Abstract
Basic helix-loop-helix (bHLH) gene family, as one of the largest transcription factor families in plants, played essential roles in regulating plant growth and development as well as in response to various environmental stress. However, the bHLH gene family in R. simsii has not yet been reported. In this study, 116 RsbHLH genes were identified in the R. simsii genome, which were divided into 13 groups based on the sequence similarity and phylogenetic relationships. Analysis of gene/protein structure, chromosome location, cis-acting elements and synteny of the RsbHLH family genes were conducted using the bioinformatic methods. Gene duplication analysis showed that 99 RsbHLH genes were expanded and retained after dispersed and WGD/segmental duplication events. Investigation of cis-acting elements within promoters of RsbHLHs indicated that many RsbHLH genes might be involved in regulating the diverse physiological processes in R. simsii. The expression patterns of RsbHLHs in different tissues and in different stages of flower development were investigated based on the RNA-seq data. Further analysis revealed that 13 candidate RsbHLH genes might be involved in regulating the flower development of R. simsii. In addition, the results of qRT-PCR showed that five RsbHLH genes (RsbHLH033, RsbHLH016, RsbHLH048, RsbHLH114, and RsbHLH115) may be involved in positively and negatively regulating the high- and low-temperature stress. These results provide a basis for the functional characterization of RsbHLH genes and investigations on the molecular mechanisms of flower development of R. simsii.