Genome-wide identification of the bHLH gene family in Scutellaria baicalensis and their relationship with baicalin biosynthesis under drought stress

The bHLH gene family plays a critical role in regulating internal responses in plants. Although the pharmacological properties of <i>Scutellaria baicalensis</i> have been extensively studied, its bHLH gene family remains poorly investigated. In this study, 142 <i>SbbHLH</i> genes were identified using the complete genome data of <i>S. baicalensis</i>. Phylogenetic and conserved motif analyses were performed. Gene duplication events were analyzed, and cis-element analysis was conducted to explore regulatory factors. The expression patterns of these genes in different tissues and under drought stress were investigated using transcriptome data and qRT-PCR analysis. Phylogenetic and conserved motif analyses revealed that the gene structures within each <i>SbbHLH</i> clade are relatively conserved. Gene duplication analysis identified 29 duplication events in the SbbHLH gene family, most of which involved gene pairs under purifying selection. Cis-element analysis revealed that these genes are regulated by various environmental and hormonal factors. Transcriptomic data and qRT-PCR results demonstrated tissue-specific expression patterns for the 142 <i>SbbHLH</i> genes. Additionally, <i>bHLH</i> genes potentially involved in baicalin biosynthesis were identified under drought stress. The findings suggest that under drought stress, <i>SbbHLH74, SbbHLH98</i>, and <i>SbbHLH142</i> are regulated by a network centered on <i>SbbHLH53</i>, which enhances baicalin biosynthesis. In conclusion, this study provides a comprehensive analysis of the bHLH gene family in <i>S. baicalensis</i> and identifies 4 potential <i>SbbHLH</i> genes involved in regulating baicalin biosynthesis under drought stress.