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Title: Genome-wide analysis of the MYB transcription factor superfamily in soybean
Authors: Du, H
Yang, S.-S
Liang, Z 
Feng, B.-R
Liu, L
Huang, Y.-B
Tang, Y.-X
Keywords: Arabidopsis
Glycine max
Arabidopsis protein
BOTRYTIS SUSCEPTIBLE1 protein, Arabidopsis
transcription factor
alternative RNA splicing
amino acid sequence
comparative study
gene duplication
gene expression profiling
gene expression regulation
genetic selection
molecular genetics
multigene family
nucleotide sequence
plant chromosome
plant gene
protein motif
Alternative Splicing
Amino Acid Motifs
Amino Acid Sequence
Arabidopsis Proteins
Chromosomes, Plant
Conserved Sequence
Gene Duplication
Gene Expression Profiling
Gene Expression Regulation, Plant
Genes, Plant
Molecular Sequence Data
Multigene Family
Selection, Genetic
Transcription Factors
Issue Date: 2012
Citation: Du, H, Yang, S.-S, Liang, Z, Feng, B.-R, Liu, L, Huang, Y.-B, Tang, Y.-X (2012). Genome-wide analysis of the MYB transcription factor superfamily in soybean. BMC Plant Biology 12 : 106. ScholarBank@NUS Repository.
Rights: Attribution 4.0 International
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 (d N/d S) 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. © 2012 Du et al.; licensee BioMed Central Ltd.
Source Title: BMC Plant Biology
ISSN: 14712229
DOI: 10.1186/1471-2229-12-106
Rights: Attribution 4.0 International
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