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Background  Aspartic proteases (APs) are a large family of proteolytic enzymes found in almost all organisms. In plants, they are involved in many biological processes, such as senescence, stress responses, programmed cell death, and reproduction. Prior to the present study, no grape AP gene(s) had been reported, and their research on woody species was very limited.    Results  In this study, a total of 50 AP genes ( VvAP ) were identified in the grape genome, among which 30 contained the complete ASP domain. Synteny analysis within grape indicated that segmental and tandem duplication events contributed to the expansion of the grape AP family. Additional analysis between grape and  Arabidopsis  demonstrated that several grape AP genes were found in the corresponding syntenic blocks of  Arabidopsis , suggesting that these genes arose before the divergence of grape and  Arabidopsis . Phylogenetic relationships of the 30  VvAPs  with the complete ASP domain and their  Arabidopsis  orthologs, as well as their gene and protein features were analyzed and their cellular localization was predicted. Moreover, expression profiles of  VvAP  genes in six different tissues were determined, and their transcript abundance under various stresses and hormone treatments were measured. Twenty-seven  VvAP  genes were expressed in at least one of the six tissues examined; nineteen  VvAPs  responded to at least one abiotic stress, 12  VvAPs  responded to powdery mildew infection, and most of the  VvAPs  responded to SA and ABA treatments. Furthermore, integrated synteny and phylogenetic analysis identified orthologous AP genes between grape and  Arabidopsis , providing a unique starting point for investigating the function of grape AP genes.    Conclusions  The genome-wide identification, evolutionary and expression analyses of grape AP genes provide a framework for future analysis of AP genes in defining their roles during stress response. Integrated synteny and phylogenetic analyses provide novel insight into the functions of less well-studied genes using information from their better understood orthologs.

Genome-wide identification, evolutionary and expression analysis of the aspartic protease gene superfamily in grape