Genome-Wide Identification and Characterization of bHLH Transcription Factors in Zanthoxylum bungeanum and Their Expression Analysis in Response to Salt Stress

The basic helix-loop-helix (bHLH) transcription factors represent one of the largest gene families and play critical roles in plant development and stress response modulation. However, the bHLH gene family in Zanthoxylum bungeanum (ZB)-a species with notable economic and medicinal importance-remains unexplored. In this study, we conducted a thorough genome-wide analysis of the ZBbHLH family. Our findings revealed that 415 ZBbHLH genes are distributed across 60 different chromosomes and are classified into 24 subfamilies based on phylogenetic analysis. Gene structure and protein motif analyses demonstrated the conservation of these genes. Duplication events indicated that ZBbHLH genes have undergone strong purifying selection during evolution. Codon usage analysis showed a bias toward A/T-ending codons, suggesting a significant influence of natural selection. Exposure to salt stress for different durations (0, 3, 9, and 24 h) facilitated the identification of 100 differentially expressed genes (DEGs), which were significantly enriched in plant hormone signal transduction (KO04075) and MAPK signaling pathways (KO04016). Moreover, the qRT-PCR results were largely in agreement with the transcriptome sequencing results, confirming the accuracy of the findings. This study provides valuable insights into the structural features, functional roles, and evolutionary divergence of the ZBbHLH gene family. It lays a foundation for further exploring the physiological and molecular mechanisms underlying bHLH transcription factors in ZB.