Identification and expression analysis of the apple (Malus × domestica) basic helix-loop-helix transcription factor family

Abstract

Basic helix-loop-helix (bHLH) proteins, which are characterized by a conserved bHLH domain, comprise one of the largest families of transcription factors in both plants and animals, and have been shown to have a wide range of biological functions. However, there have been very few studies of bHLH proteins from perennial tree species. We describe here the identification and characterization of 175 bHLH transcription factors from apple (Malus × domestica). Phylogenetic analysis of apple bHLH (MdbHLH) genes and their Arabidopsis thaliana (Arabidopsis) orthologs indicated that they can be classified into 23 subgroups. Moreover, integrated synteny analysis suggested that the large-scale expansion of the bHLH transcription factor family occurred before the divergence of apple and Arabidopsis. An analysis of the exon/intron structure and protein domains was conducted to suggest their functional roles. Finally, we observed that MdbHLH subgroup III and IV genes displayed diverse expression profiles in various organs, as well as in response to abiotic stresses and various hormone treatments. Taken together, these data provide new information regarding the composition and diversity of the apple bHLH transcription factor family that will provide a platform for future targeted functional characterization.

Genomic Characterization and Expression Analysis of Basic Helix-Loop-Helix (bHLH) Family Genes in Traditional Chinese Herb Dendrobium officinale

“…We found that four clades in Arabidopsis were not present in D. officinale. The similar results were found in other plants such as C. tinctorius [48], apple [51], and wheat [42], which suggests those genes were lost during their evolution. Clades 14 and 15 of the bHLH family in D. officinale contained 14 and 15 members, respectively, which accounted for as many as 28.57% members of the family.…”

Comparative transcriptome analysis of leaves from two grapevine species reveals an early gene expression profile associated with Elsinoe ampelina resistance

“…6). Most of them play critical roles in plant defense against biotic stress in previous reports [7,[31][32][33][34], and many were induced by E. ampelina infection in the HR grape at the earlier stages (Fig. 6).…”

Transcriptomic analysis reveals insights into the response to Hop stunt viroid (HSVd) in sweet cherry (Prunus avium L.) fruits

“…The bHLH family has been characterized by its function in anthocyanin biosynthesis, phytochrome signaling and fruit dehiscence (Yang et al, 2017). Members of MYB/bHLH TFs or their complexes regulate distinct cellular processes such as responses to biotic stress, hormone signaling and cell death (Stracke, Werber & Weisshaar, 2001;Toledo-Ortiz, Huq & Quail, 2003).…”