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

Abstract

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 An and Cn subgenomes may also lead to biased An 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.

Genome-wide identification of MBD gene family members in Eleutherococcus senticosus with their expression motifs under drought stress and DNA demethylation

“…Therefore, we speculated that the functional differences in MBD genes among different branches might be significant, indicating that the functional differences among MBD proteins were gradually realized during the evolutionary process. This result is consistent with the conclusions of previous studies that MBD genes have a long evolutionary history, with MBD genes existing and beginning to differentiate as early as the formative stages of monocotyledons and dicots [ 26 ].…”

“…It was speculated that this was due to the different functional differentiation of MBD genes during the process of evolution. Moreover, the 20 EsMBD protein sequences obtained from the screening also presented conserved motifs in most EsMBDs , which is consistent with the results of earlier studies comparing conserved motifs of MBD in B. napus [ 26 ]. These conserved motifs of different MBD genes in E. senticosus also showed different similarities.…”

“…Cellular metabolism in organisms is largely regulated at the transcriptional level, and promoters are responsible for basic regulation of transcription initiation [ 32 ]. The promoters of the MBD genes in E. senticosus were found to contain a large number of cis-acting elements, and the quantity of different cis-acting elements in adjacent branches showed some similarity, suggesting that there is a certain degree of functional differentiation among the MBD genes in E. senticosus , which is consistent with a previous hypothesis that there is functional differentiation of MBD genes during the evolutionary process [ 26 ]. Among the various cis-acting elements of the promoter, light response elements were the most abundant, followed by anaerobic induction elements, indicating that the EsMBD genes of E. senticosus were subjected to maximum regulation by light and anaerobic conditions (Supplementary Table S1).…”

“…Twenty EsMBD genes and ten AeMBD genes were identified in E. senticosus and A. elata . Together with the 13 AtMBD genes in A. thaliana , a phylogenetic tree was constructed and branched according to a previously constructed phylogenetic tree between Brassica napus L. and A. thaliana [ 26 ]. Although there was only AtMBD8 , EsMBD4 , and EsMBD20 in one branch, the MBD gene family members of E. senticosus and A. elata were identified in all the other branches.…”

Genome-Wide Characterization of the Methyl CpG Binding Domain-Containing Proteins in Watermelon and Functional Analysis of Their Roles in Disease Resistance Through Ectopic Overexpression in Arabidopsis thaliana

“…Generally, the MBD proteins recognize 5-mC and recruit histone deacetylases, chromatin remodelers, and histone methyltransferases to repress transcription ( Gigek et al, 2016 ). Genes coding for MBD proteins have been characterized in some plant species including Arabidopsis, rice, maize, poplar, potato, tomato, petunia, common bean, soybean, and rapeseed ( Grafi et al, 2007 ; Parida et al, 2018 ; Coelho et al, 2022 ; Shi et al, 2022 ; Xiao et al, 2022 ); for example, 13 AtMBDs in Arabidopsis, 17 OsMBDs in rice, 14 ZmMBDs in maize, and 14 PtMBDs in poplar were identified ( Grafi et al, 2007 ). The Arabidopsis AtMBD proteins can be divided into different subclasses ( Zemach and Grafi, 2003 ; Springer and Kaeppler, 2005 ).…”