杏扁PaCBF1基因密码子偏好性分析
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摘要
为了研究杏扁PaCBF1基因密码子偏好性,以及为其选择适合的受体,本研究利用CHIPS、CUSP在线程序以及Codon W1.4.2软件对杏扁PaCBF1基因密码子偏好性进行分析;利用SPSS 22.0软件、MEGA5.0软件对各树种CBF基因进行聚类分析。结果表明,杏扁PaCBF1基因ENc值和CAI值分别为54.053、0.163;编码区G+C含量高于A+T含量,并且偏向于G/C结尾的密码子;其他树种CBF基因也偏向于G/C结尾的密码子。聚类分析表明,杏扁与梅的密码子使用偏性的相似性较高。密码子使用频率比较分析,发现杏扁PaCBF1基因密码子使用频率与酵母、大肠杆菌、烟草、拟南芥基因组密码子之间存在一定的差异。因此,要使杏扁PaCBF1基因在4种模式生物中高效表达,需将杏扁PaCBF1基因改造成宿主基因组偏爱的密码子。此研究为PaCBF1基因选择适合的受体提供了依据,同时也为进一步研究杏扁PaCBF1基因的表达、功能以及对非生物逆境的抵抗机制提供理论依据。
In order to study codon bias of PaCBF1 gene in Prunus armeniaca L. and select the suitable receptor for it, the codon bias of PaCBF1 gene in P. armeniaca was analyzed by CHIPS and CUSP online programs and Codon W1.4.2 software. At the same time, CBFs of various tree species were clustered by SPSS 22.0 software and MEGA5.0 software. The results showed that ENc and CAI values of PaCBF1 gene in P. armeniaca were 54.053 and 0.163, respectively. The content of G+C was higher than the content of A+T in encoding region, and it was biased towards the codon with the end of G/C. The CBF genes of other tree species also favored the codon with the end of G/C. Cluster analysis indicated that codon bias of CBF gene in P. armeniaca was quite similar to that in P.mume. A comparative analysis of codon usage frequency revealed that the usage frequency of PaCBF1 gene of P.armeniaca was different with genomes condon of Saccharomyces cerevisiae, Escherichia coli, Nicotiana sylvestris,and Arabidopsis thaliana. Therefore, in order to efficiently express P. armeniaca PaCBF1 gene in 4 kinds of model organisms, we needed to transform P. armeniaca PaCBF1 gene into a host genome preference codon. This study provided the basis for the selection of the suitable receptor for the PaCBF1 gene, as well as the basis for further study of the expression, function and resistance mechanism of P. armeniaca PaCBF1 gene to abiotic stress.
In order to study codon bias of PaCBF1 gene in Prunus armeniaca L. and select the suitable receptor for it, the codon bias of PaCBF1 gene in P. armeniaca was analyzed by CHIPS and CUSP online programs and Codon W1.4.2 software. At the same time, CBFs of various tree species were clustered by SPSS 22.0 software and MEGA5.0 software. The results showed that ENc and CAI values of PaCBF1 gene in P. armeniaca were 54.053 and 0.163, respectively. The content of G+C was higher than the content of A+T in encoding region, and it was biased towards the codon with the end of G/C. The CBF genes of other tree species also favored the codon with the end of G/C. Cluster analysis indicated that codon bias of CBF gene in P. armeniaca was quite similar to that in P.mume. A comparative analysis of codon usage frequency revealed that the usage frequency of PaCBF1 gene of P.armeniaca was different with genomes condon of Saccharomyces cerevisiae, Escherichia coli, Nicotiana sylvestris,and Arabidopsis thaliana. Therefore, in order to efficiently express P. armeniaca PaCBF1 gene in 4 kinds of model organisms, we needed to transform P. armeniaca PaCBF1 gene into a host genome preference codon. This study provided the basis for the selection of the suitable receptor for the PaCBF1 gene, as well as the basis for further study of the expression, function and resistance mechanism of P. armeniaca PaCBF1 gene to abiotic stress.
