Methylation Analysis of Mycelium and Sclerotium Genome in Pleurotus tuber-regium

doi:10.16420/j.issn.0513-353x.2020-1018

Acta Horticulturae Sinica ›› 2022, Vol. 49 ›› Issue (1): 148-156.doi: 10.16420/j.issn.0513-353x.2020-1018

• Research Notes • Previous Articles Next Articles

Methylation Analysis of Mycelium and Sclerotium Genome in Pleurotus tuber-regium

WU Junyue, SUN Xueyan, YANG Zhenhua, LUO Lu, MO Cuiyuan, MA Aimin()

College of Food Science and Technology,Huazhong Agricultural University,Wuhan 430070,China

Received:2021-05-08 Revised:2021-11-08 Online:2022-01-25 Published:2022-01-24
Contact: MA Aimin E-mail:aiminma@mail.hzau.edu.cn

Abstract

Abstract:

The mycelium and sclerotium of Pleurotus tuber-regium（Fr.）Singer were used as materials,the methylation levels were analyzed by MSAP technology,and the differentially methylated fragments were recovered and sequenced to explore the relationship between the growth of P. tuber-regium and DNA whole genome methylation.The results showed that the DNA methylation rates of mycelium and sclerotium were 7.94% and 9.54%,respectively;the hemi-methylation rates were 4.50% and 4.09%,and the fully methylation rates were 3.44% and 5.45%,respectively.That is,the formation of sclerotium was accompanied by an increase in the methylation level,the full methylation level was more representative of the overall methylation status.Partially methylated differential fragments were recovered,cloned and sequenced.The NCBI homology comparison showed that the homologous genes or proteins are mainly related to metabolism,cell growth,and stress resistance.It is speculated that P. tuber-regium might regulate the expression of these genes or proteins through methylation to form sclerotium to adapt to environmental changes.

Key words: Pleurotus tuber-regium, mycelium, sclerotium, DNA methylation, methylation-sensitive amplified polymorphism（MSAP）

CLC Number:

WU Junyue, SUN Xueyan, YANG Zhenhua, LUO Lu, MO Cuiyuan, MA Aimin. Methylation Analysis of Mycelium and Sclerotium Genome in Pleurotus tuber-regium[J]. Acta Horticulturae Sinica, 2022, 49(1): 148-156.

Figures/Tables 5

References 46

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作用 Action	编号 Number	序列（5′-3′） Sequence	作用 Action	编号 Number	序列（5′-3′） Sequence
接头	EA-01	CTCGTAGACTGCGTACC	选择性扩增	E1	GTAGACTGCGTACCAATTCATA
Adapter	EA-02	AATTGGTACGCAGTCTAC	Selective	E2	GTAGACTGCGTACCAATTCAGT
	HMA-01	GATCATGAGTCCTGCT	amplification	E3	GTAGACTGCGTACCAATTCACC
	HMA-02	CGAGCAGGACTCATGA		E4	GTAGACTGCGTACCAATTCAAG
预扩增	EY	GTAGACTGCGTACCAATTCA		E5	GTAGACTGCGTACCAATTCAAC
Pre-amplification	HMY	CGAGCAGGACTCATGA		E6	GTAGACTGCGTACCAATTCAGC
				E7	GTAGACTGCGTACCAATTCACA
				E8	GTAGACTGCGTACCAATTCACT
				HM1	TCATGAGTCCTGCTCGGTAC
				HM2	TCATGAGTCCTGCTCGGTCC

作用 Action	编号 Number	序列（5′-3′） Sequence	作用 Action	编号 Number	序列（5′-3′） Sequence
接头	EA-01	CTCGTAGACTGCGTACC	选择性扩增	E1	GTAGACTGCGTACCAATTCATA
Adapter	EA-02	AATTGGTACGCAGTCTAC	Selective	E2	GTAGACTGCGTACCAATTCAGT
	HMA-01	GATCATGAGTCCTGCT	amplification	E3	GTAGACTGCGTACCAATTCACC
	HMA-02	CGAGCAGGACTCATGA		E4	GTAGACTGCGTACCAATTCAAG
预扩增	EY	GTAGACTGCGTACCAATTCA		E5	GTAGACTGCGTACCAATTCAAC
Pre-amplification	HMY	CGAGCAGGACTCATGA		E6	GTAGACTGCGTACCAATTCAGC
				E7	GTAGACTGCGTACCAATTCACA
				E8	GTAGACTGCGTACCAATTCACT
				HM1	TCATGAGTCCTGCTCGGTAC
				HM2	TCATGAGTCCTGCTCGGTCC

材料 Material	总扩增条带数 Total amplified bands	半甲基化条带数（占比/%） Hemi-methylated bands （ratio/%）	全甲基化条带数（占比/%） Fully methylated bands （ratio/%）	总甲基化条带数（占比/%） Total methylated bands （ratio/%）
菌丝体Mycelium	378	17（4.50）	13（3.44）	30（7.94）
菌核Sclerotium	367	15（4.09）	20（5.45）	35（9.54）

