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Background  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. 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.    Results  We 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.    Conclusions  This 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 material  The online version of this article (doi:10.1186/s12870-014-0249-8) contains supplementary material, which is available to authorized users.

Genome-wide identification and characterisation of R2R3-MYB genes in sugar beet (Beta vulgaris)