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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

Size distribution of sequences in the All-Unigenes.
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pone.0124382.g001: Size distribution of sequences in the All-Unigenes.

Mentions: To obtain a comprehensive transcriptome database, our unigenes dataset was further assembled with the ESTs deposited in the GenBank database (the last update time: Feb. 8, 2014), and the transcriptome dataset (29,056 unique sequences) assembled in a previous study [13] using Phrap (Release 23.0) [21]. A total of 81,951 unigenes (designated All-Unigene) was obtained with a mean size of 665 bp, including 15,714 unigenes ≥1,000 bp (Fig 1). Compared with the leaf unigenes, the quantity of reads ≥1000 increased by 49% (from 10,560 to 15,714), although the mean length of unigenes in All-Unigene decreased slightly by 4.6% (from 697 to 665 bp).


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)

Size distribution of sequences in the All-Unigenes.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0124382.g001: Size distribution of sequences in the All-Unigenes.
Mentions: To obtain a comprehensive transcriptome database, our unigenes dataset was further assembled with the ESTs deposited in the GenBank database (the last update time: Feb. 8, 2014), and the transcriptome dataset (29,056 unique sequences) assembled in a previous study [13] using Phrap (Release 23.0) [21]. A total of 81,951 unigenes (designated All-Unigene) was obtained with a mean size of 665 bp, including 15,714 unigenes ≥1,000 bp (Fig 1). Compared with the leaf unigenes, the quantity of reads ≥1000 increased by 49% (from 10,560 to 15,714), although the mean length of unigenes in All-Unigene decreased slightly by 4.6% (from 697 to 665 bp).

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