Genome-Wide Identification and Characterization of bHLH Family in Kandelia obovata Under Salt Stress

Background/Objectives: bHLH transcription factors regulate key plant processes including development, stress adaptation, and metabolism. In Kandelia obovata, a mangrove species well known for its high tolerance to harsh environments, the bHLH gene family has not been systematically investigated. Here, this study aims to perform genome-wide identification and expression profiling of KobHLH genes under normal and saline conditions. Methods: bHLH members were identified by homology searches (HMMER and BLASTp) against the K. obovata protein dataset and verified with SMART-based domain analysis. Subsequent analyses covered physicochemical features, conserved motif composition, and phylogenetic relationships. Transcript abundance was quantified via RNA-seq in various organs (roots, stems, leaves, flowers, and fruits) as well as under saline conditions. Differentially expressed transcripts were selected for co-expression network construction. Results: Phylogenetic analysis of the 118 identified KobHLH loci assigned them into 18 distinct clades. Organ-preferential expression patterns were observed, leading to their classification into three putative functional categories. Upon salinity exposure (10–30‰), 61 of the 118 KobHLH genes exhibited differential expression, grouped into ten significant clusters. A co-expression network comprising 20 hub genes and 198 edges was constructed. Conclusions: This study provides the first genome-wide characterization of the bHLH family in K. obovata, revealing its evolutionary divergence and identifying 61 salt-responsive candidates, notably KobHLH108 and KobHLH5 associated with secondary metabolism, for further functional validation. The findings provide a foundation for future functional studies on stress adaptation mechanisms in this ecologically valuable mangrove species.