利用加权基因共表达网络分析(WGCNA)的方法挖掘偃松种子萌发过程关键基因
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摘要
【目的】挖掘偃松种子萌发过程关键基因,为揭示偃松种子难于萌发的生理学和遗传学机制提供理论依据,并为进一步进行偃松资源开发利用提供技术保障。【方法】利用偃松种子萌发RNA-Seq数据,通过加权基因共表达网络分析的方法构建网络。【结果】进一步将该网络划分为4个模块,并寻找到2个特异性模块,分别为brown模块和turquoise模块。对两个模块进行GO富集分析和KEGG通路分析,发现二者均在代谢过程和细胞过程等生物学过程中发挥主要作用,其主要的细胞组分为细胞、细胞器和膜等,并均在催化反应、连接和运输中起显著作用;相比于turquoise模块,brown模块中基因信息处理过程所占比重有所提升,而相比于brown模块,turquoise模块在代谢过程中所占比重较大。利用cytoscape软件绘图,筛选特异性模块中的核心基因,并利用在线blast对其功能进行预测,其中brown模块的核心基因可能参与了ABA信号转导和固氮等过程;turquoise模块的核心基因可能参与了苯丙氨酸代谢途径、萜烯合成、果胶酶降解以及植物抗逆反应等。【结论】找到36个潜在的与偃松种子萌发相关的核心基因,其中brown模块基因为15个,turquoise模块基因为21个,但基因的具体功能有待于进一步的生物学验证。
【Objective】In order to provide a theoretical basis for revealing the physiological and genetic mechanism of the diffi cult germination of the seeds of Pinus pumila,and provide technical support for development and utilization of the resources of P. pumila,we detected the key genes of seed germination of P. pumila.【Method】A network was constructed by weighted gene co-expression network analyses(WGCNA)using RNA-Seq data of seed germination of P. pumila.【Result】The network was divided into 4 modules and two specific modules were found,which are the brown module and the turquoise module,respectively. Through the analysis of the GO concentration and the KEGG pathway of the two modules,it was found that both of the two modules played a major role in the biological processes such as the metabolic process and the cellular process. The main cellular components were the cell,the organelles and the membrane,etc.,and the main functions were catalytic activity,binding and transporter activity. Compared with the turquoise module,the proportion of genetic information processing in the brown module increased,while the turquoise module accounted for a large proportion in the metabolic compared to the brown module.The hub genes of specific modules were obtained by cytoscape,and calculate the function by online blast,which the hub genes of the brown module may be involved in the process of ABA signal transduction and nitrogen fi xation; the hub genes of the turquoise module may be involved in phenylalanine metabolism pathway,terpene synthesis,pectinase degradation and stress resistance of plant.【Conclusion】36 hub genes related to seed germination of P. pumila were identified,of which 15 were brown module bases and 21 were turquoise module bases,but the specific functions of the genes need to be further verified by biological means.
【Objective】In order to provide a theoretical basis for revealing the physiological and genetic mechanism of the diffi cult germination of the seeds of Pinus pumila,and provide technical support for development and utilization of the resources of P. pumila,we detected the key genes of seed germination of P. pumila.【Method】A network was constructed by weighted gene co-expression network analyses(WGCNA)using RNA-Seq data of seed germination of P. pumila.【Result】The network was divided into 4 modules and two specific modules were found,which are the brown module and the turquoise module,respectively. Through the analysis of the GO concentration and the KEGG pathway of the two modules,it was found that both of the two modules played a major role in the biological processes such as the metabolic process and the cellular process. The main cellular components were the cell,the organelles and the membrane,etc.,and the main functions were catalytic activity,binding and transporter activity. Compared with the turquoise module,the proportion of genetic information processing in the brown module increased,while the turquoise module accounted for a large proportion in the metabolic compared to the brown module.The hub genes of specific modules were obtained by cytoscape,and calculate the function by online blast,which the hub genes of the brown module may be involved in the process of ABA signal transduction and nitrogen fi xation; the hub genes of the turquoise module may be involved in phenylalanine metabolism pathway,terpene synthesis,pectinase degradation and stress resistance of plant.【Conclusion】36 hub genes related to seed germination of P. pumila were identified,of which 15 were brown module bases and 21 were turquoise module bases,but the specific functions of the genes need to be further verified by biological means.
