R2R3-MYB Transcription Factor Family in Boehmeria nivea (L.) Gaudich: Potential Associations between Cd2+ Stress and Flavonoid Metabolism

Abstract Background: The characterization of gene families especially MYB being the largest transcription factor (TFs) families in plants is a crucial step for functional studies. The completion of ramie genome sequencing provides a great opportunity to investigate the organization and evolutionary traits of ramie MYB genes at the genome-wide level. Results: A total of 105 BnGR2R3-MYB genes were identified in ramie and divided into 35 distinct subfamilies according to phylogeny divergence and sequences similarity. These genes were unevenly distributed among 14 chromosomes. 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. 88 BnGR2R3-MYB genes showed syntenic relationship with those in Apocynum venetum, followed by Cannabis sativa (58), Arabidopsis (53), maize (8) and rice (4). 103 of the 105 BnGMYB proteins were predicted nuclear subcellular, the remaining two were in either chloroplast or cytoplasm. The combination of transcriptome data and phylogenetic tree allows us to propose some powerful MYB candidates that might be involved in the regulation of secondary wall-associated cellulose synthases (BnGMYB14) secondary cell wall thickening (BnGMYB66/67) and flavonoids synthesis (BnGMYB60). The MYBs subgroups involve in regulating anthocyanin were different from arabidopsis and tomato pointing that BnGMYB in other groups play a role in regulating anthocyanin synthesis. qPCR results revealed 8 MYB TFs candidate genes for cadmium stress in ramie. There was an increased in synthesis of procyanidins under the cadmium stress, which suggest a new regulatory pathway in response to the stress. The predicted network identifies the interface between flavonoid metabolic pathways and adversity stress, and found evidence for the involvement of flavonoid synthetic pathways in the stress regulation.Conclusions: This work provides a basic understanding of BnGR2R3-MYB gene family characteristics and provides valuable information that may contribute in improving the tolerance of ramie to cadmium stress and fiber quality.