Exploring the guardian of abiotic stress: Genome-wide identification of the basic helix-loop-helix transcription factor family in Juglans mandshurica

The Basic helix-loop-helix (bHLH) transcription factors are wildly involved in many physiological processes in plants, such as tissue/organ development, metabolite synthesis, signal transduction and abiotic stress response. However, the structure, characteristics, and functions of bHLH genes remain unknown in Juglans mandshurica. This study identified 118 bHLH gene family members using a genome-wide database and classified into 16 subfamilies. Gene structure and conserved motifs analysis revealed that the protein structure of each JmbHLH subfamily was relatively conserved. Four pairs of tandem replication genes (JmbHLH015-JmbHLH016, JmbHLH022-JmbHLH023-JmbHLH024, JmbHLH092-JmbHLH093, and JmbHLH108-JmbHLH109) were identified, which could explain the functional diversity of JmbHLH genes. The Ka/Ks values of the intraspecific collinear gene pairs were less than 1, indicating that the genes were relatively conserved during evolution. Protein interaction network analysis predicted the key genes in the JmbHLH functional network. JmbHLH genes that regulate tissues/organs development and light stress were screened using transcriptomic data, the expression pattern of JmbHLH genes differed significantly. Additionally, twelve JmbHLH genes were expressed differently under drought, salt, and cadmium stress, demonstrating that these genes may have multiple biological functions. The results provide new insights into the characteristics and regulatory functions of JmbHLH genes in J. mandshurica.