引文
Cheng L.,Li Y.K.,Li X.D.,Qian B.B.,Xu S.,Xia B.,and Wang R.,2017,Codon usage bias and cluster analysis of plan CPR genes,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),15(5):1672-1682(程丽,李宜奎,李晓丹,钱彬彬,徐晟,夏冰,汪仁,2017,植物CPR基因密码子偏好性及聚类分析,分子植物育种,15(5):1672-1682)
Fu J.M.,Suo Y.J.,Liu H.M.,and Tan X.F.,2017,Analysis on codon usage in the chloroplast protein-coding genes of Diospyros spp.,Jingjilin Yanjiu(Nonwood Forest Research),35(2):38-44(傅建敏,索玉静,刘慧敏,谭晓风,2017,柿属植物叶绿体蛋白质编码基因密码子用法,经济林研究,35(2):38-44)
Ingvarsson P.K.,2010,Natural selection on synonymous and nonsynonymous mutations shapes patterns of polymorphism in Populus tremula,Mol.Biol.Evol.,27(3):650-660
Karlin S.,Campbell A.M.,and Mrazek J.,1998,Comparative DNA analysis across diverse genomes,Annual Review Genetics,32:185-225
Li Z.,Li Y.G.,Bo L.,Wang D.H.,and Li W.B.,2014,Analysis of synonymous codon bias of NFYB gene family in soybean and Arabidopsis,Zuowu Zazhi(Crops),(3):14-21(李真,李永光,薄蕾,王鼎慧,李文滨,2014,大豆和拟南芥NFYB基因家族同义密码子使用偏好性的比较,作物杂志,(3):14-21)
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
Liu Q.P.,2005,Analysis of codon usage bias and effects of sequence patterns proximal to translation initiation and termination codons on gene expression in Oryza sativa,Dissertation for Ph.D.,College of Agriculture and Biotechnology,Zhejiang University,Supervisor:Xue Q.Z.,pp.38-46(刘庆坡,2005,水稻的密码子用法及起始和终止密码子侧翼序列对基因表达的影响,博士学位论文,浙江大学农业与生物技术学院,导师:薛庆中,pp.38-46)
Liu Q.P.,Feng Y.,Zhao X.A.,Dong H.,and Xue Q.Z.,2004,Synonymous codon usage bias in Oryza sativa,Plant Sci.,167(1):101-105
Luo H.,Hu S.S.,Wu Q.,and Yao H.P.,2015,Analysis of buckwheat chloroplast gene codon bias,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(11):2457-2464(罗洪,胡莎莎,吴琦,姚慧鹏,2015,甜荞叶绿体基因密码子偏爱性分析,基因组学与应用生物学,35(11):2457-2464)
Mizoi J.,Shinozaki K.,and Yamaguchi-Shinozaki K.,2012,AP2/ERF family transcription factors in plant abiotic stress responses,Biochimica et Biophysica Acta,1819(2):86-96
Moriyama E.N.,and Powell J.R.,1997,Codon usage bias and t R-NA abundance in Drosophila,J.Mol.Evol.,45(5):514-523
Qu J.J.,Huang Y.,Lu J.,Wei Z.,and Yin L.,2017,Codon usage bias of banana genome,Nanfang Nongye Xuebao(Journal of Southern Agriculture),48(1):14-19(曲俊杰,黄羽,卢江,魏征,尹玲,2017,香蕉基因组密码子使用偏好性分析,南方农业学报,48(1):14-19)
Wu Y.Q.,Li Z.Y.,Zhao D.Q.,and Tao J.,2017,Comparative analysis of codon usage patterns in APETALA1 gene across several plant species,Yuanyi Xuebao(Acta Horticulturae Sinica),44(3):504-514(吴彦庆,李志远,赵大球,陶俊,2017,几种植物花分生组织决定基因APETALA1密码子使用模式比较,园艺学报,44(3):504-514)
