Global analysis of transcriptome responses and gene expression profiles to cold stress of Jatropha curcas L.
Global analysis of transcriptome responses and gene expression profiles to cold stress of Jatropha curcas L.
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麻疯树转录组响应和基因表达谱对冷胁迫的整体分析。
DOI：
10.1371/journal.pone.0082817
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Gong M
中科院分区：
文献类型：
--
作者：
Wang H;Zou Z;Wang S;Gong M
麻疯树（Jatropha curcas L.），也被称为小桐子，是一种富含油脂的灌木，具有多种用途，包括生物柴油生产，目前在许多国家被作为一种可再生能源加以开发利用。然而，由于其起源于热带中美洲地区，麻疯树具有一种固有的但不良的特性（抗寒性低），这可能会严重限制其大规模推广。通过阐明植物耐寒的机制，可以从基因上改善这种适应性缺陷。新开发的Illumina Hiseq™ 2000 RNA测序和数字基因表达（DGE）是在转录组水平进行基因表达分析的深度高通量方法，我们利用这些方法仔细研究了麻疯树在冷胁迫下的基因表达谱，以深入了解麻疯树冷响应的分子机制。
通过对麻疯树转录组进行RNA测序分析所产生的干净数据进行组装，总共获得了45251个单基因。通过蛋白质数据库比对和ESTScan预测，分别确定了33363个和912个完整或部分编码序列（CDS）。在这些单基因中，超过41.52%参与了大约128个已知的代谢或信号通路，其中4185个可能与抗寒性有关。利用DGE分析评估了在12°C的寒冷条件下暴露12、24和48小时时基因表达的变化。结果显示，在冷胁迫下，3178个基因显著上调，1244个基因显著下调。然后根据RNA测序分析得到的转录组数据对这些基因进行了功能注释。
这项研究提供了麻疯树在冷胁迫下转录组响应和基因表达谱的全局视图。研究结果有助于提高我们目前对植物抗寒机制的理解，并有利于筛选对麻疯树进行基因改良以增强其抗寒性的关键基因。
Jatropha curcas L., also called the Physic nut, is an oil-rich shrub with multiple uses, including biodiesel production, and is currently exploited as a renewable energy resource in many countries. Nevertheless, because of its origin from the tropical MidAmerican zone, J. curcas confers an inherent but undesirable characteristic (low cold resistance) that may seriously restrict its large-scale popularization. This adaptive flaw can be genetically improved by elucidating the mechanisms underlying plant tolerance to cold temperatures. The newly developed Illumina Hiseq™ 2000 RNA-seq and Digital Gene Expression (DGE) are deep high-throughput approaches for gene expression analysis at the transcriptome level, using which we carefully investigated the gene expression profiles in response to cold stress to gain insight into the molecular mechanisms of cold response in J. curcas. In total, 45,251 unigenes were obtained by assembly of clean data generated by RNA-seq analysis of the J. curcas transcriptome. A total of 33,363 and 912 complete or partial coding sequences (CDSs) were determined by protein database alignments and ESTScan prediction, respectively. Among these unigenes, more than 41.52% were involved in approximately 128 known metabolic or signaling pathways, and 4,185 were possibly associated with cold resistance. DGE analysis was used to assess the changes in gene expression when exposed to cold condition (12°C) for 12, 24, and 48 h. The results showed that 3,178 genes were significantly upregulated and 1,244 were downregulated under cold stress. These genes were then functionally annotated based on the transcriptome data from RNA-seq analysis. This study provides a global view of transcriptome response and gene expression profiling of J. curcas in response to cold stress. The results can help improve our current understanding of the mechanisms underlying plant cold resistance and favor the screening of crucial genes for genetically enhancing cold resistance in J. curcas.
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DOI：
10.1073/pnas.0406069101
发表时间：
2004-10-19
影响因子：
11.1
作者：
Cook, D;Fowler, S;Thomashow, MF
通讯作者：
Thomashow, MF
影响因子：
2.4
作者：
Deore, Ajay C.;Johnson, T. Sudhakar
通讯作者：
Johnson, T. Sudhakar
影响因子：
7.2
作者：
Gilmour, SJ;Zarka, DG;Thomashow, MF
通讯作者：
Thomashow, MF
影响因子：
6.5
作者：
Guo, Z.;Ou, W.;Zhong, Q.
通讯作者：
Zhong, Q.
DOI：
10.1007/s00249-008-0260-9
发表时间：
2008-09-01
影响因子：
2
作者：
Bogdanovic, J.;Mojovic, M.;Spasojevic, I.
通讯作者：
Spasojevic, I.