Abstract
BackgroundThe R2R3-MYB genes comprise one of the largest transcription factor gene families in plants, playing regulatory roles in plant-specific developmental processes, metabolite accumulation and defense responses. Although genome-wide analysis of this gene family has been carried out in some species, the R2R3-MYB genes in Beta vulgaris ssp. vulgaris (sugar beet) as the first sequenced member of the order Caryophyllales, have not been analysed heretofore.ResultsWe present a comprehensive, genome-wide analysis of the MYB genes from Beta vulgaris ssp. vulgaris (sugar beet) which is the first species of the order Caryophyllales with a sequenced genome. A total of 70 R2R3-MYB genes as well as genes encoding three other classes of MYB proteins containing multiple MYB repeats were identified and characterised with respect to structure and chromosomal organisation. Also, organ specific expression patterns were determined from RNA-seq data. The R2R3-MYB genes were functionally categorised which led to the identification of a sugar beet-specific clade with an atypical amino acid composition in the R3 domain, putatively encoding betalain regulators. The functional classification was verified by experimental confirmation of the prediction that the R2R3-MYB gene Bv_iogq encodes a flavonol regulator.ConclusionsThis study provides the first step towards cloning and functional dissection of the role of MYB transcription factor genes in the nutritionally and evolutionarily interesting species B. vulgaris. In addition, it describes the flavonol regulator BvMYB12, being the first sugar beet R2R3-MYB with an experimentally proven function.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0249-8) contains supplementary material, which is available to authorized users.
Highlights
The R2R3-MYB genes comprise one of the largest transcription factor gene families in plants, playing regulatory roles in plant-specific developmental processes, metabolite accumulation and defense responses
We identified six B. vulgaris MYB (BvMYB) genes which had been missed in the automatic annotation [26] and two which had been annotated with incomplete open reading frames
We created a primary data set of 70 R2R3-MYB proteins and three types of atypical multiple repeat MYB proteins distantly related to the typical R2R3-MYB proteins: three R1R2R3-MYB (MYB3R) proteins, one MYB4R protein and one CDC5like protein from the B. vulgaris genome (Table 1)
Summary
The R2R3-MYB genes comprise one of the largest transcription factor gene families in plants, playing regulatory roles in plant-specific developmental processes, metabolite accumulation and defense responses. Transcriptional control of gene expression influences almost all biological processes in eukaryotic cells or organisms. Transcription factors perform this function, alone or complexed with other proteins, by activating or repressing (or both) the recruitment of RNA polymerase to specific genes. MYB proteins are widely distributed in all eukaryotic organisms and constitute one of the largest transcription factor families in the plant kingdom. Plant R1R2R3-type MYB (MYB3R) proteins have been proposed to play divergent roles in cell cycle control [6,7], similar to the functions of their animal homologs
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