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Background  The basic helix-loop-helix transcription factors play important roles in diverse cellular and molecular processes. Comparative functional genomics can provide powerful approaches to draw inferences about gene function and evolution among species. The comprehensive comparison of bHLH gene family in different gramineous plants has not yet been reported.    Results  In this study, a total of 183, 231 and 571  bHLH s were identified in rice, maize and wheat genomes respectively, and 1154  bHLH  genes from the three species and Arabidopsis were classified into 36 subfamilies. Of the identified genes, 110  OsbHLH s, 188  ZmbHLH s and 209  TabHLH s with relatively high mRNA abundances were detected in one or more tissues during development, and some of them exhibited tissue-specific expression such as  TabHLH454–459 ,  ZmbHLH099–101  and  OsbHLH037  in root,  TabHLH559–562 , −  046 , −  047  and  ZmbHLH010 , −  072 , −  226  in leaf,  TabHLH216–221 , −  333 , −  335 , −  340  and  OsbHLH005 , −  141  in inflorescence,  TabHLH081 ,  ZmbHLH139  and  OsbHLH144  in seed. Forty five, twenty nine and thirty one differentially expressed  bHLH s were respectively detected in wheat, maize and rice under drought stresses using RNA-seq technology. Among them, the expressions of  TabHLH046 , −  047 ,  ZmbHLH097 , −  098 ,  OsbHLH006  and −  185  were strongly induced, whereas  TabHLH303 , −  562 ,  ZmbHLH155 , −  154 ,  OsbHLH152  and −  113  showed significant down-regulation. Twenty two  TabHLH s were induced after stripe rust infection at 24 h and nine of them were suppressed at 72 hpi, whereas 28 and 6  TabHLH s exhibited obviously down- and up-regulation after powdery mildew attack respectively. Forty one  ZmbHLH s were differentially expressed in response to  F. verticillioides  infection. Twenty two co-expression modules were identified by the WGCNA, some of which were associated with particular tissue types. And GO enrichment analysis for the modules showed that some  TabHLH s were involved in the control of several biological processes, such as tapetal PCD, lipid metabolism, iron absorption, stress responses and signal regulation.    Conclusion  The present study identifies the bHLH family in rice, maize and wheat genomes, and detailedly discusses the evolutionary relationships, expression and function of  bHLH s. This study provides some novel and detail information about bHLHs, and may facilitate understanding the molecular basis of the plant growth, development and stress physiology.    Electronic supplementary material  The online version of this article (10.1186/s12870-018-1529-5) contains supplementary material, which is available to authorized users.

Comparative functional genomics analysis of bHLH gene family in rice, maize and wheat