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Open Access Highly Accessed Research article

De novo sequencing and analysis of root transcriptome using 454 pyrosequencing to discover putative genes associated with drought tolerance in Ammopiptanthus mongolicus

Yijun Zhou1, Fei Gao12*, Ran Liu1, Jinchao Feng1 and Hongjie Li3

Author Affiliations

1 College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China

2 Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

3 The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

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BMC Genomics 2012, 13:266  doi:10.1186/1471-2164-13-266

Published: 21 June 2012

Abstract

Background

De novo assembly of transcript sequences produced by next-generation sequencing technologies offers a rapid approach to obtain expressed gene sequences for non-model organisms. Ammopiptanthus mongolicus, a super-xerophytic broadleaf evergreen wood, is an ecologically important foundation species in desert ecosystems and exhibits substantial drought tolerance in Mid-Asia desert. Root plays an important role in water absorption of plant. There are insufficient transcriptomic and genomic data in public databases for understanding of the molecular mechanism underlying the drought tolerance of A. mongolicus. Thus, high throughput transcriptome sequencing from A. mongolicus root is helpful to generate a large amount of transcript sequences for gene discovery and molecular marker development.

Results

A total of 672,002 sequencing reads were obtained from a 454 GS XLR70 Titanium pyrosequencer with a mean length of 279 bp. These reads were assembled into 29,056 unique sequences including 15,173 contigs and 13,883 singlets. In our assembled sequences, 1,827 potential simple sequence repeats (SSR) molecular markers were discovered. Based on sequence similarity with known plant proteins, the assembled sequences represent approximately 9,771 proteins in PlantGDB. Based on the Gene ontology (GO) analysis, hundreds of drought stress-related genes were found. We further analyzed the gene expression profiles of 27 putative genes involved in drought tolerance using quantitative real-time PCR (qRT-PCR) assay.

Conclusions

Our sequence collection represents a major transcriptomic resource for A. mongolicus, and the large number of genetic markers predicted should contribute to future research in Ammopiptanthus genus. The potential drought stress related transcripts identified in this study provide a good start for further investigation into the drought adaptation in Ammopiptanthus.

Keywords:
Ammopiptanthus mongolicus; Drought; Root; Transcriptome; 454 pyrosequencing