Genome-wide analysis of the MYB transcription factor superfamily in soybean.

Hai Du,Si-Si Yang,Bo-Run Feng,Zhe Liang,Yi-Xiong Tang,Lei Liu,Yu-Bi Huang

doi:10.1186/1471-2229-12-106

Abstract

BackgroundThe MYB superfamily constitutes one of the most abundant groups of transcription factors described in plants. Nevertheless, their functions appear to be highly diverse and remain rather unclear. To date, no genome-wide characterization of this gene family has been conducted in a legume species. Here we report the first genome-wide analysis of the whole MYB superfamily in a legume species, soybean (Glycine max), including the gene structures, phylogeny, chromosome locations, conserved motifs, and expression patterns, as well as a comparative genomic analysis with Arabidopsis.ResultsA total of 244 R2R3-MYB genes were identified and further classified into 48 subfamilies based on a phylogenetic comparative analysis with their putative orthologs, showed both gene loss and duplication events. The phylogenetic analysis showed that most characterized MYB genes with similar functions are clustered in the same subfamily, together with the identification of orthologs by synteny analysis, functional conservation among subgroups of MYB genes was strongly indicated. The phylogenetic relationships of each subgroup of MYB genes were well supported by the highly conserved intron/exon structures and motifs outside the MYB domain. Synonymous nucleotide substitution (dN/dS) analysis showed that the soybean MYB DNA-binding domain is under strong negative selection. The chromosome distribution pattern strongly indicated that genome-wide segmental and tandem duplication contribute to the expansion of soybean MYB genes. In addition, we found that ~ 4% of soybean R2R3-MYB genes had undergone alternative splicing events, producing a variety of transcripts from a single gene, which illustrated the extremely high complexity of transcriptome regulation. Comparative expression profile analysis of R2R3-MYB genes in soybean and Arabidopsis revealed that MYB genes play conserved and various roles in plants, which is indicative of a divergence in function.ConclusionsIn this study we identified the largest MYB gene family in plants known to date. Our findings indicate that members of this large gene family may be involved in different plant biological processes, some of which may be potentially involved in legume-specific nodulation. Our comparative genomics analysis provides a solid foundation for future functional dissection of this family gene.

Highlights

The MYB genes (MYBs) superfamily constitutes one of the most abundant groups of transcription factors described in plants
In order to verify the reliability of our results, we performed PROSITE profile (PS50090) and simple modular architecture research tool (SMART) analysis to identify all of the putative MYB protein sequences in the soybean genome
It was defined that the MYB superfamily is the most abundant transcription factor family in plants, with 126 244 R2R3MYB (2R-MYB) genes in Arabidopsis[4], 109 in rice[27,32], 118 in grape[29,33], and 192 in Populus[29]

Summary

Introduction

The MYB superfamily constitutes one of the most abundant groups of transcription factors described in plants. Their functions appear to be highly diverse and remain rather unclear. Transcription factors are usually composed of at least four discrete domains: a DNA-binding domain, a nuclearlocalization signal, a transcription-activation domain, and an oligomerization site. When bound to DNA, the HTH structure intercalates in the major groove [3,4] It contains three regularly spaced tryptophan residues, which form a cluster in a hydrophobic core of each repeat, and stabilize the structure of the DNA-binding domain [5]. The C-terminus is the activation domain and varies considerably between MYB proteins, which leads to the wide range of regulatory roles of the MYB gene family [4,6,7]

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Results

Conclusion