Genome-Wide Analysis of Basic Helix-Loop-Helix Superfamily Members Reveals Organization and Chilling-Responsive Patterns in Cabbage (Brassica oleracea var. a L.).

Basic helix-loop-helix (bHLH) transcription factor (TF) family is commonly found in eukaryotes, which is one of the largest families of regulator proteins. It plays an important role in plant growth and development, as well as various biotic and abiotic stresses. However, a comprehensive analysis of the bHLH family has not been reported in . In this study, we systematically describe the in the phylogenetic relationships, expression patterns in different organs/tissues, and in response to chilling stress, and gene and protein characteristics. A total of 234 genes were identified in the genome and were further clustered into twenty-three subfamilies based on the phylogenetic analyses. A large number of genes were unevenly located on nine chromosomes of . Analysis of RNA-Seq expression profiles revealed that 21 genes exhibited organ/tissue-specific expression. Additionally, the expression of six (, , , , and ) were significantly down-regulated in chilling-sensitive cabbage (CS-D9) and chilling-tolerant cabbage (CT-923). At 24h chilling stress, was significantly down-regulated and up-regulated in chilling-treated CS-D9 and CT-923. Conserved motif characterization and exon/intron structural patterns showed that genes had similar structures in the same subfamily. This study provides a comprehensive analysis of genes and reveals several candidate genes involved in chilling tolerance of , which may be helpful to clarify the roles of bHLH family members and understand the regulatory mechanisms of genes in response to the chilling stress of cabbage.