Abstract
BackgroundMembers of the basic helix-loop-helix (bHLH) transcription factor family perform indispensable functions in various biological processes, such as plant growth, seed maturation, and abiotic stress responses. However, the bHLH family in foxtail millet (Setaria italica), an important food and feed crop, has not been thoroughly studied.ResultsIn this study, 187 bHLH genes of foxtail millet (SibHLHs) were identified and renamed according to the chromosomal distribution of the SibHLH genes. Based on the number of conserved domains and gene structure, the SibHLH genes were divided into 21 subfamilies and two orphan genes via phylogenetic tree analysis. According to the phylogenetic tree, the subfamilies 15 and 18 may have experienced stronger expansion in the process of evolution. Then, the motif compositions, gene structures, chromosomal spread, and gene duplication events were discussed in detail. A total of sixteen tandem repeat events and thirty-eight pairs of segment duplications were identified in bHLH family of foxtail millet. To further investigate the evolutionary relationship in the SibHLH family, we constructed the comparative syntenic maps of foxtail millet associated with representative monocotyledons and dicotyledons species. Finally, the gene expression response characteristics of 15 typical SibHLH genes in different tissues and fruit development stages, and eight different abiotic stresses were analysed. The results showed that there were significant differences in the transcription levels of some SibHLH members in different tissues and fruit development stages, and different abiotic stresses, implying that SibHLH members might have different physiological functions.ConclusionsIn this study, we identified 187 SibHLH genes in foxtail millet and further analysed the evolution and expression patterns of the encoded proteins. The findings provide a comprehensive understanding of the bHLH family in foxtail millet, which will inform further studies on the functional characteristics of SibHLH genes.
Highlights
Members of the basic helix-loop-helix transcription factor family perform indispensable functions in various biological processes, such as plant growth, seed maturation, and abiotic stress responses
The basic domain is located at the N-terminus of the conserved basic helix-loop-helix (bHLH) domain; its DNA-binding capacity depends on the key amino acid residues in the basic region and the number of basic amino acid residues in the basic region [5,6,7]
Many bHLH genes have been identified in the plant kingdom; for example, in model plants, 147 bHLH transcription factors in Arabidopsis were divided into 21 subgroups [9] and 167 bHLH transcription factors of rice were divided into 22 subgroups [10]
Summary
Members of the basic helix-loop-helix (bHLH) transcription factor family perform indispensable functions in various biological processes, such as plant growth, seed maturation, and abiotic stress responses. Basic-helix-loop-helix (bHLH) transcription factors are widely present in eukaryotes. They are not unique to plants, they still form one of the largest transcription factor families in plants due to their numerous members [1, 2]. The basic region is located at the N-terminus and contains approximately 15 amino acids It binds to the cis-acting element E-box (5′-CANNTG3′) and determines whether bHLH transcription factors bind to DNA [3, 4]. The HLH region is distributed at the C-terminus of the gene sequence It comprises two α-helices connected by a relatively poorly conserved loop. Whole-genome analysis of the bHLH family in different species will help to understand the evolution of organisms, such as green algae, to adapt to environmental changes, along with the evolutionary origin of flowering plants
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