Identification and Expression Analysis of Genes Related to DNA Methylation in Chrysanthemum × morifolium and C. nankingense

doi:10.16420/j.issn.0513-353x.2020-1069

Acta Horticulturae Sinica ›› 2022, Vol. 49 ›› Issue (4): 827-840.doi: 10.16420/j.issn.0513-353x.2020-1069

• Research Papers • Previous Articles Next Articles

Identification and Expression Analysis of Genes Related to DNA Methylation in Chrysanthemum × morifolium and C. nankingense

WANG Ying, AI Penghui, LI Shuailei, KANG Dongru, LI Zhongai, WANG Zicheng^**()

State Key Laboratory of Crop Stress Adaptation and Improvement,Laboratory of Plant Germplasm Resources and Genetic Engineering,Kaifeng Key Laboratory of Chrysanthemum Biology,School of Life Sciences,School of Agriculture,Henan University,Kaifeng,Henan 475004,China

Received:2021-07-16 Revised:2021-11-15 Online:2022-04-25 Published:2022-04-24
Contact: WANG Zicheng E-mail:wzc@henu.edu.cn

Abstract

Abstract:

In this study,based on the transcriptome data of the traditional chrysanthemum （Chrysanthemum × morifolium Ramat.）species‘Jinbeidahong’and the genome data of Chrysanthemum nankingense,the genes encoding DNA methylation-related enzyme were identified through bioinformatics from the‘Jinbeidahong’and C. nankingense,phylogenetic trees and gene expression were analyzed. Totally 13 DNA methyltransferase genes and 11 demethylase genes were identified from‘Jinbeidahong’,and 10 DNA methyltransferase genes and five demethylase genes were identified from C. nankingense. The evolutionary relationship demonstrated that C. lavandulifolium（Fisch. ex Trautv.）Ling et Shih were more closely associated with chrysanthemum‘Zijingling’‘Jinbeidahong’‘Hechengxinghuo’than C. nankingense and‘Quanxiangshuichang’. The transcripts levels of DNA methylation-related enzyme genes in multiple tissues and chrysanthemum varieties were quite different.

Key words: chrysanthemum, DNA methylation, DNA methyltransferase, DNA demethylase, gene identification, gene expression

CLC Number:

S682.11

WANG Ying, AI Penghui, LI Shuailei, KANG Dongru, LI Zhongai, WANG Zicheng. Identification and Expression Analysis of Genes Related to DNA Methylation in Chrysanthemum × morifolium and C. nankingense[J]. Acta Horticulturae Sinica, 2022, 49(4): 827-840.

Figures/Tables 9

References 34

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基因 Gene	上游引物序列（5′-3′） Forward primer sequence	下游引物序列（5′-3′） Reverse primer sequence
Cm-methylase1	AACTGGTCACTATACAACTG	ATCATCTGCCGTCATTAC
Cm-methylase2	GACGCTCTCCAAGATTAG	ACCACCATCATTAGATTCAA
Cm-methylase10	TGACTCCGATAGGCTACTT	GGTATCCGAATCAATATCAACATT
Cm-demethylase3	TGGAGAATGATGGAAGTG	GCCTGTTACCTTGGATAA
Cn-methylase1	TGTCAAAATCTGCTGGAGG	TTGTCATTATTGTTGGGGG
Cn-methylase2	AAAAAAGAAACGAAAGGGTC	ATAAAGAAAGCGAGAAATGG
Cn-methylase3	TACAATTCATGGTGCCTTGC	ATTTTGCGCTTCCATATGCT
Cn-methylase4	GCTTCTTCCACTTCCTCCCC	CTTAAACCCCCACCTCTCGT
Cn-methylase5	TTGCCTCAGTTTCCTTTACC	AGCACCTCCATACTCCATTT
Cn-methylase6	AATCACTTTGCTATCTCTCT	TTACTTACTTGTGTCTCTGG
Cn-methylase7	TCTTTTGCTCTTGCTCACAC	CACACACAGCCCACACATTT
Cn-methylase8	CCAAGCTAATGTGTGGCTTC	GCTGTCCATTAAACTTTGGG
Cn-methylase9	TTTTGGAAGTGAATACAGGG	ATGGTTGACATAGTGGAGAA
Cn-methylase10	ATGACAGTGAAGGACAGCGA	GAAATGAGGGGTATGAAAGG
Cn-demethylase1	CAAACCTAAGAAACCGCCAA	CAACATCTCCAAAGCCACAA
Cn-demethylase2	CTGAAGAAACTGGTAGACAA	CAAAATCAAGAACCTAATGG
Cn-demethylase3	ACAGATAAGGACCACGAATG	GGACTGAATAACCAGCAAAC
Cn-demethylase4	CCACCAGAAGGAAAATGTCG	CTCACCAGGATTGTCCCACG
Cn-demethylase5	AAACCGAAGCCAATACTGAG	TTCTAAGAGTGGGTGGGAGT
Actin	AGCTTGCATATGTTGCTCTTGA	TTACCGTAAAGGTCCTTCCTGA

