Genome-wide identification and expression analysis of bHLH transcription factor family in response to cold stress in sweet cherry (Prunus avium L.)

The basic helix-loop-helix (bHLH) family is one of the largest families of transcription factors (TFs) in plants and plays crucial roles in regulating growth, development and abiotic stress responses. However, systematic analyses of the bHLH TF family in sweet cherry (Prunus avium L.) have not been reported to date. In our study, 66 bHLH genes were identified in the sweet cherry genome, and the result of phylogenetic analysis indicated that these PavbHLHs could be classified into 17 subfamilies according to the classification of bHLHs in Arabidopsis thaliana. Sixty PavbHLH genes were unevenly distributed on 8 chromosomes, and 6 PavbHLH genes could not be mapped to any chromosome. Based on the PavbHLH’s amino acid sequences, 10 motifs were identified. Motif 1 and motif 2 were highly conserved among the almost all PavbHLH proteins. Exon-intron analysis indicated that proteins belonging to same subfamily exhibited a similar gene structure. Furthermore, promoter cis-element and protein interaction network prediction analysis suggested that most members of the PavbHLH family are involved in various processes in responses to cold stress. The results of semiquantitative reverse transcription-polymerase chain reaction (RT-PCR) showed that 62 PavbHLH genes were all expressed to varying degrees during various low-temperature treatments, of which the expression levels of approximately 20 PavbHLHs were rapidly induced in the early stages of 4 and 10 °C treatment, reached a peak and decreasing thereafter, while the expression continued to be upregulated at 16 °C. Combined with the results of the quantitative real-time PCR (qRT-PCR), it was preliminarily determined that PavbHLH1, -18, -28, -60, -61, -65 and -66 may be involved in regulating the responses to cold stress in sweet cherry. The present study offers useful perception into the sweet cherry bHLH gene family and its responses in cold stress.