Abstract
BackgroundThe basic helix-loop-helix (bHLH) proteins are a large superfamily of transcription factors, and play a central role in a wide range of metabolic, physiological, and developmental processes in higher organisms. Tomato is an important vegetable crop, and its genome sequence has been published recently. However, the bHLH gene family of tomato has not been systematically identified and characterized yet.ResultsIn this study, we identified 159 bHLH protein-encoding genes (SlbHLH) in tomato genome and analyzed their structures. Although bHLH domains were conserved among the bHLH proteins between tomato and Arabidopsis, the intron sequences and distribution of tomato bHLH genes were extremely different compared with Arabidopsis. The gene duplication analysis showed that 58.5% and 6.3% of SlbHLH genes belonged to low-stringency and high-stringency duplication, respectively, indicating that the SlbHLH genes are mainly generated via short low-stringency region duplication in tomato. Subsequently, we classified the SlbHLH genes into 21 subfamilies by phylogenetic tree analysis, and predicted their possible functions by comparison with their homologous genes of Arabidopsis. Moreover, the expression profile analysis of SlbHLH genes from 10 different tissues showed that 21 SlbHLH genes exhibited tissue-specific expression. Further, we identified that 11 SlbHLH genes were associated with fruit development and ripening (eight of them associated with young fruit development and three with fruit ripening). The evolutionary analysis revealed that 92% SlbHLH genes might be evolved from ancestor(s) originated from early land plant, and 8% from algae.ConclusionsIn this work, we systematically identified SlbHLHs by analyzing the tomato genome sequence using a set of bioinformatics approaches, and characterized their chromosomal distribution, gene structures, duplication, phylogenetic relationship and expression profiles, as well predicted their possible biological functions via comparative analysis with bHLHs of Arabidopsis. The results and information provide a good basis for further investigation of the biological functions and evolution of tomato bHLH genes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-014-1209-2) contains supplementary material, which is available to authorized users.
Highlights
The basic helix-loop-helix proteins are a large superfamily of transcription factors, and play a central role in a wide range of metabolic, physiological, and developmental processes in higher organisms
Identification and classification of tomato basic helix-loop-helix (bHLH) genes For genome-wide identification of bHLH genes in tomato, we initially identified the proteins using two approaches described in the Methods and filtered the results based on the criteria developed by Atchley et al [5] and Toledo-Ortiz et al [2]
Compared with the recent report by The Tomato Genome Consortium [21], 57 bHLH proteins were absent in this study because they did not conform to our minimal criteria for inclusion
Summary
The basic helix-loop-helix (bHLH) proteins are a large superfamily of transcription factors, and play a central role in a wide range of metabolic, physiological, and developmental processes in higher organisms. The basic helix–loop–helix (bHLH) proteins are a large superfamily of eukaryotic transcription factors, and play a central role in a wide range of metabolic, physiological, and developmental processes [1,2,3]. Their bHLH domain contains approximately 60 amino acids, including a basic region and a HLH region [4]. Group A of the bHLH proteins can bind to the E-box sequence. Group F proteins contain divergent sequences compared with other groups and another domain for dimerization and DNA binding [16]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
