De novo characterization of the alligator weed (Alternanthera philoxeroides) transcriptome illuminates gene expression under potassium deprivation
De novo characterization of the alligator weed (Alternanthera philoxeroides) transcriptome illuminates gene expression under potassium deprivation
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DOI：
10.1007/s12041-015-0493-1
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发表时间：
2015-03-01
影响因子：
1.5
通讯作者：
Lu, Liming
中科院分区：
文献类型：
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作者：
Li, Liqin;Xu, Li;Lu, Liming
钾作为三大常量营养元素之一，参与了植物生活史中的许多生理过程。最近，钾依赖转录组分析在拟南芥、水稻和大豆中得到了报道。鳄鱼杂草是众所周知的，特别是它有很强的积累钾的能力。然而，钾饥饿反应的分子机制还没有被描述。在本研究中，我们利用Illumina(Solexa)测序技术分析了低钾胁迫下鳄鱼根的转录组信息。进一步分析表明，缺钾7天后，9253个差异表达基因上调，2138个差异表达基因下调。这些因子包括121个转录因子、108个蛋白激酶、136个转运蛋白和178个与应激相关的基因。随机抽取12个转录因子进行进一步分析。定量RT-PCR证实了各转录因子的表达水平，二次分析结果与SolexA测序结果一致。浓缩分析表明，10,993个deg被归类为54个基因本体论术语和123条KEGG途径。大约24%的DEG属于次生代谢物KEGG的代谢、核糖体和生物合成途径。本研究结果全面分析了低钾胁迫下扬子鳄杂草的基因调控网络，为植物缺钾的遗传和基因组研究提供了有价值的资源。
As one of the three macronutrients, potassium participates in many physiological processes in plant life cycle. Recently, potassium-dependent transcriptome analysis has been reported in Arabidopsis, rice and soybean. Alligator weed is well known, particularly for its strong ability to accumulate potassium. However, the molecular mechanism that underlies potassium starvation responses has not yet been described. In this study, we used Illumina (Solexa) sequencing technology to analyse the root transcriptome information of alligator weed under low potassium stress. Further analysis suggested that 9253 differentially expressed genes (DEGs) were upregulated, and 2138 DEGs were downregulated after seven days of potassium deficiency. These factors included 121 transcription factors, 108 kinases, 136 transporters and 178 genes that were related to stress. Twelve transcription factors were randomly selected for further analysis. The expression level of each transcription factor was confirmed by quantitative RT-PCR, and the results of this secondary analysis were consistent with the results of Solexa sequencing. Enrichment analysis indicated that 10,993 DEGs were assigned to 54 gene ontology terms and 123 KEGG pathways. Approximately 24% of DEGs belong to the metabolic, ribosome and biosynthesis of secondary metabolite KEGG pathways. Our results provide a comprehensive analysis of the gene regulatory network of alligator weed under low potassium stress, and afford a valuable resource for genetic and genomic research on plant potassium deficiency.