Genome-wide investigation and analysis of U-box Ubiquitin–Protein ligase gene family in apple: Expression profiles during Penicillium expansum infection process

Abstract U-box is the protein domain, which was presented in proteins of yeasts to higher organisms. The U-box domain-contains proteins encoded by the U-box gene family, which is a huge gene family in plants. However, information about all U-box genes in apple, one of the most popular fruits all around the world is not clear and organized. In the present study, identification of the apple U-box genes was performed based on its whole-genome sequence. From the analysis, 69 U-box genes were found in apple according to the U-box domain. The U-box genes of apple distributed across all the 17 chromosomes at different densities. Phylogenetic analysis of U-box genes between apple and Arabidopsis thaliana suggested that the genes can be clustered into seven subgroups (I–VII) on the basis of their structural and phylogenetic features. Sixty-nine U-box genes and the structure of the encoded proteins were identified in apple. The RNA-seq results showed that 23 (56.1% of the detectable genes) U-box genes were found up-regulated and 18 (43.9% of the detectable genes) U-box genes were found down-regulated under P. expansum infection stress. RT-qPCR results showed the same trend with the transcriptome. The RT-qPCR validation showed that the results obtained in the transcriptomic analysis were accurate. The U-box genes of apple were strongly expressed during P. expansum infection. These results suggested that the U-box gene family of apple may play important role in the resistance mechanism of apple against P. expansum infection. This systematic research provided a foundation for further functional investigation of U-box genes with the aim of improving apple production.