Genome-wide analysis of basic helix-loop-helix superfamily members in peach

Abstract

The basic helix-loop-helix (bHLH) transcription factor family is a superfamily found in all eukaryotes that plays important roles in regulating growth and development. Over the past several decades, many bHLH superfamily genes have been identified and characterized in herbaceous and woody plants. However, the genes belonging to the bHLH superfamily in peach (Prunus persica) have not yet been comprehensively identified and characterized. Here, we identified 95 members of the bHLH superfamily in the peach genome, and these genes were classified into 19 subfamilies based on a phylogenetic comparison with bHLH proteins from Arabidopsis. The members within each subfamily were highly conserved according to the analysis of motif compositions and exon/intron organizations. The 95 bHLH genes were unevenly distributed on chromosomes 1 to 8 of the peach genome. We identified 57 pairs of bHLH members that were orthologous between peach and Arabidopsis. Additionally, 48 pairs of paralogous bHLH genes were identified on the eight chromosomes of the peach genome. Coupled with relative expression analysis of bHLH genes in red-fleshed peach fruit at five developmental stages, we identified several bHLH genes that might be involved in fruit development and anthocyanin biosynthesis. This study provides insight into the molecular mechanisms through which these genes are involved in the regulation of biological and biochemical processes in peach and lays the foundation for further studies on these genes.

Genome-wide analysis of basic helix-loop-helix (bHLH) transcription factors in papaya (Carica papaya L.)

“…In addition, among the 73 CpbHLHs, one protein (CpbHLH003) exhibited incomplete bHLH domains, whereas the remaining 72 bHLH proteins all presented complete bHLH domains. Similar observations have been made in other plant species, such as peach and blueberry [22,36].…”

“…Transcription factors (TFs) play key roles in the stress regulation network and signal pathways in plants. Basic/helix-loop-helix (bHLH) TFs are the second largest TFs family in plants and have been identified in many species [6,[18][19][20][21][22][23][24][25]. However, the bHLH TF family has not previously been reported in papaya (Carica papaya L.).…”

“…The detailed information on these CpbHLHs, including protein ID, locus ID, opening reading frame (ORF) lengths, amino acid sequences/lengths, molecular weight, isoelectric point and exon/intron numbers, are listed in Additional file 1. In previous studies, 129/132, 188, 159, 147, 124, 95, 94 and 56 bHLH genes were identified in peanut [18], apple [19], tomato [20], Arabidopsis [6], potato [21], peach [22], grapes [23] and sweet orange [24], respectively. Compared with the above dicotyledonous plants, the density of bHLHs superfamily genes in papaya genome was approximately 0.26%, which is lower than the density of peanut [18], apple [19], tomato [20], arabidopsis [6], potato [21] and sweet orange [24], and similar to peach [22] and wine grapes [23] (Table 1).…”

“…Phylogenetic analyses of some atypical bHLH proteins have even extended that number to 32 [5]. With the availability of genome sequence data and the rapid development of molecular biology, increasing numbers of bHLH subfamily genes have been identified and characterized in a wide range of plant species, including Arabidopsis [6], peanut [18], apple [19], tomato [20], potato [21], peach [22], grapes [23], sweet orange [24], and bamboo [25]. The results from these studies have shown that bHLH TFs have versatile biological functions, such as regulating light morphogenesis [26,27], hormone signals [28,29], the developmental of root [30] and anther [31], regulating epidermal cell fate determination [32], participating in various biotic and abiotic stress responses [21,33,34], etc.…”

Insights into the Diversification of Subclade IVa bHLH Transcription Factors in Fabaceae

“…Numerous studies have reported genome-wide identi cation and classi cation of bHLH factors in plants [18,19,28,29,30]. Although the genomes of Arabidopsis thaliana and Oryza sativa possess four and six subclade IVa members, respectively [19], more than 30 subclade IVa bHLH genes were found in the genomes of Glycine max and M. truncatula [21,28].…”