引文
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[20]孙晓丽,李勇,才华,等.拟南芥bZIP1转录因子通过与ABRE元件结合调节ABA信号传导[J].作物学报,2011,37(4):612-619.
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[27]余小林,曹家树,崔辉梅,等.植物细胞色素P450[J].中国细胞生物学学报,2004,26(6):561-566.
[28]白延红,马胜利,秦静远,等.多聚半乳糖醛酸酶(PG)与果实成熟软化的影响[J].陕西农业科学,2008,54(4):86-88.
[29]Roy S.Function of MYB domain transcription factors in abiotic stress and epigenetic control of stress response in plant genome[J].Plant Signaling&Behavior,2015,11(1):e1117723.
[30]冯志娟,徐盛春,刘娜,等.植物TCP转录因子的作用机理及其应用研究进展[J].植物遗传资源学报,2018,19(1):112-121.
[31]崔喜艳,陈众峰,陈展宇.AP2/ERF转录因子对植物非生物胁迫应答的研究进展[J].吉林农业大学学报,2015,37(4):417-423.
[32]Zhou C,Li C.A Novel R2R3-MYB Transcription Factor BpMYB106 of Birch(Betula platyphylla)Confers Increased Photosynthesis and Growth Rate through Up-regulating Photosynthetic Gene Expression[J].Frontiers in plant science,2016,7:315.
[33]鞠正,曹东艳,梁岩,等.利用加权基因共表达网络分析(WGCNA)的方法挖掘番茄果实成熟相关的转录因子[J].中国食品学报,2018,18(6):240-248.
[2]谭洪涛.偃松的分布及保护利用价值[J].内蒙古林业调查设计,2013(5):27.
[3]陈国富,韦昌雷,朱万昌,等.偃松及其价值[J].特种经济动植物,2000,3(1):28.
[4]林春芳,崔克诚.偃松资源开发利用[J].林业科技通讯,2002(1):41.
[5]尹君,曹海波,崔克城,等.偃松的观赏药用价值及加工利用[J].特种经济动植物,2002,5(2):29.
[6]林春芳,朱万昌.偃松的观赏药用价值及加工利用[J].内蒙古林业调查设计,2002,25(1):49-50.
[7]刘学爽,朱万昌.偃松籽营养成份及松籽油提取技术[J].中国林副特产,2002(3):41.
[8]林建军,杨春涛.偃松资源的合理开发和利用[J].内蒙古林业调查设计,2004,27(2):20-21.
[9]许家忠.偃松资源合理开发利用价值分析[J].中国林业经济,2005(5):10-11.
[10]乌凤章,刘桂丰,姜静,等.种子萌发调控的分子机理研究进展[J].北方园艺,2008(2):54-58.
[11]颜安,吴敏洁,甘银波.光照和温度调控种子萌发的分子机理研究进展[J].核农学报,2014,28(1):52-59.
[12]周德宝.植物种子萌发的分子调控[J].安徽农业科学,2009,37(24):11405-11407.
[13]黄振英,张新时,郑光华.光照,温度和盐分对梭梭种子萌发的影响[J].植物生理与分子生物学学报,2001(3):275-280.
[14]DiLeo M V,Strahan G D,den Bakker M,et al.Weighted correlation network analysis(WGCNA)applied to the tomato fruit metabolome[J].PLoS One,2011,6(10):e26683.
[15]Iancu O D,Colville A,Oberbeck D,et al.Cosplicing network analysis of mammalian brain RNA-Seq data utilizing WGCNA and Mantel correlations[J].Frontiers in Genetics,2015,6(6):174.
