Bioinformatics Analysis Reveals the Evolutionary Characteristics of the Phoebe bournei ARF Gene Family and Its Expression Patterns in Stress Adaptation

Auxin response factors (ARFs) are pivotal transcription factors that regulate plant growth, development, and stress responses. Yet, the genomic characteristics and functions of ARFs in <i>Phoebe bournei</i> remain undefined. In this study, 25 <i>PbARF</i> genes were identified for the first time across the entire genome of <i>P. bournei</i>. Phylogenetic analysis categorized these genes into five subfamilies, with members of each subfamily displaying similar conserved motifs and gene structures. Notably, Classes III and V contained the largest number of members. Collinearity analysis suggested that segmental duplication events were the primary drivers of <i>PbARF</i> gene family expansion. Structural analysis revealed that all <i>PbARF</i> genes possess a conserved B3 binding domain and an auxin response element, while additional motifs varied among different classes. Promoter cis-acting element analysis revealed that <i>PbARF</i> genes are extensively involved in hormonal responses-particularly to abscisic acid and jasmonic acid and abiotic stresses-as well as abiotic stresses, including heat, drought, light, and dark. Tissue-specific expression analysis showed that <i>PbARF25</i>, <i>PbARF23</i>, <i>PbARF19</i>, <i>PbARF22</i>, and <i>PbARF20</i> genes (class III), and <i>PbARF18</i> and <i>PbARF11</i> genes (class V) consistently exhibited high expression levels in the five tissues. In addition, five representative <i>PbARF</i> genes were analyzed using qRT-PCR. The results demonstrated significant differences in the expression of <i>PbARF</i> genes under various abiotic stress conditions (drought, salt stress, light, and dark), indicating their important roles in stress response. This study laid a foundation for elucidating the molecular evolution mechanism of <i>ARF</i> genes in <i>P. bournei</i> and for determining the candidate genes for stress-resistance breeding.