材料 Material	总扩增条带数 Total amplified bands	半甲基化条带数（占比/%） Hemi-methylated bands （ratio/%）	全甲基化条带数（占比/%） Fully methylated bands （ratio/%）	总甲基化条带数（占比/%） Total methylated bands （ratio/%）
菌丝体Mycelium	378	17（4.50）	13（3.44）	30（7.94）
菌核Sclerotium	367	15（4.09）	20（5.45）	35（9.54）

序列编号 Sequence number	甲基化差异片段比对结果 Comparisons of differentially methylated sequences	功能注释 Functional annotation	文献来源 Literature resource
DMF1	毛栓菌菌株6号染色体 Trametes hirsuta strain 072 chromosome 6		Vasina et al.,2017
DMF2	绣球菌丙氨酸-乙醛酸转氨酶1 Sparassis crispa Alanine--glyoxylate aminotransferase 1（SCP_0903720）,partial mRNA	参与光呼吸作用、天冬酰胺分解代谢、耐盐性等 Involved in photorespiration,asparagine catabolic,salt tolerance,etc	Yang et al.,2013
DMF3	灵芝蛋白转运蛋白sec31 Ganoderma boninense Q4X0M4 gene for protein transport protein sec31	提高水解酶活性,促进大直径物质运输 Improves the activity of hydrolase,promotes transport of large diameter materials	Bacia et al.,2011
DMF4	鲑色波斯特孔菌假设蛋白 Postia placenta MAD-698-R-SB12 hypothetical protein（POSPLADRAFT_1065496）,mRNA		Mao & Wang,2019
DMF5	裂褶菌未鉴定蛋白 Schizophyllum commune H4-8 uncharacterized protein（SCHCODRAFT_10951）,mRNA		Ohm et al.,2010
DMF6	云芝PLP-依赖性转移酶 Trametes versicolor FP-101664 SS1 PLP-dependent transferase mRNA	参与催化转氨基、α-脱羧、β-脱羧、β-消除等反应 Involved in catalytic transamination,α-decarboxylation,β-decarboxylation,β-elimination effect,etc	Samuel & Reeves,2003
DMF7	SIN3组蛋白脱乙酰基酶复合物 SIN3-histone deacetylase complex	形成多种多蛋白共阻遏物复合物,在植物生长和发育中发挥作用 Plays a variety of roles in plant growth and development by forming multiple types of multi-protein co-repressor complexes	Kim et al.,2016
DMF8	转录调节蛋白SIN3 Transcriptional regulatory protein SIN3	对蛋白质互作起重要作用 Plays an important role in protein interactions	Kadamb et al.,2013
DMF9	HDAC相互作用域包含蛋白 HDAC-interact domain-containing protein	调控细胞活性,影响基因转录 Regulates cell activity,affects gene transcription	Khochbin et al.,2001
DMF10	核黄素合酶结构域样蛋白 Riboflavin synthase domain-like protein	消除活性氧,增加抗病性并参与光激活反应 Eliminates reactive oxygen,increases disease resistance,and involved in photoactivation reactions	刘会敏,2009
DMF11	NADPH依赖性二黄素氧化还原酶1 NADPH-dependent diflavin oxidoreductase 1	参与抗过氧化、生长素和光周期调控等 Involved in anti-peroxidation,auxin and photoperiod regulation	Naranjo et al.,2016
DMF12	激酶样域包含蛋白 Kinase-like domain-containing protein	催化高能供体分子将磷酸基团转移到特定底物 Catalyzes the transfer of phosphate groups to specific substrates by high-energy donor molecules	Dudkiewicz et al.,2012
DMF13	丝氨酸/苏氨酸蛋白激酶 Serine/threonine-protein kinase MAP	参与蛋白质磷酸化,涉及光照、高盐、干旱及低温等信号传导途径 Involved in protein phosphorylation,including light, high salinity,drought,and low temperatures	Mao et al.,2010;蒋正宁等,2016
DMF14	细胞色素P450 Cytochrome P450	参与多种生物过程,如初级和次级代谢产物的产生和反硝化Involved in the production of primary and secondary metabolites and denitrification	Šrejber et al.,2018
DMF15	周期蛋白依赖性相关激酶 CDK-related kinase	调节基因转录和细胞分裂 Regulates gene transcription and cell division	Malumbres & Barbacid,2009
DMF16	多酚氧化酶 Polyphenol oxidase	参与植物抵抗逆境胁迫的防御能力 Involved in plant defense against adversity stress	Khodadadi et al.,2020
DMF17	光调控酪氨酸酶 Photo-regulated tyrosinase	调控黑色素形成,保护DNA免受紫外线损伤 Regulates the formation of melanin to protect DNA from UV damage	Kawaguchi et al.,2019
DMF18	疏水表面结合蛋白 Hydrophobic surface binding protein	自组装形成牢固而高度有序的两亲性膜,帮助真菌吸附到多种表面、适应多样性的环境 Self-assembles into amphiphilic film to help fungi adapt to environment	Sunde et al.,2008

