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

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.

MYB transcription factor genes as regulators for plant responses: an overview

“…The Populus genome contains five 3R-MYB genes and 192 R2R3-MYB genes (Wilkins et al 2009). A total of 252 MYBs, including 244 R2R-MYB (2R-MYB) genes, six R1R2R3-MYB (3R-MYB) genes, and two R0R1R2R3-MYB (4R-MYB) genes were identified in soybean (Du et al 2012b). Supriya et al (2006) and Sharma et al (2010) reported MYB TF in Brassica species.…”

A MYB-related transcription factor affects nodule formation in <i>Lotus japonicus</i>

“…In this study, we focused on one of the MYB-related genes, Ljmybr, which is expressed after M. loti infection. Although there are many reports about R2R3-MYB proteins, little is known about MYB-related genes (Du et al 2012a;Du et al 2012b;Matus et al 2008;Stracke et al 2001). In maize and soybean, MYB-related genes have roles both in development and in stress responses (Du et al 2013).…”

Caracterização Estrutural e Transcricional de Fatores de Transcrição da Família R2R3-MYB no Genoma de Glycine max

“…Após o agrupamento e a designação dos subgrupos, motivos foram detectados na poção C-terminal das sequências utilizando o software MEME 1 . 1,3,6 . Observou-se ainda subgrupos formados exclusivamente por AtMYBs, indicando a ausência de controle sobre determinadas funções por MYBs em soja (S5; S12 e S15).…”