ecosystems in the Mid-Asia region. Genome-scale gene expression profiling studies will provide deep insight into the molecular mechanism underlying the drought tolerance of A. mongolicus. In the present study, we investigated the transcriptional changes induced by drought treatment in A. mongolicus leaves by establishing a comprehensive transcriptome database and then performing a Digital Gene Expression (DGE) analysis using Solexa sequencing technology. A comprehensive transcriptome database was obtained by assembling the Illumina unigenes with expressed sequence tags (EST) available publicly, and other high throughput sequencing data. To analyze the dynamic and complicated gene regulation network during PEG6000-induced drought treatment in leaves of A. mongolicus, a time-course gene expression analysis was performed using tag-based DGE technology, which identified 437, 1,247 and 802 differentially expressed transcripts in 1, 24 and 72 h drought stress libraries, respectively. GO and KEGG analyses revealed hormone signal transduction and phenylpropanoid biosynthesis were enriched during drought treatment. A batch of drought-regulated transcription factor transcripts were identified, including the subsets of HD-ZIP, bZIP, WRKY, AP2/ERF and bHLH family members, which may play roles in drought response in A. mongolicus. The sequence collection assembled in the present study represents one of the most comprehensive transcriptome databases for A. mongolicus currently. The differentially expressed transcripts identified in our study provide a good start for identifying the key genes in stress response and performing functional analysis to reveal their roles in stress adaptation in planta.

No MeSH data available.


Related in: MedlinePlus

Gene Ontology (GO) functional classification analysis of differentially expressed transcripts (DETs) based on RNA-Seq data.GO functional classification analysis of DETs in D2 vs D1, D3 vs D1, and D4 vs D1. Based on sequence homology, 2,573 differentially expressed genes could be categorized into three main categories (biological process, cellular component, and molecular function), which include 25, 13, and 12 functional groups, respectively.
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pone.0124382.g006: Gene Ontology (GO) functional classification analysis of differentially expressed transcripts (DETs) based on RNA-Seq data.GO functional classification analysis of DETs in D2 vs D1, D3 vs D1, and D4 vs D1. Based on sequence homology, 2,573 differentially expressed genes could be categorized into three main categories (biological process, cellular component, and molecular function), which include 25, 13, and 12 functional groups, respectively.

Mentions: Gene Ontology functional classification analyses were performed to classify the functions of the DETs during drought treatment [25]. Based on sequence homology, all DETs could be categorized into 50 functional groups (Fig 6). In the three main categories [Biological process (BP), Cellular component (CC), and Molecular function (MF)] of the GO classification, there were 25, 13, and 12 functional groups, respectively (Fig 6). Among these groups, the terms metabolic process (GO: 0008152), cell part (GO: 0044464), and catalytic activity (GO: 0003824) were dominant in each of the three main categories, respectively. We also noticed a considerable quantity of genes from the functional groups of cellular process (GO: 0009987), and response to stimulus (GO: 0050896), organelle (GO: 0043226), membrane (GO: 0016020), binding (GO: 0005488), and transporter activity (GO: 0005215) (Fig 6).


Transcriptomic Analysis of Drought Stress Responses in Ammopiptanthus mongolicus Leaves Using the RNA-Seq Technique.

Gao F, Wang J, Wei S, Li Z, Wang N, Li H, Feng J, Li H, Zhou Y, Zhang F - PLoS ONE (2015)

Gene Ontology (GO) functional classification analysis of differentially expressed transcripts (DETs) based on RNA-Seq data.GO functional classification analysis of DETs in D2 vs D1, D3 vs D1, and D4 vs D1. Based on sequence homology, 2,573 differentially expressed genes could be categorized into three main categories (biological process, cellular component, and molecular function), which include 25, 13, and 12 functional groups, respectively.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4414462&req=5

pone.0124382.g006: Gene Ontology (GO) functional classification analysis of differentially expressed transcripts (DETs) based on RNA-Seq data.GO functional classification analysis of DETs in D2 vs D1, D3 vs D1, and D4 vs D1. Based on sequence homology, 2,573 differentially expressed genes could be categorized into three main categories (biological process, cellular component, and molecular function), which include 25, 13, and 12 functional groups, respectively.
Mentions: Gene Ontology functional classification analyses were performed to classify the functions of the DETs during drought treatment [25]. Based on sequence homology, all DETs could be categorized into 50 functional groups (Fig 6). In the three main categories [Biological process (BP), Cellular component (CC), and Molecular function (MF)] of the GO classification, there were 25, 13, and 12 functional groups, respectively (Fig 6). Among these groups, the terms metabolic process (GO: 0008152), cell part (GO: 0044464), and catalytic activity (GO: 0003824) were dominant in each of the three main categories, respectively. We also noticed a considerable quantity of genes from the functional groups of cellular process (GO: 0009987), and response to stimulus (GO: 0050896), organelle (GO: 0043226), membrane (GO: 0016020), binding (GO: 0005488), and transporter activity (GO: 0005215) (Fig 6).

Bottom Line: GO and KEGG analyses revealed hormone signal transduction and phenylpropanoid biosynthesis were enriched during drought treatment.The sequence collection assembled in the present study represents one of the most comprehensive transcriptome databases for A. mongolicus currently.The differentially expressed transcripts identified in our study provide a good start for identifying the key genes in stress response and performing functional analysis to reveal their roles in stress adaptation in planta.

View Article: PubMed Central - PubMed

Affiliation: College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China.

ABSTRACT
Ammopiptanthus mongolicus (Maxim. Ex Kom.) Cheng f., a relic tree of the Tertiary period, plays a critical role in maintaining desert ecosystems in the Mid-Asia region. Genome-scale gene expression profiling studies will provide deep insight into the molecular mechanism underlying the drought tolerance of A. mongolicus. In the present study, we investigated the transcriptional changes induced by drought treatment in A. mongolicus leaves by establishing a comprehensive transcriptome database and then performing a Digital Gene Expression (DGE) analysis using Solexa sequencing technology. A comprehensive transcriptome database was obtained by assembling the Illumina unigenes with expressed sequence tags (EST) available publicly, and other high throughput sequencing data. To analyze the dynamic and complicated gene regulation network during PEG6000-induced drought treatment in leaves of A. mongolicus, a time-course gene expression analysis was performed using tag-based DGE technology, which identified 437, 1,247 and 802 differentially expressed transcripts in 1, 24 and 72 h drought stress libraries, respectively. GO and KEGG analyses revealed hormone signal transduction and phenylpropanoid biosynthesis were enriched during drought treatment. A batch of drought-regulated transcription factor transcripts were identified, including the subsets of HD-ZIP, bZIP, WRKY, AP2/ERF and bHLH family members, which may play roles in drought response in A. mongolicus. The sequence collection assembled in the present study represents one of the most comprehensive transcriptome databases for A. mongolicus currently. The differentially expressed transcripts identified in our study provide a good start for identifying the key genes in stress response and performing functional analysis to reveal their roles in stress adaptation in planta.

No MeSH data available.


Related in: MedlinePlus