Transcriptomic profiling of the salt-stress response in the wild recretohalophyte Reaumuria trigyna.
Transcriptomic profiling of the salt-stress response in the wild recretohalophyte Reaumuria trigyna.
复制标题
野生泌盐植物 Reaumuria trigyna 盐胁迫反应的转录组分析
DOI：
10.1186/1471-2164-14-29
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发表时间：
2013-01-16
期刊：
影响因子：
4.4
通讯作者：
Wang YC
中科院分区：
文献类型：
--
作者：
Dang ZH;Zheng LL;Wang J;Gao Z;Wu SB;Qi Z;Wang YC
背景
红砂（Reaumuria trigyna）是内蒙古荒漠地区特有的一种濒危小灌木。这种双子叶再生盐生植物具有独特的形态特征，使其能够耐受半荒漠盐渍土施加的压力。然而，如果没有详细的基因组信息，就不可能探索这种耐受性的机制。幸运的是，新开发的高通量测序技术是从头测序的强大工具，可以获得这种物种的信息。
结果
使用短读段测序技术（Illumina）对从对照（C21）和NaCl处理的样品（T43）制备的两个测序文库进行测序，以研究R. trigyna转录组响应盐胁迫。在65340 unigenes，35495（52.27%）与基因描述，保守结构域，基因本体论术语，和代谢途径的截止E值为10-5注释。这些包括44个基因本体（GO）术语，119个京都基因和基因组百科全书（KEGG）途径，以及25个Orthopathy Group家族簇。通过比较对照和NaCl处理植物的转录组，5032个基因在盐胁迫下的转录丰度显示出显著差异（错误发现率≤ 0.001，|log 2比值|≥ 1）。这些基因在29个KEGG通路和26个GO术语中显著富集。转录谱分析表明，与离子转运和活性氧清除系统相关的基因与该物种的形态和生理特征相关。随机选取30个基因进行实时荧光定量PCR检测，结果与RNA-seq检测结果基本一致。
结论
本研究鉴定了与盐胁迫相关的基因。trigyna。全球测序的基因覆盖了相当大比例的R。三角叶转录组这些数据代表了一个遗传资源，发现耐盐相关基因在这个物种，并可能是一个有用的参考序列的来源密切相关的类群。这些结果也有助于我们进一步了解其他盐生植物在钠胁迫下的耐盐性。
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.
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