Abstract
The basic helix−loop−helix (bHLH) proteins are a superfamily of transcription factors (TFs) that can bind to specific DNA target sites, playing a central role in a wide range of metabolic, physiological, and developmental processes in higher organisms. However, no systemic analysis of bHLH TFs has been reported in banana, a typical climacteric fruit in tropical and subtropical regions. In our study, 259 MabHLH TF genes were identified in the genome of Musa acuminata (A genome), and phylogenetic analysis indicated that these MabHLHs could be classified into 23 subfamilies with the bHLHs from rice and Arabidopsis. The amino acid sequences of the bHLH domain in all MabHLH protein sequences were quite conserved, especially Arg-12, Arg-13, Leu-23, and Leu-79. Distribution mapping results showed that 258 MabHLHs were localized on the 11 chromosomes in the M. acuminata genome. The results indicated that 40.7% of gene duplication events were located in collinear fragments, and segmental duplications might have played a key role in the expansion of MabHLHs. Moreover, the expression profiles of MabHLHs in different fruit development and ripening stages and under various abiotic and biotic stresses were investigated using available RNA-sequencing data to obtain fruit development, ripening-specific, and stress-responsive candidate genes. Finally, a co-expression network of MabHLHs was constructed by weighted gene co-expression network analysis to elucidate the MabHLHs that might participate in important metabolic biosynthesis pathways in banana during development and the response to stress. A total of 259 MabHLHs were identified, and their sequence features, conserved domains, phylogenetic relationships, chromosomal distributions, gene duplications, expression profiles, and co-expression networks were investigated. This study systematically identified the MabHLHs in the M. acuminata genome at the genome-wide level, providing important candidate genes for further functional analysis. These findings improve our understanding of the molecular basis of developmental and stress tolerance in an important banana cultivar.
Highlights
Transcription factors (TFs) are important regulatory factors that interact with cis-elements to regulate the expression of genes in order to adapt to environmental stress in eukaryotes (Riechmann et al, 2000)
The MabHLHs were randomly distributed on 11 chromosomes and were named MabHLH001 to MdbHLH258 based on their chromosomal locations
We discovered that there were 11 MabHLHs involved in the above weighted co-expression network that were differentially expressed during the interaction of banana with Foc tropical race 4 (Foc TR4), and all of them decreased significantly at 2 days post-infection (DPI) in the RNA-Seq data
Summary
Transcription factors (TFs) are important regulatory factors that interact with cis-elements to regulate the expression of genes in order to adapt to environmental stress in eukaryotes (Riechmann et al, 2000). The typical bHLH domain usually contains 60 amino acids and can be divided into two functional regions: a basic area of 10–15 amino acids and a spiral area (HLH region) with 40 amino acids (Heim et al, 2003; Feller et al, 2011). The alkaline region is located at the N-end of the BHLH domain, adjacent to the HLH region, and the region is mainly associated with the binding of TFs and specific sequences. The HLH region is located in the C-end of the bHLH domain, containing two adjacent α-helices. The homologous or heterogeneous dimers of the α-helices from the same or different bHLH TFs can be combined with motifs in the promoter of the target gene, thereby regulating the expression of the target gene (Heim et al, 2003)
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