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

Abstract

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 gene family of tomato has not been systematically identified and characterized yet. Results: In this study, we identified 159 bHLH protein-encoding genes in tomato genome and analyzed their structures. Although bHLH domains were conserved among the bHLH proteins between tomato and, the intron sequences and distribution of tomato genes were extremely different compared with. The gene duplication analysis showed that 58.5% and 6.3% of genes belonged to low-stringency and high-stringency duplication, respectively, indicating that the genes are mainly generated via short low-stringency region duplication in tomato. Subsequently, we classified the genes into 21 subfamilies by phylogenetic tree analysis, and predicted their possible functions by comparison with their homologous genes of. Moreover, the expression profile analysis of genes from 10 different tissues showed that 21 genes exhibited tissue-specific expression. Further, we identified that 11 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% 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. The results and information provide a good basis for further investigation of the biological functions and evolution of tomato bHLH genes.