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Plant U-box (PUB) proteins are ubiquitin ligases (E3) involved in multiple biological processes and in response to plant stress. However, the various aspects of the genome and the differences in functions between the U-box E3 (UBE3) ubiquitin ligases remain quite obscure in  Salvia miltiorrhiza . The 60  UBE3  genes in the  S. miltiorrhiza  genome were recognized in the present study. The phylogenetic analysis, gene structure, motifs, promoters, and physical and chemical properties of the genes were also examined. Based on the phylogenetic relationship, the 60  UBE3  genes were categorized under six different groups. The U-box domain was highly conserved across the family of  UBE3  genes. Analysis of the  cis -acting element revealed that the  UBE3  genes might play an important role in a variety of biological processes, including a reaction to the abscisic acid (ABA) treatment. To investigate this hypothesis, an ABA treatment was developed for the hairy roots of  S. miltiorrhiza . Thirteen out of the  UBE3  genes significantly increased after the ABA treatment. The co-expression network revealed that nine  UBE3  genes might be associated with phenolic acids or tanshinone biosynthesis. The findings of the present study brought fresh and new understanding to the participation of the  UBE3  gene family in plants, specifically in their biological responses mediated by the ABA. In  S. miltiorrhiza , this gene family may be crucial during the ABA treatment. Significantly, the results of this study contribute novel information to the understanding of the ubiquitin ligase gene and its role in plant growth.

Genome-Wide Analysis of U-box E3 Ubiquitin Ligase Family in Response to ABA Treatment in Salvia miltiorrhiza