大薯ERF基因家族的挖掘与特征
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摘要
大薯属于薯蓣科薯蓣属,是热带和亚热带地区的一种重要的粮食作物,但其基础研究还较为薄弱。本研究基于公布的大薯转录谱序列和基因组序列,开展了对大薯ERF家族基因的挖掘和特征分析。共找到DaERF基因41个,其中14个DaERF有一个以上的外显子,其余的均为一个外显子。进一步的blastx分析发现30个DaERF基因具有保守的AP2结构域,依据AP2序列构建系统进化树,可将其分成5个亚家族。通过对AP2结构域的两个保守motif的位置和结合位点的分析,发现相同家族的ERF蛋白具有相似的结构特征。根据大薯转录谱分析DaERF在不同组织中的表达,发现一些DaERF的表达具有组织特异性,并且属于同一亚家族基因的表达具有相似性。我们对在块茎中具有高表达的DaERF-DaERF24基因,使用RT-qPCR验证其在不同组织的表达,结果与转录谱数据一致。本研究通过对大薯ERF转录因子家族特性的初步挖掘,为以后研究ERF家族全基因分布、ERF基因功能验证和薯块生长发育机理提供依据。
Great yam(Dioscorea alata), belongs to the genus Dioscorea(family Dioscoreaceae), is an important staple crop in tropical and subtropical regions. However, the researches for this crop is still weak. In this study, we used the published EST, transcriptome and genomic sequences of great yam to identify and characterize ERF gene family. A total of 41 DaERF genes were obtained, of which 14 DaERF genes have more than one exon and rest genes have one exon. Through blastx analysis of the 41 DaERF genes, we found that 30 DaERF genes have conserved AP2 domains. Phylogenesis analyses of the 30 DaERFs indicated that these genes could be divided into five subfamilies. Analysis of the location and binding sites of two motifs in DaREF genes demonstrated that DaERFs in a same subfamily tend to have same structural features and suggested that DaERFs in a same family might have similar functions. Analysis of expression profiles for these DaERFs showed that DaERFs in a same ERF family tend to have similar expression level and tissue specific patterns. DaERF24, which was highly expressed in tuber tissues based on transcriptome data, was further confirmed its expression pattern by fluorescence quantitative PCR. In this study, the characteristics of ERF transcription factor family in great yam were preliminarily excavated to lay a foundation for the future study of the whole gene distribution of ERF family, the functional verification of ERF gene and the growth and development mechanism of tuber.
Great yam(Dioscorea alata), belongs to the genus Dioscorea(family Dioscoreaceae), is an important staple crop in tropical and subtropical regions. However, the researches for this crop is still weak. In this study, we used the published EST, transcriptome and genomic sequences of great yam to identify and characterize ERF gene family. A total of 41 DaERF genes were obtained, of which 14 DaERF genes have more than one exon and rest genes have one exon. Through blastx analysis of the 41 DaERF genes, we found that 30 DaERF genes have conserved AP2 domains. Phylogenesis analyses of the 30 DaERFs indicated that these genes could be divided into five subfamilies. Analysis of the location and binding sites of two motifs in DaREF genes demonstrated that DaERFs in a same subfamily tend to have same structural features and suggested that DaERFs in a same family might have similar functions. Analysis of expression profiles for these DaERFs showed that DaERFs in a same ERF family tend to have similar expression level and tissue specific patterns. DaERF24, which was highly expressed in tuber tissues based on transcriptome data, was further confirmed its expression pattern by fluorescence quantitative PCR. In this study, the characteristics of ERF transcription factor family in great yam were preliminarily excavated to lay a foundation for the future study of the whole gene distribution of ERF family, the functional verification of ERF gene and the growth and development mechanism of tuber.
