茶树DNA去甲基化酶基因的全基因组鉴定及表达分析

doi:10.13305/j.cnki.jts.2021.01.004

摘要/Abstract

摘要： DNA去甲基化酶（dMTase）是主动去甲基化过程中具有糖基化酶和脱嘌呤裂合酶活性的双功能酶。基于茶树基因组数据,本研究利用生物信息学方法对茶树DNA去甲基化酶（CsdMTase）编码基因进行了全面鉴定和序列分析。全基因组鉴定结果表明,舒茶早基因组中包含4个CsdMTases,系统进化分析将CsdMTases分为DME和ROS两个分支,基因结构分析显示不同成员之间的基因序列长度和内含子数量存在差异。不同CsdMTases蛋白的理化性质相似,均包含ENDO3c和RRM_DME典型的保守结构域,且都定位在细胞核中。CsdMTases家族基因启动子区域包含大量光信号响应、植物激素响应、胁迫响应和生长发育等相关顺式作用元件。表达分析结果显示,CsdMTase基因在不同组织器官中均有表达,有一定的组织特异性;在炭疽菌（Colletotrichum camelliae）、拟盘多毛孢菌（Pseudopestalotiopsis camelliae-sinensis）和茶尺蠖（Ectropis oblique）等生物胁迫及干旱等非生物胁迫下,CsdMTase的表达均被显著诱导;冬季休眠过程中CsdMTases在不同品种成熟叶和越冬芽中的表达模式存在显著差异;CsDMEa、CsDMEb在花芽发育及种子萌发的不同阶段的表达存在显著上调过程。CsdMTases介导的主动去甲基化过程在调控茶树胁迫应答和生长发育中可能发挥了重要的作用,为深入揭示茶树表观调控机制提供理论依据。

关键词: 茶树, DNA去甲基化酶, 逆境胁迫响应, 生长发育, 表达分析

Abstract: DNA demethylase (dMTase) is a bifunctional enzyme with activities of glycosylase and apyrimidic lysase during active demethylation. Based on the available genome data of tea plant, bioinformatics analysis was used to comprehensively identify DNA demethylases (CsdMTase) in tea plant. The genome-wide identification results show that the tea cultivar Shuchazao contains 4 CsdMTases. These CsdMTases could be divided into two branches (DME and ROS) with differences in gene length and intron number by phylogenetic and gene structure analysis. Further analysis shows that the physical and chemical properties of different CsdMTase proteins are similar, which contain the typical conserved domains of ENCO3c and RRM_DME and are located in the nucleus. The promoter regions of CsdMTases contain a large number of cis-acting components related to light response, plant hormone response, stress response and growth and development. The CsdMTase genes are expressed in all detected tissues with certain tissue specificity. The expressions of CsdMTases were significantly up-regulated under biotic stresses, including Colletotrichum camelliae, Pseudopestalotiopsis camelliae-sinensis and Ectropis oblique treatments. During winter dormancy, different expression patterns of CsdMTases were detected in mature leaves and overwintering buds of different cultivars. The expressions of CsDMEa and CsDMEb at different stages of flower bud development and seed germination were significantly induced. The results show that active DNA demethylation process mediated by CsdMTases plays a crucial role in regulating the stress responses, growth and development of tea plant, providing a theoretical basis for discovering the epigenetic regulation mechanism in tea plant.

Key words: tea plant, DNA demethylase, stress response, growth and development, expression analysis

中图分类号:

S571.1
Q523

陈瑶, 张伟富, 任恒泽, 熊飞, 张豪杰, 姚利娜, 刘莹, 王璐, 王新超, 杨亚军, 郝心愿. 茶树DNA去甲基化酶基因的全基因组鉴定及表达分析[J]. 茶叶科学, 2021, 41(1): 28-39. doi: 10.13305/j.cnki.jts.2021.01.004.

CHEN Yao, ZHANG Weifu, REN Hengze, XIONG Fei, ZHANG Haojie, YAO Lina, LIU ying, WANG Lu, WANG Xinchao, YANG Yajun, HAO Xinyuan. Genome-wide Investigation and Expression Analysis of DNA Demethylase Genes in Tea Plant (Camellia Sinensis)[J]. Journal of Tea Science, 2021, 41(1): 28-39. doi: 10.13305/j.cnki.jts.2021.01.004.

