Genome-Wide Characterization and Analysis of the bHLH Gene Family in Perilla frutescens

<i>Perilla frutescens</i> (L.) Britt. is a traditional medicinal and culinary plant with a long history of cultivation and significant potential for broader utilization. The basic helix-loop-helix (<i>bHLH</i>) gene family is essential for regulating plant growth, development, stress responses, and secondary metabolism. However, the <i>bHLH</i> gene family in <i>P. frutescens</i> has not yet been characterized. In this study, a total of 205 <i>bHLH</i> genes were identified in <i>P. frutescens</i> through genome mining and analysis. Phylogenetic analysis classified these <i>PfbHLH</i> genes into 23 distinct subfamilies. Promoter analysis revealed an enrichment of cis-acting elements linked to plant hormone signaling and stress responses, suggesting their potential regulatory roles in development, growth, and stress adaptation. Expression profiling based on publicly available RNA-seq data demonstrated tissue-specific expression patterns of <i>PfbHLH</i> genes in roots, stems, and leaves. Four <i>PfbHLH</i> genes (<i>PfbHLH66</i>, <i>PfbHLH45</i>, <i>PfbHLH13</i>, and <i>PfbHLH5</i>) showed significant responses to methyl jasmonate (MeJA) induction. Yeast one-hybrid assays confirmed that these PfbHLH proteins could bind to the cis-acting G-box (CACGTG) element. This study offers new perspectives on the evolution, regulatory mechanisms, and functional roles of the <i>bHLH</i> gene family in <i>P. frutescens</i>. The findings deepen our understanding of the functional diversity within this gene family and establish a foundation for genetic enhancement and the biosynthesis of medicinal compounds in the species.