基因 Gene	上游引物序列（5′-3′） Forward primer sequence	下游引物序列（5′-3′） Reverse primer sequence
Cm-methylase1	AACTGGTCACTATACAACTG	ATCATCTGCCGTCATTAC
Cm-methylase2	GACGCTCTCCAAGATTAG	ACCACCATCATTAGATTCAA
Cm-methylase10	TGACTCCGATAGGCTACTT	GGTATCCGAATCAATATCAACATT
Cm-demethylase3	TGGAGAATGATGGAAGTG	GCCTGTTACCTTGGATAA
Cn-methylase1	TGTCAAAATCTGCTGGAGG	TTGTCATTATTGTTGGGGG
Cn-methylase2	AAAAAAGAAACGAAAGGGTC	ATAAAGAAAGCGAGAAATGG
Cn-methylase3	TACAATTCATGGTGCCTTGC	ATTTTGCGCTTCCATATGCT
Cn-methylase4	GCTTCTTCCACTTCCTCCCC	CTTAAACCCCCACCTCTCGT
Cn-methylase5	TTGCCTCAGTTTCCTTTACC	AGCACCTCCATACTCCATTT
Cn-methylase6	AATCACTTTGCTATCTCTCT	TTACTTACTTGTGTCTCTGG
Cn-methylase7	TCTTTTGCTCTTGCTCACAC	CACACACAGCCCACACATTT
Cn-methylase8	CCAAGCTAATGTGTGGCTTC	GCTGTCCATTAAACTTTGGG
Cn-methylase9	TTTTGGAAGTGAATACAGGG	ATGGTTGACATAGTGGAGAA
Cn-methylase10	ATGACAGTGAAGGACAGCGA	GAAATGAGGGGTATGAAAGG
Cn-demethylase1	CAAACCTAAGAAACCGCCAA	CAACATCTCCAAAGCCACAA
Cn-demethylase2	CTGAAGAAACTGGTAGACAA	CAAAATCAAGAACCTAATGG
Cn-demethylase3	ACAGATAAGGACCACGAATG	GGACTGAATAACCAGCAAAC
Cn-demethylase4	CCACCAGAAGGAAAATGTCG	CTCACCAGGATTGTCCCACG
Cn-demethylase5	AAACCGAAGCCAATACTGAG	TTCTAAGAGTGGGTGGGAGT
Actin	AGCTTGCATATGTTGCTCTTGA	TTACCGTAAAGGTCCTTCCTGA

酶 Enzyme	基因 Gene name	CDS长度/bp CDS length	蛋白质 Protein			类型 Type
酶 Enzyme	基因 Gene name	CDS长度/bp CDS length	长度/aa Length	分子量/Da Mw	等电点 pI	类型 Type
甲基转移酶	Cm-methylase1	4 800	1 599	178 739.29	5.75	MET1
Methyltransferase	Cm-methylase2	2 788	925	103 843.57	6.14	CMT
	Cm-methylase3	2 595	864	97 299.75	4.91	CMT
	Cm-methylase4	3 093	1 030	116 027.35	5.92	CMT
	Cm-methylase5	2 511	836	94 321.79	5.95	DNMT2
	Cm-methylase6	1 317	438	49 870.56	5.24	DNMT2
	Cm-methylase7	1 053	350	39 764.17	5.13	DNMT2
	Cm-methylase8	921	306	34 963.24	4.91	DNMT2
	Cm-methylase9	1 788	595	66 491.85	4.89	DRM
	Cm-methylase10	1 833	610	68 071.51	4.96	DRM
	Cm-methylase11	654	217	24 671.57	8.97	DRM
	Cm-methylase12	1 122	373	40 971.16	4.34	DRM
	Cm-methylase13	1 041	346	39 705.42	5.83	DNMT2
去甲基化酶	Cm-demethylase1	4 638	1 545	173 065.09	8.26	DME
Demethylase	Cm-demethylase2	4 503	1 500	170 278.85	6.35	DML3
	Cm-demethylase3	3 822	1 273	144 744.28	8.93	DML3
	Cm-demethylase4	1 281	426	47 988.14	5.92	ROS1
	Cm-demethylase5	2 928	975	110 623.30	5.53	ROS1
	Cm-demethylase6	1 584	527	60 170.57	5.78	ROS1
	Cm-demethylase7	3 027	1 008	115 750.42	5.78	ROS1
	Cm-demethylase8	2 751	916	103 280.83	8.51	DME
	Cm-demethylase9	3 672	1 223	137 284.38	6.74	DME
	Cm-demethylase10	4 503	1 500	169 026.50	6.05	ROS1
	Cm-demethylase11	864	287	32 569.63	4.37	DML3

