Genome-wide Identification and Expression Analysis of DNA Methyltransferase and Demethylase Gene Family in Sweetpotato

doi:10.13560/j.cnki.biotech.bull.1985.2025-0743

Abstract

Abstract:

Objective Identification and analysis of the gene family members, its structures and expression patterns of DNA methyltransferase (IbC5-MTase) and demethylase (IbdMTase) will provide theoretical support for in-depth exploration of the molecular basis and biological functions of DNA methylation in sweetpotato. Method The physicochemical properties, sequences, evolution and structures of the IbC5-MTase and IbdMTase gene family members were analyzed by bioinformatic methods. The expressions of IbC5-MTase and IbdMTase in different sweetpotato tissues, and under abiotic and biotic stress conditions were analyzed by integrating transcriptome data with RT-qPCR. Result A total of seven IbC5-MTase genes and four IbdMTase genes were identified in the whole genome of sweetpotato, distributed across 8 linkage groups. The IbC5-MTase and IbdMTase proteins contain 355-1 305 amino acids (aa), with theoretical isoelectric points (pI) ranging from 4.81 to 9.81. Subcellular localization predictions indicate that nine proteins are in the nucleus. Phylogenetic analysis showed the IbC5-MTase and IbdMTase proteins are classified into four and three subfamilies, respectively. Conserved motif analysis demonstrated distinct motif compositions between two protein types. Promoter regions of both gene families were enriched with cis-regulatory elements associated with light responsiveness, hormonal regulation, and stress adaptation. Tissue-specific expression profiling revealed relatively high expression levels of IbDRM2 and IbCMT3b, with overall higher expression of both gene families in aerial tissues as compared to roots, particularly in young tissues. Transcriptome analysis under abiotic stresses demonstrated widespread expression reprogramming of these genes during salt, drought, and cold adaptation. Stem nematode infection triggered distinct transcriptional responses, IbCMT3a and IbDRM2 were significantly downregulated, whereas IbCMT3b and IbROS1 were upregulated, as validated by RT-qPCR. Conclusion The IbC5-MTase and IbdMTase genes of sweetpotato have potential functions under biotic and abiotic stresses.

Key words: sweetpotato, C5-MTase and dMTase genes, bioinformatics, biotic and abiotic stresses, expression profile

ZHANG Ai-cen, YAN Hui, MA Ju-kui, ZHANG Yun-gang, LI Qiang. Genome-wide Identification and Expression Analysis of DNA Methyltransferase and Demethylase Gene Family in Sweetpotato[J]. Biotechnology Bulletin, 2026, 42(6): 1-12.

Figures/Tables 10

Table 1 RT-qPCR primers for gene expression analysis

基因 Gene	正向引物 Forward primer （5′-3′）	反向引物 Reverse primer （5′-3′）
Tubulin	TCAATGCTGCTGTTGCCACT	CAGTGAACGAACGCCCTCT
IbCMT3a	GGTGCCCTTCCTGGAGAAAA	CATCACCAAGGAAAAGCGCC
IbCMT3b	ACGAGGACAGCGAGTTTGTT	CTCAGTGCCCTTCTGGTAGC
IbDRM2	AACTCTTCCGGAGCAAGCAA	GTCCGTGGAGGAATGGGAAG
IbROS1	GCCCTTACCTCAGACTGTCG	GGCACTTCGACAATTGGCTC

Table 2 IbC5-MTase and IbdMTase gene families information and the physicochemical properties of their encoded proteins

