Genome-wide identification and characterization of the bHLH gene family in an ornamental woody plant Prunus mume

Abstract

The basic helix-loop-helix (bHLH) transcription factor family is the second-largest family in plants, where it plays essential roles in development, and the responses to multiple abiotic and biotic stressors. However, little information is available about this gene family in Prunus mume, which is widely cultivated in East Asia as an ornamental fruit tree. Here, 100 PmbHLH genes were identified, and their evolution and functions were explored in P. mume for the first time. The PmbHLH genes were classified into 21 subfamilies. The chromosomal distribution, physicochemical properties, bHLH domain, conserved motif, and intron/exon compositions were also analyzed. Furthermore, the evolutionary pattern, divergence time of the PmbHLH family, and genetic relationships among P. mume, Arabidopsis thaliana, and Prunus persica and Fragaria vesca of Rosaceae were explored. The functional prediction analysis of these PmbHLHs indicated that their functions varied, and included participating in the formation of organs and tissues, responding to stress, and the biosynthesis and metabolism of hormones and other secondary metabolites. Interestingly, expression analyses of PmbHLHs also revealed diverse expression patterns. Most of the PmbHLH genes were highly expressed in roots and stems, and a few were highly expressed in leaves, buds, and fruits, indicating tissue expression specificity. Eight PmbHLH genes, which were upregulated during low-temperature stress, may have critical roles in the response to cold stress. Ten PmbHLHs were differentially expressed between weeping and upright branches in a P. mume F1 population. These results shed light on the structure and evolution of the PmbHLH gene family, and lay a foundation for further functional studies of the bHLH genes.