Genome-Wide Identification and Evolution Analysis of the bHLH Gene Family in Cucurbita pepo L.

The basic helix–loop–helix (bHLH) gene family is one of the largest transcription factor families in plants and plays essential roles in growth, development, and responses to environmental stresses. However, the members and functional characteristics of the bHLH gene family in Cucurbita pepo L. remain largely unclear. In this study, a total of 175 bHLH genes were identified in Cucurbita pepo L., exhibiting considerable variation in protein length and structural features. Phylogenetic analysis classified these genes into 24 subgroups (Subgroup 1–24), with conserved motif compositions within each subgroup but clear divergence among different subfamilies, indicating functional differentiation. Gene duplication analysis revealed that WGD/segmental duplication was the primary driving force underlying the expansion of the bHLH gene family. Cis-regulatory element analysis showed that CpbHLH genes are mainly associated with light responsiveness, as well as plant growth and developmental processes. Furthermore, RNA-seq analysis revealed that CpbHLH genes exhibit tissue-specific expression patterns and dynamic responses to cold stress, and quantitative real-time PCR (qRT-PCR) analysis confirmed their tissue-specific expression patterns, together suggesting their potential roles in flower development and stress adaptation. Overall, this study provides a comprehensive overview of the CpbHLH gene family and lays a solid foundation for future functional characterization.