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Background  The basic/helix-loop-helix (bHLH) transcription factor family exists in all three eukaryotic kingdoms as important participants in biological growth and development. To date, the comprehensive genomic and functional analyses of  bHLH  genes has not been reported in cucumber ( Cucumis sativus  L.).    Results  Here, a total of 142  bHLH  genes were identified and classified into 32 subfamilies according to the conserved motifs, phylogenetic analysis and gene structures in cucumber. The sequences of CsbHLH proteins were highly conserved based on the results of multiple sequence alignment analyses. The chromosomal distribution, synteny analysis, and gene duplications of these 142  CsbHLHs  were further analysed. Many elements related to stress responsiveness and plant hormones were present in the promoter regions of  CsbHLH  genes based on a  cis -element analysis. By comparing the phylogeny of cucumber and  Arabidopsis  bHLH proteins, we found that cucumber bHLH proteins were clustered into different functional clades of  Arabidopsis  bHLH proteins. The expression analysis of selected  CsbHLHs  under abiotic stresses (NaCl, ABA and low-temperature treatments) identified five  CsbHLH  genes that could simultaneously respond to the three abiotic stresses. Tissue-specific expression profiles of these five genes were also analysed. In addition,  35S : CsbHLH041  enhanced the tolerance to salt and ABA in transgenic  Arabidopsis  and in cucumber seedlings, suggesting  CsbHLH041  is an important regulator in response to abiotic stresses. Lastly, the functional interoperability network among the CsbHLH proteins was analysed.    Conclusion  This study provided a good foundation for further research into the functions and regulatory mechanisms of CsbHLH proteins and identified candidate genes for stress resistance in cucumber.

bmc plant biology

Genome-wide identification and characterization of cucumber bHLH family genes and the functional characterization of CsbHLH041 in NaCl and ABA tolerance in Arabidopsis and cucumber