Genome-wide investigation and analysis of U-box E3 ubiquitin-protein ligase gene family in kiwifruit (Actinidia chinensis) in response to the yeast antagonist, Wickerhamomyces anomalus

Although the ubiquitin ligase U-box protein family is a vital component of plant development and stress response, the exact role of kiwifruit U-box genes family is not known. The study identified 73 putative U-box genes from the kiwifruit genome. Chromosomal localisation, phylogenetic analysis, physicochemical properties, gene structure, motifs, and promoters of these genes were analysed. Distribution of Actinidia chinensis PUB (AcPUB) genes exhibited varying densities across 27 chromosomes. The study found that U-box clusters were classified into groups I-VII in phylogenetic analyses of a variety of plants, including kiwifruit, Arabidopsis thaliana, and rice, with most of the genes in kiwifruit being related to rice. The conserved motif analyses revealed that all the AcPUB genes have typical U-box structural domains. Analysis of the cis-acting elements suggested that AcPUBs expression may be responsive to several hormones and stresses. RNA-Seq analysis showed that six kiwifruit U-box genes were differentially expressed after induction by Wickerhamomyces anomalus, suggesting a potential involvement of these U-box genes in the kiwifruit's response to W. anomalus, which might include mechanisms related to resistance. Overall, our findings provide valuable insights into the function and structure of U-box genes that will help develop new genomic technologies and study plant resistance.