Genome-wide Analysis of R2R3-MYB Transcription Factors in Boehmeria nivea (L.) Gaudich Revealed Potential Cadmium Tolerance and Anthocyanin Biosynthesis Genes

Abstract MYB transcription factor (TFs) are one of the largest families in plants, and involved in many biological processes, including growth and development, metabolism and stress response. The MYB TFs has been extensively studied in various plant species. However, comprehensive information on MYB TFs in fiber crop ramie are still unknown. In the current study, a total of 105 BnGR2R3-MYB genes were identified from ramie genome and subsequently grouped into 35 subfamilies according to phylogeny divergence and sequences similarity. Chromosomal localization, gene structure, synteny analysis, gene duplication, promoter analysis, molecular characteristics and subcellular localization were accomplished using several bioinformatics tools. Collinearity analysis showed that the segmental and tandem duplication events is the dominant form of the gene family expansion, and duplications prominent in distal telomeric regions. Highest syntenic relationship was obtained between BnGR2R3-MYB genes and that of Apocynum venetum (88). Furthermore, transcriptomic data and phylogenetic analysis revealed that BnGMYB60, BnGMYB79/80 and BnGMYB70 might inhibit the biosynthesis of anthocyanins, and UPLC-QTOF-MS data further supported the results. The quantitative real-time qRT-PCR and phylogenetic analysis indicated that the six genes (BnGMYB9, BnGMYB10, BnGMYB12, BnGMYB28, BnGMYB41, BnGMYB78) were cadmium stress responsive genes. Especially, the expression of BnGMYB10/12/41 in roots, stems and leaves all increased more than 10-fold after cadmium stress, and in addition they may interact with key genes regulating flavonoid biosynthesis. Thus, a potential link between cadmium stress response and flavonoid synthesis was identified through protein interaction network analysis. In conclusion, the studies increase our understanding of the functional roles of MYBs and provided valuable foundation for study of structural and regulatory genes in ramie.