Methylation Analysis of Mycelium and Sclerotium Genome in Pleurotus tuber-regium

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[1]	SHAO Fengqing, LUO Xiurong, WANG Qi, ZHANG Xianzhi, WANG Wencai. Advances in Research of DNA Methylation Regulation During Fruit Ripening [J]. Acta Horticulturae Sinica, 2023, 50(1): 197-208.
[2]	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.
[3]	ZHOU Chenping, YANG Min, GUO Jinju, KUANG Ruibin, YANG Hu, HUANG Bingxiong, WEI Yuerong. Dynamic Changes in DNA Methylome and Transcriptome Patterns During Papaya Fruit Ripening [J]. Acta Horticulturae Sinica, 2022, 49(3): 519-532.
[4]	NIE Wenfeng, WANG Jinyu, GAO Chunjuan, CHEN Xuehao. A Review on Epigenetic Modifications in Regulating Fruit Development of Horticultural Crops [J]. Acta Horticulturae Sinica, 2022, 49(3): 671-686.
[5]	DU Xiaoyun1，SONG Laiqing1，ZHAO Lingling1,3，LIU Meiying1，TANG Yan1，SUN Yanxia1，JIANG Zhongwu1,3,，and SHU Huairui1,2,. DNA Methylation in Red Fuji Apple Bud Sports Lines [J]. ACTA HORTICULTURAE SINICA, 2019, 46(1): 107-120.
[6]	ZHANG Zhiping，ZHANG Panpan，and WANG Chunlei. Detecting SP11* Genes DNA Methylation Rate of Brassica rapa by PCR-ELISA [J]. ACTA HORTICULTURAE SINICA, 2017, 44(3): 575-580.
[7]	LIU Qiong-yao，HUANG Hua-hong，FENG Hui-ping，LOU Xiong-zhen*，and TONG Zai-kang. Analysis of DNA Methylation Levels and Patterns in Dwarf Ornamental Cunninghamia lanceolata [J]. ACTA HORTICULTURAE SINICA, 2015, 42(10): 2015-2022.
[8]	LI Ji-hong，XING Shi-yan，ZHANG Qian，YAO Pei-juan，and WANG Cong-cong. The Changes in DNA Methylation Levels and Patterns of Ginkgo biloba var. epiphylla* [J]. ACTA HORTICULTURAE SINICA, 2014, 41(8): 1535-1544.
[9]	ZHU Qin-Qin, LI Zhong-Ai, HE Yan-Xia, ZHAO Wen-Qi, WANG Zi-Cheng. Research Progress on Epigenetic and Flowering-time Regulation [J]. ACTA HORTICULTURAE SINICA, 2013, 40(9): 1787-1794.
[10]	XU Hui-Hui, LIU Wei-Xin, SUN Yan, LIN Duo. The Effects of 5-azacytidine on DNA Methylation and Heat Tolerance of Seedlings of Non-heading Chinese Cabbage [J]. ACTA HORTICULTURAE SINICA, 2012, 39(3): 567-573.
[11]	LI Ji-hong;XING Shi-yan;WANG Cong-cong;ZHANG Qian;and FU Yin-yin . Analysis on Genomic DNA Methylation Modification of Ginkgo biloba by Methylation-sensitive Amplification Polymorphism [J]. ACTA HORTICULTURAE SINICA, 2011, 38(8): 1429-1436.
[12]	LIU Fu-ping;CHEN Chun;XU Chuan-jun. H₂O₂and Embryogen ic Callus Induction of Phalaenopsis spp. [J]. ACTA HORTICULTURAE SINICA, 2009, 36(9): 1339-1344.
[13]	CAI Wei-ming;JIN Qun-li;FENG Wei-lin;Li Nan-yi;FAN Li-jun;and ZHENG Zhong. Effects of Different Casing Soil on Mycelium Biomass and Yield of Agaricus bisporus [J]. ACTA HORTICULTURAE SINICA, 2008, 35(8): 1167-1174.
[14]	ZHANG lin-qing; and CHENG Zhi-hui. Optimization of Culturing Conditions for Toxin Production by Sclerotium cepivorum Berk. of Garlic [J]. ACTA HORTICULTURAE SINICA, 2008, 35(6): 841-846.
[15]	NIE Li-juan;WANG Zi-cheng;and HE Yan-xia. The Variation of DNA Methylation During Successive Transfer Culture of Chrysanthemum（Dendranthema ×grandiflorum） [J]. ACTA HORTICULTURAE SINICA, 2008, 35(11): 1689-1694.