Genome-wide characterisation of gene expression in rice leaf blades at 25 °C and 30 °C.
Genome-wide characterisation of gene expression in rice leaf blades at 25 °C and 30 °C.
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DOI：
10.1155/2014/917292
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发表时间：
2014
影响因子：
--
通讯作者：
Zhou J
中科院分区：
文献类型：
--
作者：
E ZG;Wang L;Qin R;Shen H;Zhou J
水稻生长受温度影响很大。为了研究温度如何在全基因组的基础上影响水稻中的基因表达，我们利用最近编译的下一代测序数据集，并在25°C和30°C下表征了水稻幼苗叶片中的一些RNA序列转录组样本。我们的分析表明，水稻基因组中所有基因的50.4%（28，296/56，143）在25°C下生长的水稻样品中表达，而在30°C下生长的水稻叶片中表达的基因略少（50.2%; 28，189/56，143）。在表达的基因中，大约3%是高表达的，而大约65%是低表达的。进一步的检查表明，在25°C下，821个基因的表达增加了两倍或更多，553个基因的表达减少了两倍或更多。基因本体（GO）和京都基因和基因组百科全书（KEGG）分析表明，核糖体途径和多种代谢途径在25°C下上调。基于这些结果，我们推断，在转录和翻译水平上的基因表达在25°C下被刺激，这可能是对次优温度条件的响应。最后，我们观察到，温度显着调节转录因子的几个超家族，包括bZIP，MYB和WRKY。
Rice growth is greatly affected by temperature. To examine how temperature influences gene expression in rice on a genome-wide basis, we utilised recently compiled next-generation sequencing datasets and characterised a number of RNA-sequence transcriptome samples in rice seedling leaf blades at 25°C and 30°C. Our analysis indicated that 50.4% of all genes in the rice genome (28,296/56,143) were expressed in rice samples grown at 25°C, whereas slightly fewer genes (50.2%; 28,189/56,143) were expressed in rice leaf blades grown at 30°C. Among the genes that were expressed, approximately 3% were highly expressed, whereas approximately 65% had low levels of expression. Further examination demonstrated that 821 genes had a twofold or higher increase in expression and that 553 genes had a twofold or greater decrease in expression at 25°C. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggested that the ribosome pathway and multiple metabolic pathways were upregulated at 25°C. Based on these results, we deduced that gene expression at both transcriptional and translational levels was stimulated at 25°C, perhaps in response to a suboptimal temperature condition. Finally, we observed that temperature markedly regulates several super-families of transcription factors, including bZIP, MYB, and WRKY.
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