参考文献

[1] Law J A, Jacobsen S E.Establishing, maintaining and modifying DNA methylation patterns in plants and animals[J]. Nat Rev Genet, 2010, 11(3): 204-220.
[2] Cao X, Jacobsen S E.Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes[J]. PNAS 2002, 99(s4): 16491-16498.
[3] Duan C G, Zhu J K, Cao X.Retrospective and perspective of plant epigenetics in China[J]. J Genet Genomics, 2018, 45(11): 621-638.
[4] Rocha P S, Sheikh M, Melchiorre R, et al.The Arabidopsis homology-dependent gene Silencing1 gene codes for an S-adenosyl-L-homocysteine hydrolase required for DNA methylation-dependent gene silencing[J]. Plant Cell, 2005, 17(2): 404-417.
[5] Jon P, Huh J H, Tracy Ballinger, et al.DNA demethylation in the Arabidopsis genome[J]. PNAS 2007, 104(16): 6752-6757.
[6] Zhang H, Lang Z, Zhu J K.Dynamics and function of DNA methylation in plants[J]. Nat Rev Mol Cell Bio, 2018, 19(8): 489-506.
[7] Yeonhee Choi M G. Demeter, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis [J]. Cell Press, 2002, 110(1): 33-42.
[8] Gong Z Z, Teresa M R, Rafael R A, et al.ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase [J]. Cell Press, 2002, 111(6): 803-814.
[9] Cao D, Ju Z, Gao C, et al.Genome-wide identification of cytosine-5 DNA methyltransferases and demethylases in Solanum lycopersicum[J]. Gene, 2014, 550(2): 230-237.
[10] Zemach A, Kim M Y, Silya P, et al.Local DNA hypomethylation activates genes in rice endosperm[J]. PNAS 2010, 107(43): 18729-18734.
[11] Conde D, Moreno C A, Dervinis C, et al.Overexpression of Demeter, a DNA demethylase, promotes early apical bud maturation in poplar[J]. Plant Cell and Environment Plant Cell Environ, 2017, 40(11): 2806-2819.
[12] 周艳华, 曹红利, 岳川, 等. 冷驯化不同阶段茶树DNA甲基化模式的变化[J]. 作物学报, 2015, 41(7): 1047-1055.
Zhou Y H, Cao H L, Yue C, et al.Changes of DNA methylation levels and patterns in tea plant (Camellia sinensis) during cold acclimation[J]. Acta Agronomica Sinica, 2015, 41(7): 1047-1055.
[13] Zhu C, Zhang S, Zhou C, et al.Genome-wide investigation and transcriptional analysis of cytosine-5 DNA methyltransferase and DNA demethylase gene families in tea plant (Camellia sinensis) under abiotic stress and withering processing[J]. Peer J, 2020, 8: e8432. doi: 10.3389/fpls.2016.00007.
[14] 熊飞, 卢秦华, 房婉萍, 等. 基于全基因组的茶树PAL家族基因鉴定及其在生物与非生物胁迫下的表达分析[J]. 园艺学报, 2020, 47(3): 517-528.
Xiong F, Lu Q H, Fang W P, et al.Genome-wide identification and expression analyses of PAL genes under biotic and abiotic stress in Camellia sinensis[J]. J Hortic, 2020, 47(3): 517-528.
[15] Xia E, Tong W, Hou Y, et al.The reference genome of tea plant and resequencing of 81 diverse accessions provide insights into genome evolution and adaptation of tea plants[J]. Mol Plant, 2020, 13(7): 1013-1026.
[16] Wei C, Yang H, Wang S, et al.Draft genome sequence of Camellia sinensis var. sinensis provides insights into the evolution of the tea genome and tea quality[J]. PNAS 2018, 115(18): E4151-E4158.
[17] Xia E H, Li F D, Tong W, et al.Tea plant information archive: a comprehensive genomics and bioinformatics platform for tea plant[J]. Plant Biotechnol J, 2019, 17(10): 1938-1953.
[18] Hao X, Horvath D P, Chao W S, et al.Identification and evaluation of reliable reference genes for quantitative real-time PCR analysis in tea plant (Camellia sinensis (L.) O. Kuntze)[J]. Int J Mol Sci, 2014, 15(12): 22155-22172.
[19] Thomas D.Analyzing real-time PCR data by the comparative C_T method[J]. Protocol, 2008, 3(6): 1101. doi: 10.1038/nprot.2008.73.
[20] Mok Y G, Uzawa R, Lee J, et al.Domain structure of the DEMETER 5-methylcytosine DNA glycosylase[J]. PNAS 2010, 107(45): 19225-19230.
[21] Ogneva Z V, Dubrovina A S, Kiselev K V .Age-associated alterations in DNA methylation and expression of methyltransferase and demethylase genes in Arabidopsis thaliana[J]. Biol Plantarum, 2016, 60(4): 628-634.
[22] Victoria D, Aliki K, Venetia K, et al.Spatial and temporal expression of cytosine-5 DNA methyltransferase and DNA demethylase gene families of the Ricinus communis during seed development and drought stress[J]. Plant Growth Regul, 2017, 84(1): 81-94.
[23] Gu T T, Ren S A, Wang Y H, et al.Characterization of DNA methyltransferase and demethylase genes in Fragaria vesca[J]. Mol Genet Genomics, 2016, 291(3): 1333-1345.
[24] Wang P F, Chao G, Bai X T, et al.Genome-wide identification and comparative analysis of cytosine-5 DNA methyltransferases and demethylase families in wild and cultivated peanut[J]. Front Plant Sci, 2016, 7: 7. doi: 10.3389/fpls.2016.00007.
[25] Yang X M, Chen X G, Wang D L.Genome-wide identification and expression analysis of DNA demethylase family in cotton[J]. J Cotton Res, 2019, 2(2): 142-150.
[26] Ulrike S, Joanne L, Kemal K, et al.DNA-demethylase regulated genes show methylation-independent spatiotemporal expression patterns[J]. Front Plant Sci, 2017, 8: 1449. doi: 10.3389/fpls.2017.01449.
[27] Fan S, Liu H, Liu J, et al.Systematic analysis of the DNA methylase and demethylase gene families in rapeseed (Brassica napus L.) and their expression variations after salt and heat stresses[J]. Int J Mol Sci, 2020, 21(3): 953. doi: 10.3390/ijms21030953.
[28] Conde D, Le G A, Perales M, et al.Chilling-responsive Demeter-Like DNA demethylase mediates in poplar bud break[J]. Plant Cell Environ, 2017, 40(10): 2236-2249.