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.