Genome-wide identification and expression analysis of the WRKY gene family in response to low-temperature and drought stresses in Cucurbita pepo L

•A total of 103 candidate WRKY gene sequences were isolated from the whole zucchini genome.•The expression profiles of tissue-specific as well as low temperature and drought stresses were anlysised using RNA-seq.•An unexpected high number of 21 CpWRKY genes likely associated with the response of zucchini seedling leaves to low temperature and drought stresses were identified by using qRT-PCR. The WRKY transcription factors are important transcriptional regulators in plants, with crucial roles affecting biotic and abiotic stress responses as well as plant growth and development. In this study, a bioinformatics-based method was used to identify WRKY genes in zucchini (Cucurbita pepo L.). The CpWRKY family was revealed to comprise 103 members divided into seven subfamilies (I, II-a, II-b, II-c, II-d, II-e, and III). The members of each subfamily encoded highly conserved protein functional domains. However, five members (i.e., CpWRKY43, CpWRKY58, CpWRKY63, CpWRKY80, and CpWRKY93) encoded a unique WRKY sequence variant (WRKYGKK). In addition, an examination of gene replication events during evolution indicated that 11 tandemly duplicated gene pairs were the primary driving force behind the evolution of the CpWRKY gene family. The PlantCARE analysis of CpWRKY genes detected various cis-regulatory elements in the promoter region, including ABRE, MeJARE, LTR, MBS, ARE, and GRE, suggesting the encoded WRKY proteins likely modulate zucchini growth, development, and stress responses. Furthermore, the CpWRKY genes were differentially expressed in diverse tissues (root, stem, leaf, flower, and fruit) and under low-temperature and drought stress conditions. According to their expression patterns, CpWRKY16, CpWRKY51, and CpWRKY80 are probably involved in the zucchini responses to cold and drought stresses. Our findings have clarified the evolution of the WRKY superfamily in C. pepo, while also providing valuable insights into the functions of the encoded WRKY proteins.