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Background Polyploidization promotes species formation and is widespread in angiosperms. Genome changes dramatically bring opportunities and challenges to plants after polyploidy. Methyl-CpG-Binding Domain (MBD) proteins can recognize and bind to methylation sites and they play an important role in the physiological process related to methylation in animals and plants. However, research on the influence of the allopolyploidization process on the  MBD  gene family is still lacking, so it is necessary to conduct a comprehensive analysis. Results In this study, twenty-two, ten and eleven  MBD  genes were identified in the genome of allotetraploid  B. napus  and its diploid ancestors,  B. rapa  and  B. oleracea , respectively. Based on the clades of the  MBD  gene in Arabidopsis, rice and maize, we divided the new phylogenetic tree into 8 clades. Among them, the true  MBD  genes in  Brassica  existed in only 5 clades. Clade IV and Clade VI were unique in term of  MBD  genes in dicotyledons. Ka/Ks calculations showed that  MBD  genes underwent purifying selection in  Brassica  and may retain genes through sequence or functional differentiation early in evolution. In the process of allopolyploidization, the number of  MBD  gene introns increased, and the protein motifs changed. The MBD proteins had their own special motifs in each clade, and the MBD domains were only conserved in their clades. At the same time, the  MBD  genes were expressed in flower, leaf, silique, and stem tissues, and the expression levels of the different genes were significantly different, while the tissue specificity was not obvious. The allopolyploidization process may increase the number of  cis -acting elements and activate the transposable elements. During allopolyploidization, the expression pattern of the  MBD  gene changes, which may be regulated by  cis -acting elements and transposable elements. The number imbalance of  cis -acting elements and transposable elements in A n  and C n  subgenomes may also lead to biased A n  subgenome expression of the  MBD  gene in  B. napus . Conclusions In this study, by evaluating the number, structure, phylogeny and expression of the  MBD  gene in  B. napus  and its diploid ancestors, we increased the understanding of  MBD  genes in allopolyploids and provided a reference for future analysis of allopolyploidization.

The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus