Identification of differentially expressed genes in cucumber (Cucumis sativus L.) root under waterlogging stress by digital gene expression profile

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 5.8million 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. ►Ethylene and auxin were implicated in waterlogging response of cucumber. ►Carbon metabolism was affected by waterlogging. ►ROS generation or scavenging related genes were involved in waterlogging response. ►qRT-PCR verified the tag-mapped results.