Comparative analysis of basic helix–loop–helix gene family among Brassica oleracea, Brassica rapa, and Brassica napus

Background: The basic helix–loop–helix (bHLH) transcription factors exist widely in eukaryotes and play important roles in development and stress response regulation in plants. The bHLH gene family has been identified in many species, except for Brassica oleracea and Brassica napus thus far. This study aims to identify the bHLH family members in B. oleracea, Brassica rapa, and B. napus and elucidate the expression, duplication, phylogeny and evolution characters of these genes. Result: A total of 268 bHLH genes in B. oleracea, 440 genes in B. napus, and 251 genes in B. rapa, including 21 new bHLH members, have been identified. Subsequently, the analysis of the phylogenetic tree, conserved motifs and gene structures showed that the members in the same subfamily were highly conserved. Most Ka/Ks values of the homologous gene were <1, which indicated that the homologous genes suffered from strong purifying selection for retention. The Ks values of the three Brassica crops were concentrated in the range of 0.3–0.5. Hence, the divergence time of the bHLH gene family between Brassica crops and Arabidopsis thaliana is approximately 10–18 MYA. The retention rates of BrabHLH and BolbHLH genes were 51.6% and 55.1%, respectively. A total of 182 genes were lost in B. napus after tetraploid. GO annotations of BolbHLH genes showed that most genes focused on DNA-binding transcription factor, DNA-binding, and protein dimerization activities. The temporal and spatial expression patterns of 50 BolbHLH genes were diverse, some of which showing high expression in the reproduction tissue, while some had high expression in the root. The comparison of expression patterns between B. rapa and B. napus showed that they had similar expression patterns in the root and contrasting patterns in the stems, leaves, and reproduction tissues. However, the expression patterns of B. oleracea and B. napus were different. Conclusion: This study is the first to report about the gene family analysis of the bHLH gene in B. oleracea and B. napus. Our results not only offer useful information on the functional analysis of the bHLH gene but also provide new insights into the evolution of Brassica spp.