梨ERF超家族全基因组鉴定及表达分析
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摘要
中国南方地区普遍存在的由于干旱等原因提早落叶导致的梨二次花现象给生产带来了很大的损失,且该过程可以通过人工摘叶处理进行模拟诱导。乙烯响应因子ERF成员被认为参与了植物的激素应答、生物和非生物胁迫以及生长发育调控过程。本研究基于公开的白梨基因组序列,利用生物信息学方法对其中的ERF因子进行鉴定,并对其分组及各组结构域进行了详细分析。结合课题组采用摘叶诱导二次花形成过程中的梨转录组数据,分析了响应该过程的ERF成员。结果表明,共获得了211个白梨ERF家族编码基因,并可根据系统进化关系和结构域保守性分为11个组,其中种特有组一个。砂梨摘叶诱导二次花过程的转录组数据分析表明,有37个ERF因子差异表达,摘叶初期(摘叶后7 d)无响应,中期(摘叶后17 d)以下调表达为主,后期上调。对其中的4个差异表达基因进行了实时荧光定量PCR分析验证,结果与转录组分析结果吻合。此研究进一步丰富了梨响应胁迫反应的ERF基因资源,为进一步探讨ERF在成花过程中的作用提供了理论依据。
The returning blooming phenomenon in pears, which is commonly found in southern China due to drought or other reasons, has brought great losses in pear production. The process can be simulated and induced by manual defoliation(DF). Ethylene response factors(ERF) are thought to be involved in plant hormone response, biotic or abiotic stress, growth and development regulation processes. In this study, based on the published genome sequence of white pear, we used the bioinformatics to identify ERF factors. Phylogeny and conserved structural domains were analyzed in detail. The transcriptome data derived from Pyrus pyrifolia Nakai cv. Hosui bud release following early defoliation were used to investigate those involved ERF members. The results showed that a total of211 ERF encoding genes were obtained. They could be divided into 11 groups based on phylogenetic relationships and structural conservation, including one species specific group. The bioinformatics analysis of the transcriptomic data revealed that 37 ERF factors were differentially expressed compared with undefoliated control. In the beginning of defoliation(7 days after DF, DF7), there were no ERF member responses. During the middle stage(DF17), most responsive genes were down-regulated. Large proportion of the responsive genes was up-regulated in the last stage. Four differentially expressed genes were picked and verified by real-time quantitative PCR. The results were consistent with the results of transcriptomic analysis. Results of this study could further enrich the ERF gene resources for pear in stress response, and also provide a theoretical basis for further exploration of the role of ERFs in the flowering process.
The returning blooming phenomenon in pears, which is commonly found in southern China due to drought or other reasons, has brought great losses in pear production. The process can be simulated and induced by manual defoliation(DF). Ethylene response factors(ERF) are thought to be involved in plant hormone response, biotic or abiotic stress, growth and development regulation processes. In this study, based on the published genome sequence of white pear, we used the bioinformatics to identify ERF factors. Phylogeny and conserved structural domains were analyzed in detail. The transcriptome data derived from Pyrus pyrifolia Nakai cv. Hosui bud release following early defoliation were used to investigate those involved ERF members. The results showed that a total of211 ERF encoding genes were obtained. They could be divided into 11 groups based on phylogenetic relationships and structural conservation, including one species specific group. The bioinformatics analysis of the transcriptomic data revealed that 37 ERF factors were differentially expressed compared with undefoliated control. In the beginning of defoliation(7 days after DF, DF7), there were no ERF member responses. During the middle stage(DF17), most responsive genes were down-regulated. Large proportion of the responsive genes was up-regulated in the last stage. Four differentially expressed genes were picked and verified by real-time quantitative PCR. The results were consistent with the results of transcriptomic analysis. Results of this study could further enrich the ERF gene resources for pear in stress response, and also provide a theoretical basis for further exploration of the role of ERFs in the flowering process.
