Genome-wide identification and expression profiling of bHLH transcription factors associated with ferulic acid biosynthesis in Angelica sinensis

This study identifies 148 <i>bHLH</i> transcription factors in <i>Angelica sinensis</i> and reveals four putative candidates associated with ferulic acid biosynthesis, providing a genetic foundation for metabolic engineering to enhance the plant's medicinal value. The basic helix-loop-helix (bHLH) proteins regulate plant growth, development, stress responses, and secondary metabolites. While well-characterized in woody plants, they remain unexplored in <i>Angelica sinensis</i> (<i>A. sinensis</i>), a medicinal plant renowned for bioactive compounds including ferulic acid. Therefore, we systematically identified and characterized <i>bHLH</i> transcription factors in <i>A. sinensis</i> through whole-genome analysis and transcriptome profiling, identifying putative genes potentially regulating ferulic acid biosynthesis. Bioinformatic analyses were employed to characterize the physicochemical properties, gene structures, conserved motifs/domains, phylogenetic relationships, chromosome localization, collinearity, cis-acting elements, and transcriptome expression patterns of <i>AsbHLHs</i>. A total of 148 <i>AsbHLH</i> genes were annotated from the genomic database of <i>A. sinensis</i>, classified into 16 subfamilies based on the phylogenetic analysis. Results revealed that these transcription factors encode hydrophilic proteins (83-741 aa; 9.6-80.8 kDa), with nearly all localized to the nucleus. Gene structure analysis showed exon numbers ranging from 1 to 18, while MEME motif analysis identified five conserved motifs (1-5) shared across most <i>AsbHLH</i> proteins. Promoter analysis uncovered abundant <i>cis</i>-elements associated with growth, secondary metabolism (including ferulic acid biosynthesis), and stress responses. WGCNA revealed turquoise module contained 40 <i>bHLH</i> and five phenylpropanoid pathway-specific genes, from which PPI and phylogenetic analyses pinpointed four putative genes potentially associated with ferulic acid production. Quantitative RT-PCR validated these candidates, showing expression patterns consistent with transcriptome data. This study provides the first comprehensive genomic/transcriptomic resource for <i>AsbHLH</i> genes in <i>A. sinensis</i>, highlighting their secondary metabolic roles. Identified candidates enable genetic engineering strategies to boost ferulic acid production, enhancing <i>A. sinensis'</i> medicinal value.