Identification of differentially expressed genes in cucumber (Cucumis sativus L.) root under waterlogging stress by digital gene expression profile
- 作者：Xiao-Hua Qi ; Xue-Wen Xu ; Xiao-Jian Lin ; Wen-Jie Zhang ; Xue-Hao Chen ; xhchen@yzu.edu.cn
- 关键词：DGE ; digital gene expression ; ERF ; ethylene responsive factor ; POD ; peroxidase ; CAT ; catalase ; SOD ; superoxide dismutase ; ETR ; ethylene receptor ; RBOH ; respiratory burst oxidase homolog
- 刊名：Genomics
- 出版年：2012
- 期刊代码：170_08887543
- 类别：bio
- 出版时间：March, 2012
- 卷：99
- 期：3
- 页码：160-168
- 文件大小：732 K
摘要
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.