引文
Allen M.D.,Yamasaki K.,Ohme-Takagi M.,Tateno M.,and Suzuki M.,1998,A novel mode of DNA recognition by aβ-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA,The EMBO J.,17(18):5484-5496
Bailey T.L.,Boden M.,Buske F.A.,Frith M.,Grant C.E.,Clementi L.,Ren J.,Li W.W.,and Noble W.S.,2009,MEME SUITE:tools for motif discovery and searching,Nucleic Acids Res.,37:202-208
Gu C.,Guo Z.H.,Hao P.P.,Wang G.M.,Jin Z.M.,and Zhang S.L.,2017,Multiple regulatory roles of AP2/ERF transcription factor in angiosperm,Bot.Stud.,58(1):6
Hao D.,Ohme-Takagi M.,and Sarai A.,1998,Unique mode of GCC box recognition by the DNA-binding domain of ethylene-responsive element-binding factor(ERF domain)in plant,J.Biol.Chem.,273(41):26857-26861
Hu L.,and Liu S.,2011.,Genome-wide identification and phylogenetic analysis of the ERF gene family in cucumbers,Genet.Mol.Biol.,34(4):624-634
Li X.,Tao S.,Wei S.,Ming M.,Huang X.,Zhang S.,and Wu J.,2018,The mining and evolutionary investigation of AP2/ERF genes in pear(Pyrus),BMC Plant Biol.,18(1):46
Licausi F.,Giorgi F.M.,Zenoni S.,Osti F.,Pezzotti M.,and Perata P.,2010,Genomic and transcriptomic analysis of the AP2/ERF superfamily in Vitis vinifera,BMC Genomics,11(1):719
Licausi F.,Ohme-Takagi M.,and Perata P.,2013,APETALA2/ethylene responsive factor(AP2/ERF)transcription factors:mediators of stress responses and developmental programs,New Phytol.,199(3):639-649
Müller T.,and Vingron M.,2000,Modeling amino acid replacement,J.Comput.Biol.,7(6):761-776
Nakano T.,Suzuki K.,Fujimura T.,and Shinshi H.,2006,Genome-wide analysis of the ERF gene family in Arabidopsis and rice,Plant Physiol.,140(2):411-432
Pena-Castro J.M.,van Zanten M.,Lee S.C.,Patel M.R.,Voesenek L.A.,Fukao T.,and Bailey-Serres J.,2011,Expression of rice SUB1A and SUB1C transcription factors in Arabidopsis uncovers flowering inhibition as a submergence tolerance mechanism,Plant J.,67(3):434-446
Swaminathan K.,Peterson K.,and Jack T.,2008,The plant B3superfamily,Trends Plant Sci.,13(12):647-655
Wang Y.,Chen Q.,Chen T.,Tang H.,Liu L.,and Wang X.,2016,Phylogenetic insights into Chinese Rubus(Rosaceae)from multiple chloroplast and nuclear DNAs,Front.Plant Sci.,7:968
Wu J.,Wang Z.,Shi Z.,Zhang S.,Ming R.,Zhu S.,Khan M.A.,Tao S.,Korban S.S.,Wang H.,Chen N.J.,Nishio T.,Xu X.,Cong L.,Qi K.,Huang X.,Wang Y.,Zhao X.,Wu J.,Deng C.,Gou C.,Zhou W.,Yin H.,Qin G.,Sha Y.,Tao Y.,Chen H.,Yang Y.,Song Y.,Zhan D.,Wang J.,Li L.,Dai M.,Gu C.,Wang Y.,Shi D.,Wang X.,Zhang H.,Zeng L.,Zheng D.,Wang C.,Chen M.,Wang G.,Xie L.,Sovero V.,Sha S.,Huang W.,Zhang S.,Zhang M.,Sun J.,Xu L.,Li Y.,Liu X.,Li Q.,Shen J.,Wang J.,Paull R.E.,Bennetzen J.L.,Wang J.,and Zhang S.,2013,The genome of the pear(Pyrus bretschneideri Rehd.),Genome Res.,23(2):396-408
Xu Z.S.,Chen M.,Li L.C.,and Ma Y.Z.,2008,Functions of the ERF transcription factor family in plants,Botany,86(9):969-977
