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Background  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. 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.    Results  In 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.    Conclusions  In 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 material  The online version of this article (doi:10.1186/s12864-014-1209-2) contains supplementary material, which is available to authorized users.

Genome-wide identification and characterization of the bHLH gene family in tomato