[16]Yin L,Cai Z,Zhu B,et al.Identifi cation of key pathways and genes in the dynamic progression of HCC based on WGCNA[J].Genes,2018,9(2):92.
[17]Hollender C A,Kang C,Darwish O,et al.Floral Transcriptomes in Woodland Strawberry Uncover Developing Receptacle and Anther Gene Networks[J].PLANT PHYSIOLOGY,2014,165(3):1062-1075.
[18]鞠正,曹东艳,梁岩,等利用加权基因共表达网络分析(WGCNA)的方法挖掘番茄果实成熟相关的转录因子[J].中国食品学报,2018(6):240-248.
[19]Kim D,Ntui V O,Xiong L.Arabidopsis YAK1 regulates abscisic acid response and drought resistance[J].FEBSLetters,2016,590(140):2201-2209.
[20]孙晓丽,李勇,才华,等.拟南芥bZIP1转录因子通过与ABRE元件结合调节ABA信号传导[J].作物学报,2011,37(4):612-619.
[21]Nieva C,Busk P K,Domínguez-puigjaner E,et al.Isolation and Functional Characterisation of Two New bZIPMaize Regulators of the ABA Responsive Gene rab28[J].Plant Molecular Biology,2005,58(6):899-914.
[22]Sun X L,Yu Q Y,Tang L L,et al.GsSRK,a G-type lectin S-receptor-like serine/threonine protein kinase,is a positive regulator of plant tolerance to salt stress[J].Journal of plant physiology,2013,170(5):505-515.
[23]Awan S Z,Chandler J O,Harrison P J,et al.Promotion of Germination Using Hydroxamic Acid Inhibitors of9-cis-Epoxycarotenoid Dioxygenase[J].Frontiers in plant science,2017,8:357.
[24]Coschigano K T,Melo-Oliveira R,Lim J,et al.Arabidopsis gls mutants and distinct Fd-GOGAT genes:implications for photorespiration and primary nitrogen assimilation[J].The Plant Cell,1998,10(5):741-752.
[25]吴翔宇,许志茹,曲春浦,等.毛果杨基因家族生物信息学分析与鉴定[J].植物研究,2014,34(1):37-43.
[26]Ruben V,Igor C,Katarzyna R,et al.Caffeoyl shikimate esterase(CSE)is an enzyme in the lignin biosynthetic pathway in Arabidopsis[J].Science,2013,341(6150):1103-1106.
[27]余小林,曹家树,崔辉梅,等.植物细胞色素P450[J].中国细胞生物学学报,2004,26(6):561-566.
[28]白延红,马胜利,秦静远,等.多聚半乳糖醛酸酶(PG)与果实成熟软化的影响[J].陕西农业科学,2008,54(4):86-88.
[29]Roy S.Function of MYB domain transcription factors in abiotic stress and epigenetic control of stress response in plant genome[J].Plant Signaling&Behavior,2015,11(1):e1117723.
[30]冯志娟,徐盛春,刘娜,等.植物TCP转录因子的作用机理及其应用研究进展[J].植物遗传资源学报,2018,19(1):112-121.
[31]崔喜艳,陈众峰,陈展宇.AP2/ERF转录因子对植物非生物胁迫应答的研究进展[J].吉林农业大学学报,2015,37(4):417-423.
[32]Zhou C,Li C.A Novel R2R3-MYB Transcription Factor BpMYB106 of Birch(Betula platyphylla)Confers Increased Photosynthesis and Growth Rate through Up-regulating Photosynthetic Gene Expression[J].Frontiers in plant science,2016,7:315.
[33]鞠正,曹东艳,梁岩,等.利用加权基因共表达网络分析(WGCNA)的方法挖掘番茄果实成熟相关的转录因子[J].中国食品学报,2018,18(6):240-248.
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