Yang Z.,Tian L.,Latoszek-Green M.,Brown D.,and Wu K.,2005,Arabidopsis ERF4 is a transcriptional repressor capable of modulating ethylene and abscisic acid responses,Plant Mol.Biol.,58(4):585-596
Zhang Q.J.,Zhong B.F.,Li W.G.,Deng J.L.,and Zhang S.L.,2016,Variation of organic nutrition on shoot and flower bud of'Hosui'pear(Pyrus pyrifolia Nakai)during reflorescence period,Xibei Zhiwu Xuebao(Acta Botanica BorealiOccidentalia Sinica),36(3):493-498(张全军,钟必凤,李文贵,邓家林,张绍铃,2016,‘丰水’梨二次开花过程中枝皮和花芽有机营养变化特征,西北植物学报,36(3):493-498)
Zhang Q.J.,Tao S.T.,Li M.,Qi X.X.,Wu J.,Yin H.,Deng J.L.,and Zhang S.L.,2015,Identification of differentially expressed genes using digital gene expression profiles in Pyrus pyrifolia Nakai cv.Hosui bud release following early defoliation,Tree Genet.Genomes,11(3):34
Zhong B.J.,Zhang Q.J.,Li W.G.,Zhang W.H.,and Deng J.L,2014,Variation of endogenous hormone of Pyrus pyrifolia Nakai in south China during returning bloomand its relationship with returing bloom,Xibei Zhiwu Xuebao(Acta Botanica Boreali-Occidentalia Sinica),34(12):2453-2458(钟必凤,张全军,李文贵,张微慧,邓家铃,2014,南方砂梨返花过程中内源激素含量变化及其与秋季返花的关系,西北植物学报,34(12):2453-2458)
Zhu Q.,Zhang J.,Gao X.,Tong J.,Xiao L.,Li W.,and Zhang H.,2010,The Arabidopsis AP2/ERF transcription factor RAP2.6 participates in ABA,salt and osmotic stress responses,Gene,457(1-2):1-12
Zhuang J.,Cai B.,Peng R.H.,Zhu B.,Jin X.F.,Xue Y.,Gao F.,Fu X.Y.,Tian Y.S.,and Zhao W.,2008,Genome-wide analysis of the AP2/ERF gene family in Populus trichocarpa,Biochem.Bioph.Res.Co.,371(3):468-474
Bailey T.L.,Boden M.,Buske F.A.,Frith M.,Grant C.E.,Clementi L.,Ren J.,Li W.W.,and Noble W.S.,2009,MEME SUITE:tools for motif discovery and searching,Nucleic Acids Res.,37:202-208
Gu C.,Guo Z.H.,Hao P.P.,Wang G.M.,Jin Z.M.,and Zhang S.L.,2017,Multiple regulatory roles of AP2/ERF transcription factor in angiosperm,Bot.Stud.,58(1):6
Hao D.,Ohme-Takagi M.,and Sarai A.,1998,Unique mode of GCC box recognition by the DNA-binding domain of ethylene-responsive element-binding factor(ERF domain)in plant,J.Biol.Chem.,273(41):26857-26861
Hu L.,and Liu S.,2011.,Genome-wide identification and phylogenetic analysis of the ERF gene family in cucumbers,Genet.Mol.Biol.,34(4):624-634
Li X.,Tao S.,Wei S.,Ming M.,Huang X.,Zhang S.,and Wu J.,2018,The mining and evolutionary investigation of AP2/ERF genes in pear(Pyrus),BMC Plant Biol.,18(1):46
Licausi F.,Giorgi F.M.,Zenoni S.,Osti F.,Pezzotti M.,and Perata P.,2010,Genomic and transcriptomic analysis of the AP2/ERF superfamily in Vitis vinifera,BMC Genomics,11(1):719
Licausi F.,Ohme-Takagi M.,and Perata P.,2013,APETALA2/ethylene responsive factor(AP2/ERF)transcription factors:mediators of stress responses and developmental programs,New Phytol.,199(3):639-649
Müller T.,and Vingron M.,2000,Modeling amino acid replacement,J.Comput.Biol.,7(6):761-776
