Abstract
MYB proteins comprise a large family of plant transcription factors, members of which perform a variety of functions in plant biological processes. To date, no genome-wide characterization of this gene family has been conducted in maize (Zea mays). In the present study, we performed a comprehensive computational analysis, to yield a complete overview of the R2R3-MYB gene family in maize, including the phylogeny, expression patterns, and also its structural and functional characteristics. The MYB gene structure in maize and Arabidopsis were highly conserved, indicating that they were originally compact in size. Subgroup-specific conserved motifs outside the MYB domain may reflect functional conservation. The genome distribution strongly supports the hypothesis that segmental and tandem duplication contribute to the expansion of maize MYB genes. We also performed an updated and comprehensive classification of the R2R3-MYB gene families in maize and other plant species. The result revealed that the functions were conserved between maize MYB genes and their putative orthologs, demonstrating the origin and evolutionary diversification of plant MYB genes. Species-specific groups/subgroups may evolve or be lost during evolution, resulting in functional divergence. Expression profile study indicated that maize R2R3-MYB genes exhibit a variety of expression patterns, suggesting diverse functions. Furthermore, computational prediction potential targets of maize microRNAs (miRNAs) revealed that miR159, miR319, and miR160 may be implicated in regulating maize R2R3-MYB genes, suggesting roles of these miRNAs in post-transcriptional regulation and transcription networks. Our comparative analysis of R2R3-MYB genes in maize confirm and extend the sequence and functional characteristics of this gene family, and will facilitate future functional analysis of the MYB gene family in maize.
Highlights
MYB transcription factor contains a conserved DNA-binding domain (DBD), which is homologous to the DBD of animal c-Myb [1]
The first plant MYB gene was isolated from maize, which encodes a c-MYB-like transcription factor involved in anthocyanin biosynthesis [7]
The remaining maize MYBs possessing incomplete open reading frames (ORFs) were excluded for further analysis
Summary
MYB transcription factor contains a conserved DNA-binding domain (DBD), which is homologous to the DBD of animal c-Myb [1]. This domain is generally composed of 1–4 imperfect repeats [2,3]. When bound to specific promoter sequences, the second and third helices form a helix-turn-helix (HTH) structure [2,4]; the third a-helix is thought to play a recognition role in binding to a short DNA sequence [5]. The first plant MYB gene was isolated from maize, which encodes a c-MYB-like transcription factor involved in anthocyanin biosynthesis [7]. The most common type of plant MYB transcription factor is R2R3-MYB (containing 2 repeats)
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