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Open Access Highly Accessed Research article

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

Hai Du123, Si-Si Yang12, Zhe Liang4, Bo-Run Feng12, Lei Liu1, Yu-Bi Huang12* and Yi-Xiong Tang3*

Author Affiliations

1 Maize Research Institute, Sichuan Agricultural University, Chengdu Sichuan, China

2 Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute of Sichuan Agricultural University, Ministry of Agriculture, Chengdu Sichuan, China

3 Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China

4 Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, PO Box 5003N-1432, Norway

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BMC Plant Biology 2012, 12:106  doi:10.1186/1471-2229-12-106

Published: 9 July 2012

Abstract

Background

The 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.

Results

A 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.

Conclusions

In 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.