基因家族 Gene family	基因 Gene	基因号 Gene ID	氨基酸数目 Amino acid length （aa）	分子量 Molecular weight （Da）	等电点 pI	亲水性平均值 GRAVY value	亚细胞定位预测 Subcellular localization prediction
IbC5-MTase	IbCMT3a	IB02G00540	566	64 206.59	4.81	-0.396	细胞核
	IbCMT3b	IB08G17210	782	87 453.08	5.10	-0.365	细胞核
	IbMET1a	IB14G25930	1 305	148 434.28	7.73	-0.431	细胞膜、细胞核
	IbMET1b	IB14G25950	406	45 303.61	6.84	-0.414	细胞核
	IbCMT2	IB04G14710	355	40 821.35	7.64	-0.280	细胞核
	IbDRM2	IB10G09160	593	66 752.48	4.85	-0.443	细胞膜、细胞质、细胞核等
	IbDNMT2	IB11G24750	389	44 472.12	5.53	-0.484	细胞核
IbdMTase	IbDME1	IB01G25690	1 294	144 598.76	7.43	-0.621	细胞核
	IbDME2	IB07G04730	601	67 543.83	6.90	-0.436	细胞核
	IbROS1	IB14G14640	419	47 514.26	5.64	-0.474	细胞核
	IbDML3	IB02G03320	861	96 384.00	4.93	-0.449	细胞核

Fig. 1 Chromosome distribution and structural analysis of the IbC5-MTase and IbdMTase gene familyA: Distribution of genes on linkage groups, red indicates the IbC5-MTase genes, blue indicates the IbdMTase genes. B: The exon-intron distribution of genes, with blue squares indicating exons and black lines representing introns

Fig. 2 Phylogenetic trees of C5-MTase and dMTase proteins in different plantsIb: Ipomoea batatas; Itf: Ipomoea trifida; Itb: Ipomoea triloba; At: Arabidopsis thaliana; Al: Arabidopsis lyrata; Sl: Solanum lycopersicum; Os: Oryza sativa; Sb:Sorghum bicolor; Zm:Zea mays; Gm: Glycine max

Fig. 3 Conserved domain and motif analysis of IbC5-MTase and IbdMTase proteinsA: Conserved domains of IbC5-MTase and IbdMTase proteins. B: Motif diagrams of IbC5-MTase and IbdMTase proteins

Fig. 4 Distribution of cis-regulatory elements in the promoter regions of the IbC5-MTase and IbdMTase gene familiesA: The number of each motif in the IbC5-MTase and IbdMTase gene families, with the depth of color indicating the number. B: Statistics of cis-acting elements related to different biological functions

Fig. 5 Potential PPI network among IbC5-MTases and IbdMTasesEach node indicates a protein. The size and color intensity of a node are proportional to the number of its interacting proteins. The edges between nodes indicate predicted interactions

Fig. 6 Tissue expression patterns of IbC5-MTase and IbdMTase genesYS: Young shoot; YL: young leaf; ML: mature leaf; S:stem; FR: fibrous root; ITR: initial tuberous root; ETR: expanding tuberous root; MTR: mature tuberous root; Xu: Xuzishu No. 3; Yan: Yan 252

Fig. 7 Expression analysis of IbC5-MTase and IbdMTase genes under abiotic stressSM: Salt-sensitive material Lizixiang. SN: Salt-resistant material ND98. DM: Drought-sensitive material 18-12-3. DN: Drought-resistant material XS161819. Salt: 200 mmol/L NaCl treatment; drought: 20% PEG treatment; cold: 4 ℃ treatment. The grey square indicates that no gene expression has been detected.A: Expression analysis of IbC5-MTase and IbdMTase gene families under salt stress treatment. B: Expression analysis of IbC5-MTase and IbdMTase gene families under drought stress treatment. C: Expression analysis of IbC5-MTase and IbdMTase gene families under cold stress treatment

Fig. 8 Expression analysis of IbC5-MTase and IbdMTase genes in stem nematode inoculation treatmentR: Stem nematode-highly resistant material Xu 18-203. S: Stem nematode-highly susceptible material Xuzi 8. Different lowercase letters above the bars indicate significant differences at the P0.05 levelA: Transcriptional level analysis of the IbC5-MTase and IbdMTase gene families under stem nematode inoculation treatment. B: RT-qPCR verification of the response of IbC5-MTase and IbdMTase genes to stem nematodes

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