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Background  Basic helix-loop-helix/helix-loop-helix (bHLH/HLH) transcription factors play important roles in plant development. Many reports have suggested that bHLH/HLH proteins participate in brassinosteroid (BR) hormone signaling pathways to promote cell elongation. Cotton fibers are single-cells and derived from seed surface. To explore the roles of bHLH/HLH proteins in cotton fiber development progress by modulating BR signaling pathway, we performed a systematic analysis of the  bHLH/HLH  gene family in upland cotton ( Gossypium hirsutum ) genome.    Results  In this study, we identified 437  bHLH/HLH  genes in upland cotton ( G. hirsutum ) genome. Phylogenetic analysis revealed that GhbHLH/HLH proteins were split into twenty six clades in the tree. These  GhbHLH/HLH  genes are distributed unevenly in different chromosomes of cotton genome. Segmental duplication is the predominant gene duplication event and the major contributor for amplification of  GhbHLH/HLH  gene family. The  GhbHLH/HLHs  within the same group have conserved exon/intron pattern and their encoding proteins show conserved motif composition. Based on transcriptome data, we identified 77  GhbHLH/HLH  candidates that are expressed at relatively high levels in cotton fibers. As adding exogenous BR (brassinolide, BL) or brassinazole (Brz, a BR biosynthesis inhibitor), expressions of these  GhbHLH/HLH  genes were up-regulated or down-regulated in cotton fibers. Furthermore, overexpression of GhbHLH282 (one of the BR-response genes) in Arabidopsis not only promoted the plant growth, but also changed plant response to BR signaling.    Conclusion  Collectively, these data suggested that these  GhbHLH/HLH  genes may participate in BR signaling transduction during cotton fiber development. Thus, our results may provide a valuable reference data as the basis for further studying the roles of these  bHLH/HLH  genes in cotton fiber development.    Electronic supplementary material  The online version of this article (10.1186/s12870-018-1523-y) contains supplementary material, which is available to authorized users.

Characterization of bHLH/HLH genes that are involved in brassinosteroid (BR) signaling in fiber development of cotton (Gossypium hirsutum)