The WRKY transcription factors play important roles in various physiological processes, especially in regulating plant resistance to environmental stresses. Watermelon (Citrullus lanatus) plants suffer from various stressful climate conditions during their growth, especially cold stress. However, little information about the exact role of WRKYs in watermelon responses to cold was available. In this study, a total of 57 candidate ClWRKY genes from watermelon genome were identified and they were distributed unevenly on 11 chromosomes. After excluding five ClWRKY genes with incomplete WRKY domains, phylogenetic analysis showed that the remaining 52 ClWRKY genes could be divided into three groups with 11 members in Group 1, 34 in Group 2, and seven in Group 3. The ClWRKY genes in group 2 could be further classified into five subgroups with three members in 2a, five in 2b, 13 in 2c, six in 2d, and seven in 2e, respectively. The expression profiles of ClWRKY genes in response to cold stress could be classified into four types: four ClWRKY genes had little or no change in transcript levels, seven ClWRKY genes had irregular expression patters, 17 ClWRKY genes were upregulated, and 25 ClWRKY genes were downregulated. The different regulation patterns of ClWRKY genes in response to low-temperature treatment revealed that the WRKY gene family was crucial for cold stress tolerance and there were multiple regulatory pathways involved in cold resistance.
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