Identification of differentially expressed genes in cucumber (Cucumis sativus L.) root under waterlogging stress by digital gene expression profile
Identification of differentially expressed genes in cucumber (Cucumis sativus L.) root under waterlogging stress by digital gene expression profile
复制标题
利用数字基因表达谱鉴定淹水胁迫下黄瓜根系差异表达基因
DOI：
10.1016/j.ygeno.2011.12.008
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发表时间：
2012-03-01
期刊：
影响因子：
4.4
通讯作者：
Chen, Xue-Hao
中科院分区：
文献类型：
--
作者：
Qi, Xiao-Hua;Xu, Xue-Wen;Chen, Xue-Hao
应用基于Solexa基因组分析仪平台的高通量标签测序（Tag-seq）分析黄瓜植株在24小时的涝渍处理期间5个时间点的基因表达谱。每个文库获得了大约 580 万个干净序列标签，其中包含 143013 个不同的干净标签序列。大约 23.69%-29.61% 的不同 clean 标签被明确映射到 unigene 数据库，53.78%-60.66% 的不同 clean 标签被映射到黄瓜基因组数据库。对差异表达基因的分析表明，大多数基因在涝渍阶段下调，差异表达基因主要与碳代谢、光合作用、活性氧产生/清除、激素合成/信号传导有关。最后，使用九个基因的定量实时聚合酶链反应独立验证了标签映射结果。本研究揭示了黄瓜涝害响应转录的综合机制。 (C) 2011 Elsevier Inc. 保留所有权利。
High-throughput tag-sequencing (Tag-seq) analysis based on the Solexa Genome Analyzer platform was applied to analyze the gene expression profiling of cucumber plant at 5 time points over a 24 h period of waterlogging treatment. Approximately 5.8 million total clean sequence tags per library were obtained with 143013 distinct clean tag sequences. Approximately 23.69%-29.61% of the distinct clean tags were mapped unambiguously to the unigene database, and 53.78%-60.66% of the distinct clean tags were mapped to the cucumber genome database. Analysis of the differentially expressed genes revealed that most of the genes were down-regulated in the waterlogging stages, and the differentially expressed genes mainly linked to carbon metabolism, photosynthesis, reactive oxygen species generation/scavenging, and hormone synthesis/signaling. Finally, quantitative real-time polymerase chain reaction using nine genes independently verified the tag-mapped results. This present study reveals the comprehensive mechanisms of waterlogging-responsive transcription in cucumber. (C) 2011 Elsevier Inc. All rights reserved.