Genome-wide analysis of the basic Helix-Loop-Helix (bHLH) transcription factor family in maize

Abstract

BackgroundIn plants, the basic helix-loop-helix (bHLH) transcription factors play key roles in diverse biological processes. Genome-wide comprehensive and systematic analyses of bHLH proteins have been well conducted in Arabidopsis, rice, tomato and other plant species. However, only few of bHLH family genes have been functional characterized in maize.ResultsIn this study, our genome-wide analysis identified 208 putative bHLH family proteins (ZmbHLH proteins) in maize (Zea mays). We classified these proteins into 18 subfamilies by comparing the ZmbHLHs with Arabidopsis thaliana bHLH proteins. Phylogenetic analysis, conserved protein motifs, and exon-intron patterns further supported the evolutionary relationships among these bHLH proteins. Genome distribution analysis found that the 208 ZmbHLH loci were located non-randomly on the ten maize chromosomes. Further, analysis of conserved cis-elements in the promoter regions, protein interaction networks, and expression patterns in roots, leaves, and seeds across developmental stages, suggested that bHLH family proteins in maize are probably involved in multiple physiological processes in plant growth and development.ConclusionWe performed a genome-wide, systematic analysis of bHLH proteins in maize. This comprehensive analysis provides a useful resource that enables further investigation of the physiological roles and molecular functions of the ZmbHLH transcription factors.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1441-z) contains supplementary material, which is available to authorized users.

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

“…Patterns f, a and k are the three types accounting for the majority of BnbHLHs (41.2%, 26.2% and 20.1% respectively). This trend is similar to the results in other species, such as Arabidopsis, rice, potato, poplar and tomato [8][9][10][11]13].…”

“…As an important plant transcription factor super gene family, genome-wide analysis of bHLHs has already been widely performed in a mass of species [7][8][9][10]. However, we find that there is still lacking a uniform subfamily classification of this gene family in plants, resulting in many sorts of classification.…”

“…For further comparative analysis across different species, we identified 255 bHLHs in B. oleracea genome by the same method (Additional file 2: Table S2). Sequence information of the bHLHs in other species like Arabidopsis, Brassica rapa, tomato, potato and rice are obtained from published researches [8][9][10][11]13].…”

“…Consequently, an obvious decrease of orphan gene proportions (total 15 genes, 2%) was observed, suggesting a relative better solution for the classfication of orpan genes. To date, this gene family have been genome-wide characterized in various plants, such as Z. mays [8], tomato [9], and B. rapa [10], etc., and the classification in most of those studies referred to that of Pires and Dolan. As a result, there did exist several inadequacies for the subfamily classification in those researches.…”

“…As one of the largest transcription factor gene families in plants, the number of bHLH genes (bHLHs) were largely increased during the evolution. For example, there was only one bHLH gene in Cyanidioschyzon Merolae [6], 98 bHLHs in moss [7], 208 in Zea mays [8], 167…”