引文
Cai J.,Liu M.J.,Wang Z.,and Ju Y.,2002,Apoptosis induced by dioscin in hela cells,Biological&Pharmaceutical Bulletin,25(2):193-196
Dong W.,Ai X.H.,Xu F.,Quan T.Y.,Liu S.W.,and Xia G.M.,2012,Isolation and characterization of a bread wheat salinity responsive ERF transcription factor,Gene,511(1):38-45
Huang M.,Cheng S.Y.,Zhang Z.X.,and Du H.W.,2014,Genome-wide analysis of the AP2/ERF gene family in maize waterlogging stress response,Euphytica,198(1):115-126
Elliott R.C.,Betzner A.S.,Huttner E.,Oakes M.P.,Tucker W.Q.J.,Gerentes D.,Perez P.,and Smyth D.R.,1996,AIN-TEGUMENTA,an APETALA2-like gene of Arabidopsis with pleiotropic roles in ovule development and floral organ growth,Plant Cell,8(2):155-168
Gu Y.,Wildermuth M.C.,Chakravarthy S.,Loh Y.,Yang C.,He X.,Han Y.,and Martin G.B.,2002,Tomato transcription factors Pti4,Pti5,and Pti6 activate defense responses when expressed in Arabidopsis,Plant Cell,14(4):817-831
Hu L.F.,and Liu S.Q.,2011,Genome-wide identification and phylogenetic analysis of the ERF gene family in cucumbers,Genet.Mol.Biol.,34(4):624-634
Hu Y.X.,Wang Y.H.,Liu X.F.,and Li J.,2004,Arabidopsis RAV1 is down-regulated by brassinosteroid and may act as a negative regulator during plant development,Cell Research,14(1):8-15
Ji Q.,Zhou F.,Zhou J.,Wang D.W.,Hu M.H.,Li D.,Shen B.Q.,Deng L.,Gao X.Y.,and Du Z.Y.,2018,Whole genome identification and bioinformatics analysis of AP2/EREBPtranscription factors in Chinese jujube,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),37(7):2983-2997(纪晴,周凡,周军,王大玮,胡孟豪,李丹,沈兵琪,邓浪,高晓宇,杜宗义,2018,枣AP2/EREBP转录因子的全基因组鉴定及生物信息学分析,基因组学与应用生物学,37(7):2983-2997)
Lakhwani D.,Pandey A.,Dhar Y.V.,Bag S.K.,Trivedi P.K.,and Asif M.H.,2016,Genome-wide analysis of the AP2/ERFfamily in Musa species reveals divergence and neofunctionalisation during evolution,Sci.Rep.,6:18878
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 Phytologist,199(3):639-649
Memelink J.,2009,Regulation of gene expression by jasmonate hormones,Phytochemistry,70(13-14):1560-1570
Muller M.,and Munne-Bosch S.,2015,Ethylene response factors:a key regulatory hub in hormone and stress signaling,Plant Physiol.,169(1):32-41
Nakano T.,Suzuki K.,Fujimura T.,and Shinshi H.,2006,Genomewide analysis of the ERF gene family in Arabidopsis and rice,Plant Physiol.,140(2):411-432
Reiner A.,Yekutieli D.,and Benjamini Y.,2003,Identifying differentially expressed genes using false discovery rate controlling procedures,Bioinformatics,19(3):368-375
Sakuma Y.,Liu Q.,Dubouzet J.G.,Abe H.,Shinozaki K.,and Yamaguchi-Shinozaki K.,2002,DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs,transcription factors involved in dehydration-and cold-inducible gene expression,Biochem.Biophys.Res.Commun.,290(3):998-1009
Tamiru M.,Natsume S.,Takagi H.,White B.,Yaegashi H.,Shimizu M.,Yoshida K.,Uemura A.,Oikawa K.,Abe A.,Urasaki N.,Matsumura H.,Babil P.,Yamanaka S.,Matsumoto R.,Muranaka S.,Girma G.,Lopez-Montes A.,Gedil M.,Bhattacharjee R.,Abberton M.,Kumar P.L.,Rabbi I.,Tsujimura M.,Terachi T.,Haerty W.,Corpas M.,Kamoun S.,Kahl G.,Takagi H.,Asiedu R.,and Terauchi R.,2017,Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination,BMC Biol.,15(1):86
