Global identification, structural analysis and expression characterization of bHLH transcription factors in wheat

• Published in: BMC plant biology Vol. 17; no. 1; p. 90
• Main Authors: Guo, Xiao-Jiang, Wang, Ji-Rui
• Format: Journal Article
• Language: English
• Published: England BioMed Central 30-05-2017; BMC
• Subjects: Amino acids; Basic Helix-Loop-Helix Transcription Factors - genetics; Basic Helix-Loop-Helix Transcription Factors - metabolism; bHLH; Categories; Classification; Clusters; Conserved sequence; Correlation analysis; Deoxyribonucleic acid; DNA; Endosperm; Expression pattern; Flowers & plants; Gene expression; Gene Expression Profiling; Gene sequencing; Genes; Genome, Plant; Genomes; Genomics; Helix-loop-helix proteins (basic); Identification; Leaves; Pattern analysis; Phylogenetics; Phylogeny; Plant Proteins - genetics; Plant Proteins - metabolism; Proteins; Reconstruction; Ribonucleic acid; Rice; RNA; RNA-Seq; Roots; Seedlings; Seeds; Shoots; Signal transduction; Spikes; Structural analysis; Synteny; Transcription factor; Transcription factors; Triticum - genetics; Triticum - metabolism; Triticum aestivum; Wheat; Transcription factor; Expression pattern; RNA-Seq; Wheat; bHLH
• ISSN: 1471-2229; 1471-2229
• DOI: 10.1186/s12870-017-1038-y

Basic helix-loop-helix (bHLH) transcription factors (TFs), which are widely distributed in eukaryotic organisms, play crucial roles in plant development. However, no comprehensive analysis of the bHLH family in wheat (Triticum aestivum L.) has been undertaken previously.
In this study, 225 bHLH TFs predicted from wheat using genomic and RNA sequencing data were subjected to identification, classification, phylogenetic reconstruction, conserved motif characterization, chromosomal distribution determination and expression pattern analysis. One basic region, two helix regions and one loop region were found to be conserved in wheat bHLH TFs. The bHLH proteins could be separated into four categories based on sequences in their basic regions. Neighbor-joining-based phylogenetic analysis of conserved bHLH domains from wheat, Arabidopsis and rice identified 26 subfamilies of bHLH TFs, of which 23 were found in wheat. A total of 82 wheat bHLH genes had orthologs in Arabidopsis (27 TFs), rice (28 TFs) and both of them (27 TFs). Seven tissue-specific bHLH TF clusters were identified according to their expression patterns in endosperm, aleurone, seedlings, heading-stage spikes, flag leaves, shoots and roots. Expression levels of six endosperm-specifically expressed TFs measured by qPCR and RNA-seq showed a good correlation.
The 225 bHLH transcription factors identified from wheat could be classed into 23 subfamilies, and those members from the same subfamily with similar sequence motifs generally have similar expression patterns.