Genome-wide analysis of PfBBXs transcription factors in Perilla frutescens and their expression responses to different light intensities.

Perilla frutescens (L.) Britt., a traditional Chinese herb used for both medicinal and culinary purposes, contained various bioactive compounds such as volatile oils, flavonoids, and phenolic acids, which contribute to its diverse pharmacological activities. BBXs (B-box zinc finger genes), a subfamily of zinc finger proteins, play critical regulatory roles in plant growth and development, abiotic stress responses, and pigment accumulation. However, research on the PfBBXs in P. frutescens remains limited. In this study, 31 PfBBXs were identified from the P. frutescens genome. Their protein physicochemical properties, phylogeny, conserved domains, motifs, cis-acting elements, and expression patterns were systematically analyzed. Phylogenetic analysis classified PfBBXs into five subfamilies, with similar conserved motifs and gene structures within each subfamily but notable divergence among them. Promoter regions of PfBBXs were enriched in cis-regulatory elements related to light responsiveness, stress responses, and phytohormone signaling. Different light intensities significantly affected the leaf area and the accumulation of anthocyanins and flavonoids. Integrated metabolomic and transcriptomic analyses revealed that light intensity modulated the biosynthesis of flavonoids and anthocyanins. Transcriptomic screening identified five highly light-responsive PfBBXs (PfBBX10, 12, 13, 17, and 18), whose light-induced expression patterns were further validated by qRT-PCR. Among them, PfBBX10, 12, and 17 exhibited significant positive correlations with anthocyanin and flavonoid contents, suggesting their pivotal roles in light signaling and secondary metabolism regulation. This study lays a foundation for functional characterization of PfBBXs in P. frutescens particularly in light signal transduction and anthocyanin accumulation.