酶 Enzyme	基因 Gene name	CDS长度/bp CDS length	蛋白质 Protein			类型 Type
酶 Enzyme	基因 Gene name	CDS长度/bp CDS length	长度/aa Length	分子量/Da Mw	等电点 pI	类型 Type
甲基转移酶	Cm-methylase1	4 800	1 599	178 739.29	5.75	MET1
Methyltransferase	Cm-methylase2	2 788	925	103 843.57	6.14	CMT
	Cm-methylase3	2 595	864	97 299.75	4.91	CMT
	Cm-methylase4	3 093	1 030	116 027.35	5.92	CMT
	Cm-methylase5	2 511	836	94 321.79	5.95	DNMT2
	Cm-methylase6	1 317	438	49 870.56	5.24	DNMT2
	Cm-methylase7	1 053	350	39 764.17	5.13	DNMT2
	Cm-methylase8	921	306	34 963.24	4.91	DNMT2
	Cm-methylase9	1 788	595	66 491.85	4.89	DRM
	Cm-methylase10	1 833	610	68 071.51	4.96	DRM
	Cm-methylase11	654	217	24 671.57	8.97	DRM
	Cm-methylase12	1 122	373	40 971.16	4.34	DRM
	Cm-methylase13	1 041	346	39 705.42	5.83	DNMT2
去甲基化酶	Cm-demethylase1	4 638	1 545	173 065.09	8.26	DME
Demethylase	Cm-demethylase2	4 503	1 500	170 278.85	6.35	DML3
	Cm-demethylase3	3 822	1 273	144 744.28	8.93	DML3
	Cm-demethylase4	1 281	426	47 988.14	5.92	ROS1
	Cm-demethylase5	2 928	975	110 623.30	5.53	ROS1
	Cm-demethylase6	1 584	527	60 170.57	5.78	ROS1
	Cm-demethylase7	3 027	1 008	115 750.42	5.78	ROS1
	Cm-demethylase8	2 751	916	103 280.83	8.51	DME
	Cm-demethylase9	3 672	1 223	137 284.38	6.74	DME
	Cm-demethylase10	4 503	1 500	169 026.50	6.05	ROS1
	Cm-demethylase11	864	287	32 569.63	4.37	DML3

酶 Enzyme	基因 Gene Name	CDS长度/bp CDS length	外显子数 Number of exons	蛋白质Protein			类型 Type
酶 Enzyme	基因 Gene Name	CDS长度/bp CDS length	外显子数 Number of exons	长度/aa Length	分子量/Da Mw	等电点 pI	类型 Type
甲基转移酶	Cn-methylase1	4 803	3	1 600	178 962.60	5.78	MET1
Methyltransferase	Cn-methylase2	1 029	4	342	39 472.94	9.68	DRM
	Cn-methylase3	2 019	12	672	75 038.30	5.01	DRM
	Cn-methylase4	1 470	9	489	54 992.14	5.19	DRM
	Cn-methylase5	879	10	292	32 439.25	7.63	CMT
	Cn-methylase6	2 730	20	909	101 888.25	6.20	CMT
	Cn-methylase7	1 887	18	628	71 372.50	4.99	CMT
	Cn-methylase8	543	4	181	20 947.95	7.57	DNMT2
	Cn-methylase9	1 155	9	384	44 105.80	6.36	DNMT2
	Cn-methylase10	1 038	9	345	39 700.18	5.27	DNMT2
去甲基化酶	Cn-demethylase1	4 254	18	1 417	160 835.45	7.46	DML3
Demethylase	Cn-demethylase2	2 805	14	934	106 836.11	8.79	DML3
	Cn-demethylase3	2 613	15	870	99 036.82	9.20	DML3
	Cn-demethylase4	5 244	20	1 747	194 573.45	6.65	DME
	Cn-demethylase5	4 707	18	1 568	175 882.89	5.96	ROS1

Identification and Expression Analysis of Genes Related to DNA Methylation in Chrysanthemum × morifolium and C. nankingense

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