Transcriptome- and genome-wide systematic characterization of bHLH transcription factor family identifies promising members that respond to abiotic stress in tomato

Abstract The bHLH (basic helix-loop-helix) transcription factors function as crucial regulators in numerous biological processes including abiotic stress responses and plant development. According to our RNA-seq analysis of tomato seedlings under salt stress, we found that although bHLH gene family in tomato has been studied, there are still so many tomato bHLH genes have not been identified and named, which will hinder the later study of SlbHLHs. Therefore, the identification of tomato bHLH gene family is lagging and further genome-wide systematical identification and characterization is necessary for tomato bHLH genes. Here, numerous members of different gene families were identified to be the potential and significant candidates that respond to salt stress by RNA-seq analysis. 195 SlbHLHs that unevenly distributed onto 12 chromosomes were identified from tomato genome and were classified into 26 subfamilies based on their molecular features. The collinearity between SlbHLHs and interrelated orthologs from ten plants further revealed evolutionary insights into SlbHLHs. Cis-elements investigations of SlbHLHs promotors futhrer suggested the potential roles of SlbHLHs in tomato development and stress responses. 30 SlbHLHs were defined as the differentially expressed genes in response to salt stress by RNA-seq. The expression profiles of selected SlbHLHs were varyingly and markedly induced by multiple abiotic stresses and hormone treatments. These results provide valuable foundations for further exploring the salt resistance mechanism of tomato and functional characterizations of SlbHLHs, and numerous SlbHLHs may function as the key regulators to enhance plant tolerance to abiotic stress.