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Background  The WRKY gene family is one of the most important families in higher plants. As transcription factors, they actively respond to biotic and abiotic stress and are also involved in plant development. Chinese jujube ( Ziziphus jujuba  Mill.) is the largest type of dried fruit tree in China in terms of production, but its production is largely limited by phytoplasma infection, and the information about the role of  WRKY  genes under phytoplasma stress was still limited.    Results  We identified 54  ZjWRKYs  in the jujube genome and classified them into three subgroups according to conserved WRKY domains and zinc-finger structure. 41  ZjWRKYs  were distributed on 11 of 12 pseudo chromosomes in Chinese jujube. The majority of  ZjWRKYs  were highly expressed in the seven examined tissues, indicating that they play multiple roles in these vegetative and reproductive organs. Transcriptome data showed that most of the characterised  ZjWRKYs  were highly expressed at later stages of fruit development. RT-qPCR demonstrated that the expression of 23  ZjWRKYs  changed following phytoplasma infection, suggesting that they are involved in signalling pathways that respond to phytoplasma stress. Then, STRING analysis and yeast two-hybrid screening proved that some ZjWRKY proteins were interacting with ZjMAPKK proteins, which were also involved in phytoplasma invasion. Moreover, their differential expressions were further confirmed in resistant and susceptible jujube varieties under phytoplasma stress. These results suggest that  ZjWRKYs  play significant roles in phytoplasma tolerance and should be crucial candidate genes for jujube-phytoplasma interaction.    Conclusions  54  ZjWRKYs  in Chinese jujube were identified and classified into three subgroups. 41  ZjWRKYs  were unevenly distributed along the chromosomes. The majority of  ZjWRKYs  were highly expressed in various tissues. Most of the  ZjWRKYs  were positive responses to phytoplasma invasion, and that provided candidate genes for the future studies of jujube-phytoplasma interaction.    Electronic supplementary material  The online version of this article (10.1186/s12864-019-5789-8) contains supplementary material, which is available to authorized users.

Genome-wide analysis of the WRKY gene family and their positive responses to phytoplasma invasion in Chinese jujube