Nakano T.,Suzuki K.,Fujimura T.,and Shinshi H.,2006,Genome-wide analysis of the ERF gene family in Arabidopsis and rice,Plant Physiol.,140(2):411-432
Pena-Castro J.M.,van Zanten M.,Lee S.C.,Patel M.R.,Voesenek L.A.,Fukao T.,and Bailey-Serres J.,2011,Expression of rice SUB1A and SUB1C transcription factors in Arabidopsis uncovers flowering inhibition as a submergence tolerance mechanism,Plant J.,67(3):434-446
Swaminathan K.,Peterson K.,and Jack T.,2008,The plant B3superfamily,Trends Plant Sci.,13(12):647-655
Wang Y.,Chen Q.,Chen T.,Tang H.,Liu L.,and Wang X.,2016,Phylogenetic insights into Chinese Rubus(Rosaceae)from multiple chloroplast and nuclear DNAs,Front.Plant Sci.,7:968
Wu J.,Wang Z.,Shi Z.,Zhang S.,Ming R.,Zhu S.,Khan M.A.,Tao S.,Korban S.S.,Wang H.,Chen N.J.,Nishio T.,Xu X.,Cong L.,Qi K.,Huang X.,Wang Y.,Zhao X.,Wu J.,Deng C.,Gou C.,Zhou W.,Yin H.,Qin G.,Sha Y.,Tao Y.,Chen H.,Yang Y.,Song Y.,Zhan D.,Wang J.,Li L.,Dai M.,Gu C.,Wang Y.,Shi D.,Wang X.,Zhang H.,Zeng L.,Zheng D.,Wang C.,Chen M.,Wang G.,Xie L.,Sovero V.,Sha S.,Huang W.,Zhang S.,Zhang M.,Sun J.,Xu L.,Li Y.,Liu X.,Li Q.,Shen J.,Wang J.,Paull R.E.,Bennetzen J.L.,Wang J.,and Zhang S.,2013,The genome of the pear(Pyrus bretschneideri Rehd.),Genome Res.,23(2):396-408
Xu Z.S.,Chen M.,Li L.C.,and Ma Y.Z.,2008,Functions of the ERF transcription factor family in plants,Botany,86(9):969-977
Yang Z.,Tian L.,Latoszek-Green M.,Brown D.,and Wu K.,2005,Arabidopsis ERF4 is a transcriptional repressor capable of modulating ethylene and abscisic acid responses,Plant Mol.Biol.,58(4):585-596
Zhang Q.J.,Zhong B.F.,Li W.G.,Deng J.L.,and Zhang S.L.,2016,Variation of organic nutrition on shoot and flower bud of'Hosui'pear(Pyrus pyrifolia Nakai)during reflorescence period,Xibei Zhiwu Xuebao(Acta Botanica BorealiOccidentalia Sinica),36(3):493-498(张全军,钟必凤,李文贵,邓家林,张绍铃,2016,‘丰水’梨二次开花过程中枝皮和花芽有机营养变化特征,西北植物学报,36(3):493-498)
Zhang Q.J.,Tao S.T.,Li M.,Qi X.X.,Wu J.,Yin H.,Deng J.L.,and Zhang S.L.,2015,Identification of differentially expressed genes using digital gene expression profiles in Pyrus pyrifolia Nakai cv.Hosui bud release following early defoliation,Tree Genet.Genomes,11(3):34
Zhong B.J.,Zhang Q.J.,Li W.G.,Zhang W.H.,and Deng J.L,2014,Variation of endogenous hormone of Pyrus pyrifolia Nakai in south China during returning bloomand its relationship with returing bloom,Xibei Zhiwu Xuebao(Acta Botanica Boreali-Occidentalia Sinica),34(12):2453-2458(钟必凤,张全军,李文贵,张微慧,邓家铃,2014,南方砂梨返花过程中内源激素含量变化及其与秋季返花的关系,西北植物学报,34(12):2453-2458)
Zhu Q.,Zhang J.,Gao X.,Tong J.,Xiao L.,Li W.,and Zhang H.,2010,The Arabidopsis AP2/ERF transcription factor RAP2.6 participates in ABA,salt and osmotic stress responses,Gene,457(1-2):1-12
Zhuang J.,Cai B.,Peng R.H.,Zhu B.,Jin X.F.,Xue Y.,Gao F.,Fu X.Y.,Tian Y.S.,and Zhao W.,2008,Genome-wide analysis of the AP2/ERF gene family in Populus trichocarpa,Biochem.Bioph.Res.Co.,371(3):468-474