Genome-Wide Identification and Expression Analysis of the Plant U-Box Protein Gene Family in Phyllostachys edulis

Abstract

The <i>U-box</i> gene encodes a ubiquitin ligase that contains a U-box domain. The plant U-box (PUB) protein plays an important role in the plant stress response; however, very few studies have investigated the role of these proteins in Moso bamboo (<i>Phyllostachys edulis</i>). Thus, more research on PUB proteins is necessary to understand the mechanisms of stress tolerance in <i>P. edulis</i>. In this study, we identified 121 members of the PUB family in <i>P. edulis</i> (<i>PePUB</i>), using bioinformatics based on the <i>P. edulis</i> V2 genome build. The <i>U-box</i> genes of <i>P. edulis</i> showed an uneven distribution among the chromosomes. Phylogenetic analysis of the <i>U-box</i> genes between <i>P. edulis</i> and <i>Arabidopsis thaliana</i> suggested that these genes can be classified into eight subgroups (Groups I-VIII) based on their structural and phylogenetic features. All <i>U-box</i> genes and the structure of their encoded proteins were identified in <i>P. edulis</i>. We further investigated the expression pattern of <i>PePUB</i> genes in different tissues, including the leaves, panicles, rhizomes, roots, and shoots. The qRT-PCR results showed that expression of three genes, <i>PePUB15</i>, <i>PePUB92,</i> and <i>PePUB120</i>, was upregulated at low temperatures compared to that at 25°C. The expression levels of two <i>PePUBs</i>, <i>PePUB60</i> and <i>PePUB120</i>, were upregulated under drought stress. These results suggest that the <i>PePUB</i> genes play an important role in resistance to low temperatures and drought in <i>P. edulis</i>. This research provides new insight into the function, diversity, and characterization of <i>PUB</i> genes in <i>P. edulis</i> and provides a basis for understanding their biological roles and molecular mechanisms.