Genome-Wide Characterization and Light-Responsive Expression Patterns of B-Box Transcription Factors in Artemisia argyi

For over 3000 years, the perennial herb mugwort (Artemisia argyi) has served as a cornerstone of traditional Asian medicine. Its clinical efficacy is driven by a diverse array of specialized metabolites, most notably flavonoids and volatile oils. While B-box (BBX) transcription factors are known to dictate photomorphogenic development and secondary metabolic pathways in plants, this specific gene family has not yet been systematically analyzed in A. argyi. Leveraging a chromosome-level genomic assembly, we comprehensively identified and analyzed the complete repertoire of AarBBX genes, profiling their structural organization, physicochemical attributes, conserved motifs, promoter architecture, and spatial expression dynamics. The AarBBX family segregates into five distinct evolutionary clades and comprises 114 members, exceeding the gene counts in the diploid relatives Artemisia annua (27) and Arabidopsis thaliana (32), a numerical increase potentially attributable to the tetraploid genome architecture of A. argyi. Promoter scanning revealed a high density of cis-acting elements linked to light perception and environmental stress responses. Integrating RNA-seq transcriptomics with tissue-specific expression profiling, we identified prominent candidate light-responsive AarBBX genes that are highly active in green, photosynthetic tissues and acutely responsive to shifts in light conditions, providing a foundation for future exploration of their potential relationship with secondary metabolic pathways, including flavonoid and terpenoid biosynthesis. Furthermore, we validated the potential operational compartments and structural interactions of these proteins utilizing green fluorescent protein (GFP) subcellular localization and yeast two-hybrid (Y2H) screenings. Collectively, these findings provide new insights into the evolutionary trajectory and regulatory potential of the B-box (BBX) proteins in A. argyi, offering a prioritized candidate gene set for subsequent investigations into their potential roles in light-regulated secondary metabolism, including flavonoid and terpenoid pathways.