Genome-wide identification of basic helix-loop-helix (bHLH) genes in Pinellia ternata and their responses to abiotic stress and hormone treatments

Background Basic helix-loop-helix (bHLH) transcription factors constitute the second-largest transcription factor family in plants. They are widely distributed across plant genomes and play vital regulatory roles in plant growth and development, secondary metabolism, and responses to abiotic stress. Although the bHLH gene family has been widely identified and analyzed in many plant species, systematic genome-wide identification and functional analysis of bHLH genes in Pinellia ternata are still lacking. Results In this study, a total of 140 PtbHLH genes were identified, of which 135 were unevenly distributed on 13 chromosomes. Phylogenetic analysis with Arabidopsis thaliana divided the PtbHLH genes into 24 subfamilies, with no members clustered in subfamily VI. Gene structure and conserved motif analysis showed that members of the same subfamily had highly similar structural characteristics. Collinearity analysis identified three paralogous pairs among the 140 PtbHLH genes. Cross-species collinearity analysis revealed eight syntenic pairs between P. ternata and A. thaliana , 76 between P. ternata and Nicotiana tabacum , and 50 between P. ternata and Oryza sativa . Cis-element prediction showed that all PtbHLH promoters contained hormone-responsive elements, stress-responsive elements and transcription factor binding sites. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment indicated that PtbHLH genes were mainly involved in hormone signal transduction, environmental signal response and transcriptional regulation. Protein–protein interaction (PPI) analysis suggested that PtbHLH68 was predicted as a putative interaction hub interacting with multiple family members. Tissue expression profiles showed that PtbHLH genes had diverse expression patterns, with most highly expressed in roots and tubers. Under high-temperature and drought stress, PtbHLH9 was most sensitive to high temperature, and PtbHLH85 was most sensitive to drought. Under methyl jasmonate (MeJA), abscisic acid (ABA) and salicylic acid (SA) treatments, PtbHLH73 responded most strongly to MeJA, PtbHLH7 to ABA, and PtbHLH48 responded significantly to all three hormones. These four genes serve as core candidates for exploring PtbHLH functions in abiotic stress tolerance and hormone signal transduction. Conclusion This study provides a solid foundation for understanding the functional mechanism of PtbHLH transcription factors in Pinellia ternata , and offers a valuable reference for the further screening of PtbHLH genes related to abiotic stress tolerance and hormone signaling pathways.