Xia W.,Wu W.Q.,Xu Y.,Xie J.,Huang X.L.,and Huang D.Y.,2017,Advances in the study of germplasm diversity of Dioscorea,Zhiwu Shengli Xuebao(Plant Physiology Journal),53(5):781-784(夏薇,吴文嫱,许云,谢俊,黄小龙,黄东益,2017,大薯种质资源多样性研究进展,植物生理学报,53(5):781-784)
Yu X.,Cao B.B.,Qin J.H.,Gao Y.,and Li A.,2018,Cloning and expression vector construction of LkERF-B2 gene from larch,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),37(8):3482-3488(于雪,曹贝贝,秦家慧,高英,李爱,2018,落叶松LkERF-B2基因的克隆及表达载体的构建,基因组学与应用生物学,37(8):3482-3488)
Zarei A.,Korbes A.P.,Younessi P.,Montiel G.,Champion A.,and Memelink J.,2011,Two GCC boxes and AP2/ERF-domain transcription factor ORA59 in jasmonate/ethylene-mediated activation of the PDF1.2 promoter in Arabidopsis,Plant Mol.Biol.,75(4-5):321-331
Zhang Z.,and Huang R.,2010,Enhanced tolerance to freezing in tobacco and tomato overexpressing transcription factor TERF2/LeERF2 is modulated by ethylene biosynthesis,Plant Molecular Biology,73(3):241-249
Zhao X.H.,Wang Q.J.,Li C.,Chen X.D.,Xiao W.,Gao D.S.,and Fu X.L.,2018,Tao ERF transcription factor family bioinformatics analysis and germination-related gene screening,Zhiwu Xuebao(Acta Botanica Sinica),53(5):612-624(赵雪惠,王庆杰,李晨,陈修德,肖伟,高东升,付喜玲,2018.桃ERF转录因子家族生物信息学分析及芽萌发相关基因筛选,植物学报,53(5):612-624)
Zhao Y.,Chang X.,Qi D.,Dong L.,Wang G.,Fan S.,Jiang L.,Cheng Q.,Chen X.,Han D.,Xu P.,and Zhang S.,2017,Anovel soybean ERF transcription factor,Gm ERF113,increases resistance to Phytophthora sojae infection in soybean,Front Plant Sci.,8:299
Dong W.,Ai X.H.,Xu F.,Quan T.Y.,Liu S.W.,and Xia G.M.,2012,Isolation and characterization of a bread wheat salinity responsive ERF transcription factor,Gene,511(1):38-45
Huang M.,Cheng S.Y.,Zhang Z.X.,and Du H.W.,2014,Genome-wide analysis of the AP2/ERF gene family in maize waterlogging stress response,Euphytica,198(1):115-126
Elliott R.C.,Betzner A.S.,Huttner E.,Oakes M.P.,Tucker W.Q.J.,Gerentes D.,Perez P.,and Smyth D.R.,1996,AIN-TEGUMENTA,an APETALA2-like gene of Arabidopsis with pleiotropic roles in ovule development and floral organ growth,Plant Cell,8(2):155-168
Gu Y.,Wildermuth M.C.,Chakravarthy S.,Loh Y.,Yang C.,He X.,Han Y.,and Martin G.B.,2002,Tomato transcription factors Pti4,Pti5,and Pti6 activate defense responses when expressed in Arabidopsis,Plant Cell,14(4):817-831
Hu L.F.,and Liu S.Q.,2011,Genome-wide identification and phylogenetic analysis of the ERF gene family in cucumbers,Genet.Mol.Biol.,34(4):624-634
Hu Y.X.,Wang Y.H.,Liu X.F.,and Li J.,2004,Arabidopsis RAV1 is down-regulated by brassinosteroid and may act as a negative regulator during plant development,Cell Research,14(1):8-15
Ji Q.,Zhou F.,Zhou J.,Wang D.W.,Hu M.H.,Li D.,Shen B.Q.,Deng L.,Gao X.Y.,and Du Z.Y.,2018,Whole genome identification and bioinformatics analysis of AP2/EREBPtranscription factors in Chinese jujube,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),37(7):2983-2997(纪晴,周凡,周军,王大玮,胡孟豪,李丹,沈兵琪,邓浪,高晓宇,杜宗义,2018,枣AP2/EREBP转录因子的全基因组鉴定及生物信息学分析,基因组学与应用生物学,37(7):2983-2997)
