Genome-Wide Analysis of Basic Helix-Loop-Helix (bHLH) TFs in Sea Buckthorn (Hippophae rhamnoides)

Abstract

Background The basic helix-loop-helix (bHLH) transcription factor gene family is one of the largest gene families and extensively involved in plant growth, organ development, and stress responses. However, limited studies are available on the gene family in sea buckthorn. Results In this study, we focused on 144 HrbHLH genes, exploring their DNA and protein sequences and physicochemical properties. According to their protein sequence similarities, we classified the genes into 15 groups with specific motif structures. In order to explore their expressions, we performed gene expression profiling using RNA-Seq and identified 108 HrbHLH genes that expressed in five sea buckthorn tissue, including root nodule, root, leaf, stem and fruit. Furthermore, we found 11 increased expressed HrbHLH genes during sea buckthorn fruit development. We validated the expression pattern of HrbHLH genes using reverse transcription quantitative real-time PCR. Conclusions This study lays the foundation for future studies on gene cloning, transgenes, and biological mechanisms. We performed a genome-wide, systematic analysis of bHLH proteins in sea buckthorn. This comprehensive analysis provides a useful resource that enables further investigation of the physiological roles and molecular functions of the HrbHLH TFs.