Genome-wide identification and analysis of UBP gene family in Quercus robur

Ubiquitin-specific proteases (UBPs), the largest group of deubiquitinating enzymes (DUBs), play pivotal roles in various aspects of plant physiology including growth, development, and stress response by maintaining the ubiquitin molecule pool or removing ubiquitin from targeted proteins. While numerous studies exist on UBPs across various plant species, studies focusing on the Fagaceae family remain scarce. In this study, 20 UBP genes were identified in Quercus robur and phylogenetically classified into 12 groups, supported by domain organization and conserved motif composition. The gene structures and chromosomal localizations of these genes were elucidated. To understand the evolution of the QrUBP gene family, synteny analysis was conducted among Q. robur and five other plant species. Notably, four QrUBP genes (QrUBP3, QrUBP12A, QrUBP16, and QrUBP23) were found to have at least four isogenous gene pairs, implying important roles in the phylogenetic process of the UBP gene family. Moreover, cis-acting elements analysis reveals that the QrUBP promoters contain a large number of hormone-response elements and stress-response elements. The RT-qPCR analysis of roots, stems, and leaves indicates that some of the QrUBP genes were expressed ubiquitously, while others were organ-specific. For example, QrUBP15* was primarily expressed in roots, while QrUBP8 showed tissue-specific expression in stems. Additionally, comprehensive physicochemical and subcellular localization analyses were conducted. Collectively, this comprehensive study provides insights into the UBP gene family in Q. robur, laying a solid foundation for future investigations elucidating the functional roles of QrUBP genes in plant growth and stress responses.