Lakhwani D.,Pandey A.,Dhar Y.V.,Bag S.K.,Trivedi P.K.,and Asif M.H.,2016,Genome-wide analysis of the AP2/ERFfamily in Musa species reveals divergence and neofunctionalisation during evolution,Sci.Rep.,6:18878
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 Phytologist,199(3):639-649
Memelink J.,2009,Regulation of gene expression by jasmonate hormones,Phytochemistry,70(13-14):1560-1570
Muller M.,and Munne-Bosch S.,2015,Ethylene response factors:a key regulatory hub in hormone and stress signaling,Plant Physiol.,169(1):32-41
Nakano T.,Suzuki K.,Fujimura T.,and Shinshi H.,2006,Genomewide analysis of the ERF gene family in Arabidopsis and rice,Plant Physiol.,140(2):411-432
Reiner A.,Yekutieli D.,and Benjamini Y.,2003,Identifying differentially expressed genes using false discovery rate controlling procedures,Bioinformatics,19(3):368-375
Sakuma Y.,Liu Q.,Dubouzet J.G.,Abe H.,Shinozaki K.,and Yamaguchi-Shinozaki K.,2002,DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs,transcription factors involved in dehydration-and cold-inducible gene expression,Biochem.Biophys.Res.Commun.,290(3):998-1009
Tamiru M.,Natsume S.,Takagi H.,White B.,Yaegashi H.,Shimizu M.,Yoshida K.,Uemura A.,Oikawa K.,Abe A.,Urasaki N.,Matsumura H.,Babil P.,Yamanaka S.,Matsumoto R.,Muranaka S.,Girma G.,Lopez-Montes A.,Gedil M.,Bhattacharjee R.,Abberton M.,Kumar P.L.,Rabbi I.,Tsujimura M.,Terachi T.,Haerty W.,Corpas M.,Kamoun S.,Kahl G.,Takagi H.,Asiedu R.,and Terauchi R.,2017,Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination,BMC Biol.,15(1):86
Xia W.,Wu W.Q.,Xu Y.,Xie J.,Huang X.L.,and Huang D.Y.,2017,Advances in the study of germplasm diversity of Dioscorea,Zhiwu Shengli Xuebao(Plant Physiology Journal),53(5):781-784(夏薇,吴文嫱,许云,谢俊,黄小龙,黄东益,2017,大薯种质资源多样性研究进展,植物生理学报,53(5):781-784)
Yu X.,Cao B.B.,Qin J.H.,Gao Y.,and Li A.,2018,Cloning and expression vector construction of LkERF-B2 gene from larch,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),37(8):3482-3488(于雪,曹贝贝,秦家慧,高英,李爱,2018,落叶松LkERF-B2基因的克隆及表达载体的构建,基因组学与应用生物学,37(8):3482-3488)
Zarei A.,Korbes A.P.,Younessi P.,Montiel G.,Champion A.,and Memelink J.,2011,Two GCC boxes and AP2/ERF-domain transcription factor ORA59 in jasmonate/ethylene-mediated activation of the PDF1.2 promoter in Arabidopsis,Plant Mol.Biol.,75(4-5):321-331
Zhang Z.,and Huang R.,2010,Enhanced tolerance to freezing in tobacco and tomato overexpressing transcription factor TERF2/LeERF2 is modulated by ethylene biosynthesis,Plant Molecular Biology,73(3):241-249
Zhao X.H.,Wang Q.J.,Li C.,Chen X.D.,Xiao W.,Gao D.S.,and Fu X.L.,2018,Tao ERF transcription factor family bioinformatics analysis and germination-related gene screening,Zhiwu Xuebao(Acta Botanica Sinica),53(5):612-624(赵雪惠,王庆杰,李晨,陈修德,肖伟,高东升,付喜玲,2018.桃ERF转录因子家族生物信息学分析及芽萌发相关基因筛选,植物学报,53(5):612-624)
Zhao Y.,Chang X.,Qi D.,Dong L.,Wang G.,Fan S.,Jiang L.,Cheng Q.,Chen X.,Han D.,Xu P.,and Zhang S.,2017,Anovel soybean ERF transcription factor,Gm ERF113,increases resistance to Phytophthora sojae infection in soybean,Front Plant Sci.,8:299