Genome-Wide Identification and Evolutionary Analysis of the bHLH Transcription Factor Family in Rosa roxburghii

The basic/helix-loop-helix (bHLH) transcription factors are crucial regulators of plant development and stress responses. In this study, we conducted a genome-wide analysis of the bHLH family in Rosa roxburghii, an economically important fruit crop. A total of 89 non-redundant RrbHLHs were identified and unevenly distributed across the seven chromosomes. Phylogenetic analysis classified them into 23 subfamilies and 7 Arabidopsis subfamilies were absent, indicating lineage-specific evolutionary trajectories. Conserved motif and gene structure analyses showed that members within the same subfamily generally shared similar architectures, yet subfamily-specific variations were evident, suggesting potential functional diversification. Notably, key residues involved in DNA-binding and dimerization were highly conserved within the bHLH domain. Promoter analysis identified multiple cis-acting elements related to hormone response, stress adaptation, and tissue-specific regulation, hinting at broad regulatory roles. Expression profiling across fruit developmental stages and in response to GA₃ treatment revealed dynamic expression patterns. Furthermore, 21 duplicated gene pairs (17 segmental and 4 tandem duplicated pairs) were identified, with most evolving under purifying selection. Detailed analysis of these pairs revealed that segmental duplication, coupled with structural variations such as exon indels, dissolution/joining, and exonization/pseudoexonization, substantially contributed to their functional divergence during evolution. Our results provide a basis for understanding the evolution and potential functions of the RrbHLHs.