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Title: Transcriptomic profiling of the salt-stress response in the wild recretohalophyte 'Reaumuria trigyna'
Contributor(s): Dang, Zhen-hua (author); Zheng, Lin-lin (author); Wang, Jia (author); Gao, Zhe (author); Wu, Shubiao  (author)orcid ; Qi, Zhi (author); Wang, Ying-chun (author)
Publication Date: 2013
Open Access: Yes
DOI: 10.1186/1471-2164-14-29Open Access Link
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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.
Publication Type: Journal Article
Source of Publication: BMC Genomics, v.14, p. 1-16
Publisher: BioMed Central Ltd
Place of Publication: United Kingdom
ISSN: 1471-2164
Field of Research (FOR): 060405 Gene Expression (incl Microarray and other genome-wide approaches)
060704 Plant Pathology
Socio-Economic Objective (SEO): 960899 Flora, Fauna and Biodiversity of Environments not elsewhere classified
960699 Environmental and Natural Resource Evaluation not elsewhere classified
Peer Reviewed: Yes
HERDC Category Description: C1 Refereed Article in a Scholarly Journal
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