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Open Access Highly Accessed Research article

Transcriptomic profiling of the salt-stress response in the wild recretohalophyte Reaumuria trigyna

Zhen-hua Dang1, Lin-lin Zheng1, Jia Wang1, Zhe Gao1, Shu-biao Wu2, Zhi Qi1 and Ying-chun Wang1*

Author affiliations

1 Key Laboratory of Herbage & Endemic Crop Biotechnology, and College of Life Sciences, Inner Mongolia University, Hohhot, 010020, PR China

2 School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia

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Citation and License

BMC Genomics 2013, 14:29  doi:10.1186/1471-2164-14-29

Published: 16 January 2013

Abstract

Background

Reaumuria trigyna is an endangered small shrub endemic to desert regions in Inner Mongolia. This dicotyledonous recretohalophyte has unique morphological characteristics that allow it to tolerate the stress imposed by semi-desert saline soil. However, it is impossible to explore the mechanisms underlying this tolerance without detailed genomic information. Fortunately, newly developed high-throughput sequencing technologies are powerful tools for de novo sequencing to gain such information for this species.

Results

Two sequencing libraries prepared from control (C21) and NaCl-treated samples (T43) were sequenced using short reads sequencing technology (Illumina) to investigate changes in the R. trigyna transcriptome in response to salt stress. Among 65340 unigenes, 35495 (52.27%) were annotated with gene descriptions, conserved domains, gene ontology terms, and metabolic pathways with a cut-off E-value of 10-5. These included 44 Gene Ontology (GO) terms, 119 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and 25 Clusters of Orthologous Groups families. By comparing the transcriptomes from control and NaCl-treated plants, 5032 genes showed significantly differences in transcript abundance under salt stress (false discovery rate ≤ 0.001 and |log2Ratio| ≥ 1). These genes were significantly enriched in 29 KEGG pathways and 26 GO terms. The transcription profiles indicated that genes related to ion transport and the reactive oxygen species scavenging system were relevant to the morphological and physiological characteristics of this species. The expression patterns of 30 randomly selected genes resulted from quantitative real-time PCR were basically consistent with their transcript abundance changes identified by RNA-seq.

Conclusions

The present study identified potential genes involved in salt tolerance of R. trigyna. The globally sequenced genes covered a considerable proportion of the R. trigyna transcriptome. These data represent a genetic resource for the discovery of genes related to salt tolerance in this species, and may be a useful source of reference sequences for closely related taxa. These results can also further our understanding of salt tolerance in other halophytes surviving under sodic stress.

Keywords:
Reaumuria trigyna; Recretohalophyte; Transcriptome; Illumina sequencing; Salt-stress response