Genome-Wide Comparative Analysis of the R2R3-MYB Gene Family in Six Ipomoea Species and the Identification of Anthocyanin-Related Members in Sweet Potatoes

• Published in: Plants (Basel) Vol. 12; no. 8; p. 1731
• Main Authors: Li, Maoxing, Zhou, Yuanping, Li, Kaifeng, Guo, Huachun
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 21.04.2023; MDPI
• Subjects: Amino acids; anthocyanin biosynthesis; Anthocyanins; Arabidopsis; Bioaccumulation; Biological activity; Biological evolution; Biosynthesis; Chromosomes; Collinearity; Comparative analysis; Diploids; Exons; expression analysis; Fruits; Gene duplication; Gene rearrangement; Genes; Genomes; Ipomoea; Ipomoea batatas; Ipomoea species; Localization; Metabolism; Metabolites; Molecular weight; MYB gene; Phylogenetics; Phylogeny; Potatoes; Proteins; R2R3-MYB gene family; Reproduction (copying); Software; Species; sweet potato; Sweet potatoes; Trees; Vegetables; China; sweet potato; R2R3-MYB gene family; expression analysis; Ipomoea species; anthocyanin biosynthesis
• ISSN: 2223-7747; 2223-7747
• DOI: 10.3390/plants12081731

Sweet potatoes ( ) are one of the important tuberous root crops cultivated worldwide, and thier storage roots are rich in antioxidants, such as anthocyanins. is a large gene family involved in various biological processes, including anthocyanin biosynthesis. However, few reports about the gene family of sweet potatoes have been released to date. In the present study, a total of 695 typical genes were identified in six species, including 131 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 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 -specific clades. The identified genes were unevenly distributed on all chromosomes in six species genomes, and the collinearity analysis among hexaploid and another five diploid 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 gene family expansion of 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 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 genes ( and ) 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 gene family in sweet potatoes and five other species.