Genome-wide analysis of basic/helix-loop-helix gene family in peanut and assessment of its roles in pod development.

Chao Gao,Chongqi Wang,Shouhua Xiao,Zigao Jiao,Xingjun Wang,Jianlei Sun,Yumei Dong,Zhong-Hua Chen

doi:10.1371/journal.pone.0181843

Chao Gao, Chongqi Wang + Show 6 more

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https://doi.org/10.1371/journal.pone.0181843

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Abstract

The basic/helix-loop-helix (bHLH) proteins constitute a superfamily of transcription factors that are known to play a range of regulatory roles in eukaryotes. Over the past few decades, many bHLH family genes have been well-characterized in model plants, such as Arabidopsis, rice and tomato. However, the bHLH protein family in peanuts has not yet been systematically identified and characterized. Here, 132 and 129 bHLH proteins were identified from two wild ancestral diploid subgenomes of cultivated tetraploid peanuts, Arachis duranensis (AA) and Arachis ipaensis (BB), respectively. Phylogenetic analysis indicated that these bHLHs could be classified into 19 subfamilies. Distribution mapping results showed that peanut bHLH genes were randomly and unevenly distributed within the 10 AA chromosomes and 10 BB chromosomes. In addition, 120 bHLH gene pairs between the AA-subgenome and BB-subgenome were found to be orthologous and 101 of these pairs were highly syntenic in AA and BB chromosomes. Furthermore, we confirmed that 184 bHLH genes expressed in different tissues, 22 of which exhibited tissue-specific expression. Meanwhile, we identified 61 bHLH genes that may be potentially involved in peanut-specific subterranean. Our comprehensive genomic analysis provides a foundation for future functional dissection and understanding of the regulatory mechanisms of bHLH transcription factors in peanuts.

Highlights

Basic/helix-loop-helix transcription factors are a superfamily of proteins that are widely distributed in all eukaryotic organisms and have been found to play an increasing number of functions in a wide range of essential metabolic, physiological and developmental processes, such as photosynthesis, light signaling, pigment biosynthesis, seed development and stress resistance [1,2,3,4]
Identification of bHLH genes in two wild type peanuts The bHLH gene family is one of the largest families in plants, and the members are only fewer than the MYB family [28]
In order to define the peanut bHLH gene family, in this study, a total of 132 and 129 bHLH proteins were identified in the Arachis duranensis (AA)- and BB-subgenomes, respectively, based on the Hidden Markov Model BLAST, according to the criteria developed by Atchley and Toledo-Ortiz [3,7]

Summary

Introduction

Basic/helix-loop-helix (bHLH) transcription factors are a superfamily of proteins that are widely distributed in all eukaryotic organisms and have been found to play an increasing number of functions in a wide range of essential metabolic, physiological and developmental processes, such as photosynthesis, light signaling, pigment biosynthesis, seed development and stress resistance [1,2,3,4]. Two highly conserved domains, namely the basic region and the HLH region, which are approximately 60 amino acids in length [5,6]. The basic region contains approximately 15 amino acids and typically includes six basic residues, located at the N-terminus of the bHLH domain, which functions as a DNA binding motif [7]. The HLH region, located at the C-terminal end, is composed of two amphipathic α helices consisting of hydrophobic residues linked by a divergent loop. It functions as a dimerization domain, promoting protein-protein interactions and allowing for the formation of homodimeric or heterodimeric complexes to control gene transcription [8]. Several conserved amino acids within the basic region determine recognition of the core consensus site of different E-boxes [10]

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