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Background  The bHLH (basic helix-loop-helix) transcription factor is one of the largest families of transcription factors in plants, containing a large number of members with diverse functions. Chinese jujube ( Ziziphus jujuba  Mill.) is the species with the highest economic value in the family Rhamnaceae. However, the characteristics of the bHLH family in the jujube genome are still unclear. Hence,  ZjbHLHs  were first searched at a genome-wide level, their expression levels under various conditions were investigated systematically, and their protein-protein interaction networks were predicted.    Results  We identified 92  ZjbHLHs  in the jujube genome, and these genes were classified into 16 classes according to bHLH domains. Ten ZjbHLHs with atypical bHLH domains were found. Seventy  ZjbHLHs  were mapped to but not evenly distributed on 12 pseudo- chromosomes. The domain sequences among  ZjbHLH s were highly conserved, and their conserved residues were also identified. The tissue-specific expression of 37  ZjbHLH  genes in jujube and wild jujube showed diverse patterns, revealing that these genes likely perform multiple functions. Many  ZjbHLH  genes were screened and found to be involved in flower and fruit development, especially in earlier developmental stages. A few genes responsive to phytoplasma invasion were also verified. Based on protein-protein interaction prediction and homology comparison, protein-protein interaction networks composed of 92 ZjbHLHs were also established.    Conclusions  This study provides a comprehensive bioinformatics analysis of 92 identified  ZjbHLH  genes. We explored their expression patterns in various tissues, the flowering process, and fruit ripening and under phytoplasma stress. The protein-protein interaction networks of ZjbHLHs provide valuable clues toward further studies of their biological functions.    Electronic supplementary material  The online version of this article (10.1186/s12864-019-5936-2) contains supplementary material, which is available to authorized users.

Genome-wide analysis of the bHLH gene family in Chinese jujube (Ziziphus jujuba Mill.) and wild jujube