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Background  Grapevine is an important fruit crop grown worldwide, and its cultivars are mostly derived from the European species  Vitis vinifera , which has genes for high fruit quality and adaptation to a wide variety of climatic conditions. Disease resistance varies substantially across grapevine species; however, the molecular mechanisms underlying such variation remain uncharacterized.    Results  The anatomical structure and disease symptoms of grapevine leaves were analyzed for two grapevine species, and the critical period of resistance of grapevine to pathogenic bacteria was determined to be 12 h post inoculation (hpi). Differentially expressed genes (DEGs) were identified from transcriptome analysis of leaf samples obtained at 12 and 36 hpi, and the transcripts in four pathways (cell wall genes, LRR receptor-like genes,  WRKY  genes, and pathogenesis-related (PR) genes) were classified into four co-expression groups by using weighted correlation network analysis (WGCNA). The gene  VdWRKY53 , showing the highest transcript level, was introduced into Arabidopsis plants by using a vector containing the CaMV35S promoter. These procedures allowed identifying the key genes contributing to differences in disease resistance between a strongly resistant accession of a wild grapevine species  Vitis davidii  ( VID ) and a susceptible cultivar of  V. vinifera , ‘Manicure Finger’ ( VIV ).  Vitis davidii,  but not  VIV,  showed a typical hypersensitive response after infection with a fungal pathogen ( Coniella diplodiella ) causing white rot disease. Further, 20 defense-related genes were identified, and their differential expression between the two grapevine species was confirmed using quantitative real-time PCR analysis.  VdWRKY53 , showing the highest transcript level, was selected for functional analysis and therefore over-expressed in Arabidopsis under the control of the CaMV35S promoter. The transgenic plants showed enhanced resistance to  C. diplodiella  and to two other pathogens,  Pseudomonas syringae  pv.  tomato  DC3000 and  Golovinomyces cichoracearum .    Conclusion  The consistency of the results in  VID  and transgenic Arabidopsis indicated that  VdWRKY53  might be involved in the activation of defense-related genes that enhance the resistance of these plants to pathogens. Thus, the over-expression of  VdWRKY53  in transgenic grapevines might improve their resistance to pathogens.    Electronic supplementary material  The online version of this article (10.1186/s41065-019-0089-5) contains supplementary material, which is available to authorized users.

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Identification of the defense-related gene VdWRKY53 from the wild grapevine Vitis davidii using RNA sequencing and ectopic expression analysis in Arabidopsis