Genome-wide analysis of basic helix-loop-helix (bHLH) transcription factors in Brachypodium distachyon

Abstract

BackgroundAs a superfamily of transcription factors (TFs), the basic helix-loop-helix (bHLH) proteins have been characterized functionally in many plants with a vital role in the regulation of diverse biological processes including growth, development, response to various stresses, and so on. However, no systemic analysis of the bHLH TFs has been reported in Brachypodium distachyon, an emerging model plant in Poaceae.ResultsA total of 146 bHLH TFs were identified in the Brachypodium distachyon genome and classified into 24 subfamilies. BdbHLHs in the same subfamily share similar protein motifs and gene structures. Gene duplication events showed a close relationship to rice, maize and sorghum, and segment duplications might play a key role in the expansion of this gene family. The amino acid sequence of the bHLH domains were quite conservative, especially Leu-27 and Leu-54. Based on the predicted binding activities, the BdbHLHs were divided into DNA binding and non-DNA binding types. According to the gene ontology (GO) analysis, BdbHLHs were speculated to function in homodimer or heterodimer manner. By integrating the available high throughput data in public database and results of quantitative RT-PCR, we found the expression profiles of BdbHLHs were different, implying their differentiated functions.ConclusionOne hundred fourty-six BdbHLHs were identified and their conserved domains, sequence features, phylogenetic relationship, chromosomal distribution, GO annotations, gene structures, gene duplication and expression profiles were investigated. Our findings lay a foundation for further evolutionary and functional elucidation of BdbHLH genes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-4044-4) contains supplementary material, which is available to authorized users.

Genome-wide survey of the bHLH super gene family in Brassica napus

“…Expression differences in BnabHLHs following hormone treatments was assessed by the Welch's t-test (*P < 0.05; **P < 0.01). Comparison between treatments and control (CK, 0 h) according to Welch's t-test (*P < 0.05; **P < 0.01) presence of highly conserved intron patterns and motif distribution within each subfamily [42,43]. In this study, the bHLH sequence characteristics within each subfamily were also highly conserved, which independently supports our phylogeny analysis and classification results.…”

“…By contrast, there was a total of 162 AtbHLHs in the study by Pires and Dolan [6] resulting in 12 newly identified orphan genes, such as AtbHLH022/ DYT1, AtbHLH159/P1r2, and AtbHLH102/BIM2 etc. Generally, the division of a gene family is based on the topology and bootstrap value of the phylogenetic tree [42,43]. However, we found that subfamilies VII (a + b), IX, and IIIf in the results of Pires and Dolan [6] did not consist of a consensus node, but were across different branches/clades instead.…”

Genome-wide Survey of the bHLH Super Gene Family in Brassica napus

“…Several other genetic characteristics must be considered when performing subfamily classifications, including the presence of highly conserved intron patterns and motif distribution within each subfamily [42,43]. In this study, the bHLH sequence characteristics within each subfamily were also highly conserved, which independently supports our phylogeny analysis and classification results.…”

Genome-wide Survey of bHLH Super Gene Family in Brassica napus and Their Roles in Roots

“…The difference may be attributed to more sequences from Brassicaceae species applied that have close evolutionary relationship. It is reported that many other characteristics of candidates generally supply important clues to support the subfamily classification, including highly conserved intron pattern and motif distribution within each subfamily [40,41]. Similarly, the sequence characteristics within each subfamily are also highly conserved in our results, which provides an independent support to our phylogeny analysis and classification as well.…”

“…By contrast, there was a total of 162 AtbHLHs in the study of Pires and Dolan resulting in 12 newly identified orphan genes, such as AtbHLH022/DYT1, AtbHLH159/P1r2 and AtbHLH102/BIM2 etc. Generally, the division of gene family is performed on the basis of the topology and bootstrap value of the phylogenetic tree [40,41]. However, we find that subfamilies VII (a+b), IX and IIIf in the result of Pires and Dolan did not consist of a consensus node, but across different branches/clades instead [6].…”