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

Abstract

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.

A Co-Opted Hormonal Cascade Activates Dormant Adventitious Root Primordia upon Flooding in Solanum dulcamara

“…This results in detrimental effects on cellular metabolic homeostasis, but at the same time these changes in gas concentrations are used as cues to alter gene expression leading to acclimation. In many plant species, genes involved in (hormonal) signaling, photosynthesis, anaerobic metabolism, and secondary metabolism are rapidly modulated in response to flooding (Zhang et al, 2006;Lee et al, 2007;Christianson et al, 2010;Lee et al, 2011;Nanjo et al, 2011;Qi et al, 2012). To prevent or shorten the imminent energy crisis, plant species from wetland habitats show morphological adaptations such as elongation of the shoot, formation of aerenchyma in existing tissues, or development of new, aerenchymatous adventitious roots (ARs), all of which are aimed at improving gas exchange between plant tissues and the atmosphere (Bailey-Serres and Voesenek, 2008).…”

Waterlogging-induced increase in fermentation and related gene expression in the root of cucumber (Cucumis sativus L.)

“…The relative quantitation of gene expressions was calculated and normalized to Actin. Specific primers pairs used to amplify gene-specific primers (Table 1) were designed according to the Cucurbit Genomics Database (http://www.icugi.org), and digital gene expression profiles (Qi et al, 2012) were determined using Primer Premier 5.0 (Premier Biosoft International, Palo Alto, CA, USA).qRT-PCR was performed using a Takara SYBR ® PrimeScript TM RT-PCR kit according to the manufacturer's specifications (Takara, China). SYBR Green PCR cycling was performed on an iQ TM 5 Multicolor real-time PCR detection system (Bio-RAD, USA) using 25 L samples with a programme of denaturation at 95 • C for 10 s and 40 cycles of 95 • C for 5 s and 52 • C for 30 s. Three replicates of the waterlogging stress and control treatments were used for real-time PCR.…”

“…However, cucumber is waterlogging-sensitive, and easily affected by heavy rain and subsequent periods of soil flooding during summer, especially in Southern China, due to its shallow root system and strict oxygen requirement (Qi et al, 2012). To the best of our knowledge, little was known about morphological and molecular studies on the effects of waterlogging stress in cucumber.…”

Characterization and Identification of Differentially Expressed Genes Involved in Thermal Adaptation of the Hong Kong Oyster Crassostrea hongkongensis by Digital Gene Expression Profiling

“…It is more advantageous than previous microarrays technology which has several limitations, including the accuracy of low abundance expression measurements, the differences of hybridization properties, and limitation to known genes (Wheelan et al, 2008). This technique has been widely used in transcriptomic studies in various species, including Caenorhabditis elegans (Nesbitt et al, 2010), Physcomitrella patens (Nishiyama et al, 2012), Cucumis sativus (Qi et al, 2012), Microsporum canis , Bombyx mori (Zhang et al, 2014), and Mus musculus (Zhang et al, 2013). Aiming to elucidate the molecular mechanisms of thermal stress tolerance in C. hongkongensis, a DGE based gene expression analysis was performed with Hong Kong oysters.…”