| Summary: | Sweet potatoes (<i>Ipomoea batatas</i>) are one of the important tuberous root crops cultivated worldwide, and thier storage roots are rich in antioxidants, such as anthocyanins. <i>R2R3-MYB</i> is a large gene family involved in various biological processes, including anthocyanin biosynthesis. However, few reports about the <i>R2R3-MYB</i> gene family of sweet potatoes have been released to date. In the present study, a total of 695 typical <i>R2R3-MYB</i> genes were identified in six <i>Ipomoea</i> species, including 131 <i>R2R3-MYB</i> genes in sweet potatoes. A maximum likelihood phylogenetic analysis divided these genes into 36 clades, referring to the classification of 126 R2R3-MYB proteins of Arabidopsis. Clade C25(S12) has no members in six <i>Ipomoea</i> species, whereas four clades (i.e., clade C21, C26, C30, and C36), including 102 members, had no members in Arabidopsis, and they were identified as <i>Ipomoea</i>-specific clades. The identified <i>R2R3-MYB</i> genes were unevenly distributed on all chromosomes in six <i>Ipomoea</i> species genomes, and the collinearity analysis among hexaploid <i>I. batatas</i> and another five diploid <i>Ipomoea</i> species suggested that the sweet potato genome might have undergone a larger chromosome rearrangement during the evolution process. Further analyses of gene duplication events showed that whole-genome duplication, transposed duplication, and dispersed duplication events were the primary forces driving the <i>R2R3-MYB</i> gene family expansion of <i>Ipomoea</i> plants, and these duplicated genes experienced strong purifying selection because of their Ka/Ks ratio, which is less than 1. Additionally, the genomic sequence length of 131 <i>IbR2R3-MYBs</i> varied from 923 bp to ~12.9 kb with a mean of ~2.6 kb, and most of them had more than three exons. The Motif 1, 2, 3, and 4 formed typical R2 and R3 domains and were identified in all IbR2R3-MYB proteins. Finally, based on multiple RNA-seq datasets, two <i>IbR2R3-MYB</i> genes (<i>IbMYB1/g17138.t1</i> and <i>IbMYB113/g17108.t1</i>) were relatively highly expressed in pigmented leaves and tuberous root flesh and skin, respectively; thus, they were identified to regulate tissue-specific anthocyanin accumulation in sweet potato. This study provides a basis for the evolution and function of the <i>R2R3-MYB</i> gene family in sweet potatoes and five other <i>Ipomoea</i> species.
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