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. 2025 Aug 1;14(15):2370.
doi: 10.3390/plants14152370.

Genome-Wide Identification of DNA Methyltransferase and Demethylase in Populus sect. Turanga and Their Potential Roles in Heteromorphic Leaf Development in Populus euphratica

Chen Qiu  1   2   3 , Jianhao Sun  1   2   3 , Mingyu Jia  1   2   3 , Xiaoli Han  1   2   3 , Jia Song  1   2   3 , Zhongshuai Gai  1   2   3 , Zhijun Li  1   2   3
Affiliations

Genome-Wide Identification of DNA Methyltransferase and Demethylase in Populus sect. Turanga and Their Potential Roles in Heteromorphic Leaf Development in Populus euphratica

Chen Qiu et al. Plants (Basel). .

Abstract

DNA methylation, mediated by DNA methyltransferases (DMTs) and demethylases (DMLs), is an important epigenetic modification that maintains genomic stability and regulates gene expression in plant growth, development, and stress responses. However, a comprehensive characterization of these gene families in Populus sect. Turanga remains lacking. In this study, eight PeDMT and two PeDML genes were identified in Populus euphratica, and six PpDMT and three PpDML genes in Populus pruinosa. Phylogenetic analysis revealed that DMTs and DMLs could be classified into four and three subfamilies, respectively. The analysis of cis-acting elements indicated that the promoter regions of both DMTs and DMLs were enriched with elements responsive to growth and development, light, phytohormones, and stress. Collinearity analysis detected three segmentally duplicated gene pairs (PeDMT5/8, PeDML1/2, and PpDML2/3), suggesting potential functional diversification. Transcriptome profiling showed that several PeDMTs and PeDMLs exhibited leaf shape- and developmental stage-specific expression patterns, with PeDML1 highly expressed during early stages and in broad-ovate leaves. Whole-genome bisulfite sequencing revealed corresponding decreases in DNA methylation levels, suggesting that active demethylation may contribute to heteromorphic leaf formation. Overall, this study provides significant insights for exploring the functions and expression regulation of plant DMTs and DMLs and will contribute to future research unraveling the molecular mechanisms of epigenetic regulation in P. euphratica.

Keywords: DML gene family; DMT gene famliy; Populus euphratica; Populus pruinosa; heteromorphic leaf.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Genomic distribution of DMTs and DMLs across chromosomes of (a) P. euphratica and (b) P. pruinosa.
Figure 2
Figure 2
Phylogenetic tree of (a) DMT and (b) DML gene family among A. thaliana, P. euphratica, and P. pruinosa. Branch support was assessed using bootstrap values based on 1000 replicates.
Figure 3
Figure 3
Analysis of phylogenetic relationships, conserved motifs, gene structure, and protein domains among (a) DMTs and (b) DMLs in P. euphratica and P. pruniosa.
Figure 4
Figure 4
Collinearity analysis of DMTs and DMLs gene family. (a) P. euphratica vs. A. thaliana, (b) P. pruinosa vs. A. thaliana, (c) P. euphratica vs. P. pruinosa, (d) intraspecific collinearity in P. euphratica, (e) intraspecific collinearity in P. pruinosa. The red lines highlight collinear DMT pairs, while the blue lines highlight collinear DML pairs.
Figure 5
Figure 5
Analysis of cis-acting elements in DMT and DML. (a) Predicted cis-acting elements in the 2000 bp upstream regions of DMT and DML genes. (b) The abundance of cis-acting elements in each gene.
Figure 6
Figure 6
Expression of PeDMT and PeDML genes in RNA-seq and relative expression level. Heatmaps showing relative expression levels of seven PeDMT and PeDML genes in (a) 30 groups and in (b) the different comparison groups. (c) The relative expression level of PeDMT1, PeDMT5, PeDMT6, and PeDML1 in 4 samples. (d) The DNA methylation rates in the different comparison groups. Tree stages: A Stage (3 years): only Li; B Stage (5 years): Li and La; C Stage (7 years): Li, La, and Ov; D Stage (8 years): Li, La, Ov, and Bo. Leaf stages: P1: complete leaf flattening; P2: intermediate stage; P3: maturation phase. Significant differences were determined by ANOVA with the 0.05 p-value threshold. Comparison letters were shown only when differences were statistically significant.
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