• • 170 bHLH transcription factors with complete HLH domains were identified across 14 chromosomes, with protein lengths of 67–885 aa and molecular masses of 7,910.58–98,854.78; this comprehensive inventory enables targeted functional genomics for phillygenin yield improvement.
• • Phylogenetic clustering resolved 13 subfamilies, with subfamily III containing the most members; this structural diversity suggests functional specialization that can be exploited for precise breeding or metabolic engineering.
• • Cis-acting element profiling revealed light-, hormone-, and stress-responsive elements in FsbHLHs, indicating that phillygenin accumulation can be modulated by environmental and hormonal inputs, with direct implications for controlled cultivation.
• • MeJA treatment for 48 h followed by qRT-PCR and correlation with phillygenin content identified FsbHLH26 and FsbHLH139 as key regulatory candidates; these two genes represent high-value targets for genetic validation and marker-assisted selection.