Genome-Wide Identification and Expression Analysis of the Ginkgo biloba B-Box Gene Family in Response to Hormone Treatments, Flavonoid Levels, and Water Stress

B-box (BBX) transcription factors, which are specific to the plant kingdom, play a crucial role in regulating light-dependent growth, development, secondary metabolite biosynthesis, and the response to biotic and abiotic stresses. Despite their significance, there has been a lack of systematic investigation into the BBX gene family in <i>Ginkgo biloba</i>. In the present study, we identified nine BBX genes within the <i>G. biloba</i> reference genome, distributed across seven chromosomes, and classified them into four groups based on their phylogenetic relationships with the BBX gene families of <i>Arabidopsis thaliana</i>. Our analysis of gene structure, conserved domains, and motifs suggests that <i>GbBBX</i>s exhibit a high degree of conservation throughout evolutionary history. Additionally, synteny analysis revealed that dispersed duplication events have contributed to the expansion of the BBX gene family in <i>G. biloba</i>. An examination of cis-regulatory elements indicated that numerous <i>GbBBX</i> genes contain motifs associated with light, hormones, and stress, suggesting their potential roles in responding to these signals and environmental adaptation. Expression profiles obtained from RNA-Seq data and quantitative Real-Time PCR (qRT-PCR) analyses of <i>GbBBX</i> genes across various organs, hormone treatments, and leaves with differing flavonoid content, as well as during both short-term and long-term water stress, demonstrated their potential roles in flavonoid regulation and responses to hormones and water stress. Subcellular localization studies indicated that the proteins GbBBX5, GbBBX7, GbBBX8, and GbBBX9 are localized within the nucleus. This study is the first thorough analysis of the BBX gene family in <i>G. biloba</i>, providing a valuable foundation for further understanding their evolutionary context and functional roles in flavonoid regulation and responses to water stress.