Li Maoxing, Zhou Yuanping, Li Kaifeng, Guo Huachun
College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China.
Yunnan Engineering Research Center of Tuber and Root Crop Bio-Breeding and Healthy Seed Propagation, Yunnan Agricultural University, Kunming 650201, China.
Plants (Basel). 2023 Apr 21;12(8):1731. 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.
甘薯（Ipomoea batatas）是全球广泛种植的重要块根作物之一，其贮藏根富含花青素等抗氧化剂。MYB是一个参与包括花青素生物合成在内的各种生物学过程的大基因家族。然而，迄今为止，关于甘薯MYB基因家族的报道很少。在本研究中，在六个甘薯属物种中总共鉴定出695个典型的MYB基因，其中甘薯中有131个MYB基因。根据拟南芥126个R2R3-MYB蛋白的分类，最大似然系统发育分析将这些基因分为36个进化枝。进化枝C25(S12)在六个甘薯属物种中没有成员，而包括102个成员的四个进化枝（即进化枝C21、C26、C30和C36）在拟南芥中没有成员，它们被鉴定为甘薯属特有的进化枝。在六个甘薯属物种基因组中，鉴定出的MYB基因在所有染色体上分布不均，六倍体甘薯与其他五个二倍体甘薯属物种之间的共线性分析表明，甘薯基因组在进化过程中可能经历了较大的染色体重排。对基因复制事件的进一步分析表明，全基因组复制、转座复制和分散复制事件是推动甘薯属植物MYB基因家族扩张的主要力量，并且由于它们的Ka/Ks比值小于1，这些复制基因经历了强烈的纯化选择。此外，131个MYB的基因组序列长度从923 bp到约12.9 kb不等，平均约为2.6 kb，并且它们中的大多数具有三个以上的外显子。基序1、2、3和4形成典型的R2和R3结构域，并且在所有IbR2R3-MYB蛋白中都有鉴定。最后，基于多个RNA-seq数据集，两个MYB基因（IbMYB113和IbMYB114）分别在有色叶片和块根果肉及表皮中相对高表达；因此，它们被鉴定为调控甘薯中组织特异性花青素积累的基因。本研究为甘薯和其他五个甘薯属物种中MYB基因家族的进化和功能提供了依据。
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