Genome-wide analysis of theWRKYgene family in the cucumber genome and transcriptome-wide identification of WRKY transcription factors that respond to biotic and abiotic stresses

Background Cucumber (Cucumis sativusL.) is an economically important vegetable crop species. However, it is susceptible to various abiotic and biotic stresses. WRKY transcription factors play important roles in plant growth and development, particularly in the plant response to biotic and abiotic stresses. However, little is known about the expression pattern ofWRKYgenes under different stresses in cucumber. Results In the present study, an analysis of the new assembly of the cucumber genome (v3.0) allowed the identification of 61 cucumberWRKYgenes. Phylogenetic and synteny analyses were performed using related species to investigate the evolution of the cucumberWRKYgenes. The 61CsWRKYswere classified into three main groups, within which the gene structure and motif compositions were conserved. Tissue expression profiles of theWRKYgenes demonstrated that 24CsWRKYgenes showed constitutive expression (FPKM > 1 in all samples), and someWRKYgenes showed organ-specific expression, suggesting that theseWRKYsmight be important for plant growth and organ development in cucumber. Importantly, analysis of theCsWRKYgene expression patterns revealed that fiveCsWRKYgenes strongly responded to both salt and heat stresses, 12 genes were observed to be expressed in response to infection from downy mildew and powdery mildew, and threeCsWRKYgenes simultaneously responded to all treatments analysed. SomeCsWRKYgenes were observed to be induced/repressed at different times after abiotic or biotic stress treatment, demonstrating that cucumberWRKYgenes might play different roles during different stress responses and that their expression patterns vary in response to stresses. Conclusions Sixty-oneWRKYgenes were identified in cucumber, and insight into their classification, evolution, and expression patterns was gained in this study. Responses to different abiotic and biotic stresses in cucumber were also investigated. Our results provide a better understanding of the function ofCsWRKYgenes in improving abiotic and biotic stress resistance in cucumber.