Genome-wide analysis of the bHLH family and identification of bHLH genes involved in fruit development and ripening of cultivated octoploid strawberry

Abstract Objectives The basic helix–loop–helix (bHLH) transcription factors (TFs) regulate fruit growth in many plants. However, there is no available study on the bHLH gene family in the haplotype-resolved genome of cultivated strawberry (Fragaria × ananassa). Materials and Methods The 131 FabHLH genes identified in the strawberry cultivar ‘Yanli’ haplotype-resolved genome were classified into 24 subfamilies according to their phylogenetic relationships. Gene structure, conserved motifs, and chromosomal locations were investigated using bioinformatics. Results In total, 15 FabHLH genes potentially involved in fruit development were screened based on transcriptome analysis of different stages of fruit development. We also identified the cis-regulatory elements of these 15 FabHLH genes, predicted upstream transcription factors, and identified protein–protein interactions. Conclusions The findings of this study improve our understanding of the regulation mediated by bHLH TFs during strawberry fruit growth and maturation.