Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.
Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.
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利用下一代测序对萝卜 (Raphanus sativus L.) 根进行转录组分析并鉴定参与铅 (Pb) 应激反应的基因
DOI：
10.1371/journal.pone.0066539
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Liu L
中科院分区：
文献类型：
--
作者：
Wang Y;Xu L;Chen Y;Shen H;Gong Y;Limera C;Liu L
铅（Pb）是毒性最强的重金属之一，可被植物根部吸收和积累，然后进入食物链，对人类造成潜在的健康风险。萝卜（Raphanus sativus L.）是一种重要的块根蔬菜作物，以肉质主根为食用部分。人们对萝卜在分子水平上响应铅胁迫的机制知之甚少。在本研究中，采用基于下一代测序（NGS）的RNA-seq技术来表征萝卜根的从头转录组，并识别铅胁迫期间的差异表达基因（DEG）。从萝卜根 cDNA 样本中获得了总共 68,940 个组装的独特转录本，其中包括 33,337 个 unigenes。根据组装的从头转录组，在未处理 (CK) 和铅处理 (Pb1000) 根的两个文库之间检测到 4,614 个 DEG。基因本体（GO）和通路富集分析表明，Pb胁迫下上调的DEG主要参与细胞壁的防御反应和谷胱甘肽代谢相关过程，而下调的DEG主要参与碳水化合物代谢相关的通路。通过实时定量PCR验证了22个选定基因的表达模式，结果与Solexa分析高度一致。此外，成功鉴定了许多参与防御和解毒机制的候选基因，包括信号蛋白激酶、转录因子、金属转运蛋白和螯合化合物生物合成相关酶，以响应重金属Pb。参与 Pb 胁迫反应的潜在 DEG 的鉴定显着反映了主要生物过程和代谢途径的变化。全面表征了萝卜对铅胁迫响应的分子基础。为研究根类蔬菜作物重金属Pb积累和耐受性的分子调控机制提供了有用的信息和新的见解。
Lead (Pb), one of the most toxic heavy metals, can be absorbed and accumulated by plant roots and then enter the food chain resulting in potential health risks for human beings. The radish (Raphanus sativus L.) is an important root vegetable crop with fleshy taproots as the edible parts. Little is known about the mechanism by which radishes respond to Pb stress at the molecular level. In this study, Next Generation Sequencing (NGS)–based RNA-seq technology was employed to characterize the de novo transcriptome of radish roots and identify differentially expressed genes (DEGs) during Pb stress. A total of 68,940 assembled unique transcripts including 33,337 unigenes were obtained from radish root cDNA samples. Based on the assembled de novo transcriptome, 4,614 DEGs were detected between the two libraries of untreated (CK) and Pb-treated (Pb1000) roots. Gene Ontology (GO) and pathway enrichment analysis revealed that upregulated DEGs under Pb stress are predominately involved in defense responses in cell walls and glutathione metabolism-related processes, while downregulated DEGs were mainly involved in carbohydrate metabolism-related pathways. The expression patterns of 22 selected genes were validated by quantitative real-time PCR, and the results were highly accordant with the Solexa analysis. Furthermore, many candidate genes, which were involved in defense and detoxification mechanisms including signaling protein kinases, transcription factors, metal transporters and chelate compound biosynthesis related enzymes, were successfully identified in response to heavy metal Pb. Identification of potential DEGs involved in responses to Pb stress significantly reflected alterations in major biological processes and metabolic pathways. The molecular basis of the response to Pb stress in radishes was comprehensively characterized. Useful information and new insights were provided for investigating the molecular regulation mechanism of heavy metal Pb accumulation and tolerance in root vegetable crops.
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