IntroductionAlkaloids are one of the main medicinal components ofDendrobiumspecies.Dendrobiumalkaloids are mainly composed of terpene alkaloids. Jasmonic acid (JA) induce the biosynthesis of such alkaloids, mainly by enhancing the expression of JA-responsive genes to increase plant resistance and increase the content of alkaloids. Many JA-responsive genes are the target genes of bHLH transcription factors (TFs), especially the MYC2 transcription factor.MethodsIn this study, the differentially expressed genes involved in the JA signaling pathway were screened out fromDendrobium huoshanenseusing comparative transcriptomics approaches, revealing the critical roles of basic helix-loop-helix (bHLH) family, particularly the MYC2 subfamily.Results and discussionMicrosynteny-based comparative genomics demonstrated that whole genome duplication (WGD) and segmental duplication events drovebHLHgenes expansion and functional divergence. Tandem duplication accelerated the generation ofbHLHparalogs. Multiple sequence alignments showed that all bHLH proteins included bHLH-zip and ACT-like conserved domains. The MYC2 subfamily had a typical bHLH-MYC_N domain. The phylogenetic tree revealed the classification and putative roles of bHLHs. The analysis ofcis-acting elements revealed that promoter of the majority ofbHLHgenes contain multiple regulatory elements relevant to light response, hormone responses, and abiotic stresses, and thebHLHgenes could be activated by binding these elements. The expression profiling andqRT-PCR results indicated thatbHLHsubgroups IIIe and IIId may have an antagonistic role in JA-mediated expression of stress-related genes.DhbHLH20andDhbHLH21were considered to be the positive regulators in the early response of JA signaling, whileDhbHLH24andDhbHLH25might be the negative regulators. Our findings may provide a practical reference for the functional study ofDhbHLHgenes and the regulation of secondary metabolites.