甘薯DNA甲基转移酶和去甲基化酶基因家族的全基因组鉴定与表达分析

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

摘要/Abstract

摘要：

目的鉴定甘薯DNA甲基转移酶（IbC5-MTase）及去甲基化酶（IbdMTase）基因家族成员并分析其结构及表达模式，为深入探究甘薯DNA甲基化的分子基础及生物学功能提供理论支撑。方法利用生物信息学方法对IbC5-MTase及IbdMTase基因家族成员进行理化性质、序列、进化及结构分析，并结合转录组和RT-qPCR技术分析IbC5-MTase及IbdMTase在甘薯不同组织、非生物及生物胁迫下的表达情况。结果在甘薯全基因组中共鉴定出7个C5-MTase基因和4个dMTase基因，分布于8个连锁群上。IbC5-MTase和IbdMTase蛋白含有355-1 305个氨基酸，理论等电点（pI）介于4.81-9.81，亚细胞定位预测结果表明其中9个蛋白位于细胞核；系统进化分析将IbC5-MTase和IbdMTase蛋白分别分为4个和3个亚族；保守基序分析结果显示，IbC5-MTase和IbdMTase蛋白具有完全不同的motif；启动子分析发现，IbC5-MTase和IbdMTase基因启动子区富含光响应、激素响应及应激响应元件。组织特异性表达分析表明，IbDRM2和IbCMT3b表达量较高，两类基因家族在甘薯地上部表达水平高于根部，且在幼嫩组织中表达量更高。甘薯非生物胁迫转录组数据显示，IbC5-MTase和IbdMTase基因在甘薯响应盐、干旱、冷胁迫中表达模式发生显著变化。茎线虫接种后转录组及RT-qPCR结果表明，IbC5-MTase和IbdMTase家族基因也受到生物胁迫诱导，其中，IbCMT3a和IbDRM2表达量显著降低，IbCMT3b与IbROS1基因表达量升高。结论甘薯C5-MTase和dMTase基因在生物及非生物胁迫中均具有潜在功能。

关键词: 甘薯, C5-MTase及dMTase基因, 生物信息学, 生物及非生物胁迫, 表达模式

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

张艾岑, 闫会, 马居奎, 张允刚, 李强. 甘薯DNA甲基转移酶和去甲基化酶基因家族的全基因组鉴定与表达分析[J]. 生物技术通报, 2026, 42(6): 1-12.

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.

图/表 10

表1 基因表达分析的实时荧光定量引物

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

表2 IbC5-MTase和IbdMTase家族基因信息及其编码蛋白理化性质

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

图1 IbC5-MTase和IbdMTase基因家族染色体分布及结构分析A：基因在连锁群上的分布，红色为IbC5-MTase家族基因，蓝色为IbdMTase家族基因；B：基因外显子-内含子分布，蓝色方块代表外显子，黑线代表内含子

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

图2 不同植物C5-MTase和dMTase蛋白的系统进化树Ib：甘薯；Itf：三浅裂野牵牛；Itb：三裂叶薯；At：拟南芥；Al：琴叶拟南芥；Sl：番茄；Os：水稻；Sb：高粱；Zm：玉米；Gm：大豆

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

图3 IbC5-MTase和IbdMTase蛋白保守结构域及基序分析A：IbC5-MTase和IbdMTase蛋白保守结构域； B：IbC5-MTase和IbdMTase蛋白基序图

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

图4 IbC5-MTase和IbdMTase基因家族启动子区顺式调控元件的分布A：IbC5-MTase和IbdMTase基因家族中每个基序的数目，颜色的深浅表示数目。B：不同生物学功能相关的顺式作用元件统计

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

图5 IbC5-MTases和IbdMTases潜在的蛋白-蛋白相互作用网络节点表示蛋白质，其大小与颜色深度代表与之相互作用的蛋白质数量；边表示蛋白质间存在的相互作用

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

图6 IbC5-MTase和IbdMTase基因组织表达模式YS：幼苗地上部；YL：幼叶；ML：成熟叶；S：茎；FR：须根；ITR：初期块根；ETR：膨大期块根；MTR：成熟块根；Xu：徐紫薯3号；Yan：烟252

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

图7 IbC5-MTase和IbdMTase基因在非生物胁迫下的表达分析SM：盐敏感材料栗子香；SN：耐盐材料ND98；DM：干旱敏感材料18-12-3；DN：耐旱材料XS161819；盐：200 mmol/L NaCl处理；旱：20% PEG处理；冷：4 ℃处理；灰色方块代表未检测到基因表达A：盐胁迫处理下IbC5-MTase和IbdMTase基因家族表达分析；B：干旱胁迫处理下IbC5-MTase和IbdMTase基因家族表达分析；C：冷胁迫处理下IbC5-MTase和IbdMTase基因家族表达分析

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

图8 IbC5-MTase和IbdMTase基因茎线虫接种处理表达分析R：高抗茎线虫材料徐18-203；S：高感茎线虫材料徐紫薯8号；柱状图上不同小写字母表示在P0.05水平时显著差异A：茎线虫接种处理下IbC5-MTase和IbdMTase基因家族转录水平分析；B：IbC5-MTase和IbdMTase基因响应茎线虫的RT-qPCR验证

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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