Genome-Wide Comparative Analysis of the <i>R2R3-MYB</i> Gene Family in Six <i>Ipomoea</i> Species and the Identification of Anthocyanin-Related Members in Sweet Potatoes
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 anthoc...
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MDPI AG
2023-04-01
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| Online Access: | https://www.mdpi.com/2223-7747/12/8/1731 |
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| author | Maoxing Li Yuanping Zhou Kaifeng Li Huachun Guo |
| author_facet | Maoxing Li Yuanping Zhou Kaifeng Li Huachun Guo |
| author_sort | Maoxing Li |
| collection | DOAJ |
| description | 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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| spelling | doaj.art-871b4cd9257a413bb8723f0ad3f1fa702023-11-17T21:00:51ZengMDPI AGPlants2223-77472023-04-01128173110.3390/plants12081731Genome-Wide Comparative Analysis of the <i>R2R3-MYB</i> Gene Family in Six <i>Ipomoea</i> Species and the Identification of Anthocyanin-Related Members in Sweet PotatoesMaoxing Li0Yuanping Zhou1Kaifeng Li2Huachun Guo3College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, ChinaCollege of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, ChinaCollege of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, ChinaCollege of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, ChinaSweet 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.https://www.mdpi.com/2223-7747/12/8/1731<i>Ipomoea</i> speciessweet potato<i>R2R3-MYB</i> gene familyexpression analysisanthocyanin biosynthesis |
| spellingShingle | Maoxing Li Yuanping Zhou Kaifeng Li Huachun Guo Genome-Wide Comparative Analysis of the <i>R2R3-MYB</i> Gene Family in Six <i>Ipomoea</i> Species and the Identification of Anthocyanin-Related Members in Sweet Potatoes Plants <i>Ipomoea</i> species sweet potato <i>R2R3-MYB</i> gene family expression analysis anthocyanin biosynthesis |
| title | Genome-Wide Comparative Analysis of the <i>R2R3-MYB</i> Gene Family in Six <i>Ipomoea</i> Species and the Identification of Anthocyanin-Related Members in Sweet Potatoes |
| title_full | Genome-Wide Comparative Analysis of the <i>R2R3-MYB</i> Gene Family in Six <i>Ipomoea</i> Species and the Identification of Anthocyanin-Related Members in Sweet Potatoes |
| title_fullStr | Genome-Wide Comparative Analysis of the <i>R2R3-MYB</i> Gene Family in Six <i>Ipomoea</i> Species and the Identification of Anthocyanin-Related Members in Sweet Potatoes |
| title_full_unstemmed | Genome-Wide Comparative Analysis of the <i>R2R3-MYB</i> Gene Family in Six <i>Ipomoea</i> Species and the Identification of Anthocyanin-Related Members in Sweet Potatoes |
| title_short | Genome-Wide Comparative Analysis of the <i>R2R3-MYB</i> Gene Family in Six <i>Ipomoea</i> Species and the Identification of Anthocyanin-Related Members in Sweet Potatoes |
| title_sort | genome wide comparative analysis of the i r2r3 myb i gene family in six i ipomoea i species and the identification of anthocyanin related members in sweet potatoes |
| topic | <i>Ipomoea</i> species sweet potato <i>R2R3-MYB</i> gene family expression analysis anthocyanin biosynthesis |
| url | https://www.mdpi.com/2223-7747/12/8/1731 |
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