School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, China.
Genomics. 2012 Mar;99(3):160-8. doi: 10.1016/j.ygeno.2011.12.008. Epub 2012 Jan 4.
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 24h 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.
基于 Solexa 基因组分析仪平台的高通量标签测序（Tag-seq）分析被应用于分析黄瓜植物在淹水处理 24 小时过程中的 5 个时间点的基因表达谱。每个文库获得约 580 万条总清洁序列标签，具有 143013 个独特的清洁标签序列。大约 23.69%-29.61%的独特清洁标签可以明确映射到基因数据库，53.78%-60.66%的独特清洁标签可以映射到黄瓜基因组数据库。差异表达基因分析表明，大多数基因在淹水阶段下调，差异表达基因主要与碳代谢、光合作用、活性氧生成/清除以及激素合成/信号转导有关。最后，使用 9 个基因进行的定量实时聚合酶链反应独立验证了标签映射结果。本研究揭示了黄瓜水淹响应转录的综合机制。