Xiao Z.A.,ed.,2005,Plant biotechnology,Chemical Industry Press,Beijing,China,pp.219-226(肖尊安,编著,2005,植物生物技术,化学工业出版社,中国,北京,pp.219-226)
Xu C.,Cai X.N.,Qian B.L.,and Ben A.L.,2012,Codon usage bias in Vitis vinifera,Xibei Zhiwu Xuebao(Acta Botanica Boreali-Occidentalia Sinica),32(2):409-415(续晨,蔡小宁钱保俐,贲爱玲,2012,葡萄基因组密码子使用偏好模式研究,西北植物学报,32(2):409-415)
Zhang L.,Jin L.G.,Luo L.,Wang Y.P.,Dong Z.M.,Sun S.H.and Qiu L.J.,2011,Analysis of nuclear gene codon bias on soybean genome and transcriptome,Zuowu Xuebao(Acta Agronomica Sinica),37(6):965-974(张乐,金龙国,罗玲王跃平,董志敏,孙守红,邱丽娟,2011,大豆基因组和转录组的核基因密码子使用偏好性分析,作物学报,37(6):965-974)
Zhang T.K.,Qi G.H.,Ye H.L.,Zhang M.W.,Xiao W.,and Yuan Z.H.,2017,Codon usage bias in pomegranate transcriptome,Yuanyi Xuebao(Acta Horticulturae Sinica),44(4):675-690(张太奎,起国海,叶红莲,张孟伟,肖巍,苑兆和,2017,石榴转录组密码子使用偏向性,园艺学报,44(4):675-690)
Zheng W.W.,Chen J.H.,Hao Z.D.,and Shi J.S.,2016,Analysis on codon usage bias of chloroplast genes from five conifers including Cunninghamia lanceolata,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),14(5):1091-1097(郑薇玮,陈金慧,郝兆东,施季森,2016,杉木等5种针叶树叶绿体密码子偏好性分析,分子植物育种,14(5):1091-1097)
Fu J.M.,Suo Y.J.,Liu H.M.,and Tan X.F.,2017,Analysis on codon usage in the chloroplast protein-coding genes of Diospyros spp.,Jingjilin Yanjiu(Nonwood Forest Research),35(2):38-44(傅建敏,索玉静,刘慧敏,谭晓风,2017,柿属植物叶绿体蛋白质编码基因密码子用法,经济林研究,35(2):38-44)
Ingvarsson P.K.,2010,Natural selection on synonymous and nonsynonymous mutations shapes patterns of polymorphism in Populus tremula,Mol.Biol.Evol.,27(3):650-660
Karlin S.,Campbell A.M.,and Mrazek J.,1998,Comparative DNA analysis across diverse genomes,Annual Review Genetics,32:185-225
Li Z.,Li Y.G.,Bo L.,Wang D.H.,and Li W.B.,2014,Analysis of synonymous codon bias of NFYB gene family in soybean and Arabidopsis,Zuowu Zazhi(Crops),(3):14-21(李真,李永光,薄蕾,王鼎慧,李文滨,2014,大豆和拟南芥NFYB基因家族同义密码子使用偏好性的比较,作物杂志,(3):14-21)
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
Liu Q.P.,2005,Analysis of codon usage bias and effects of sequence patterns proximal to translation initiation and termination codons on gene expression in Oryza sativa,Dissertation for Ph.D.,College of Agriculture and Biotechnology,Zhejiang University,Supervisor:Xue Q.Z.,pp.38-46(刘庆坡,2005,水稻的密码子用法及起始和终止密码子侧翼序列对基因表达的影响,博士学位论文,浙江大学农业与生物技术学院,导师:薛庆中,pp.38-46)
Liu Q.P.,Feng Y.,Zhao X.A.,Dong H.,and Xue Q.Z.,2004,Synonymous codon usage bias in Oryza sativa,Plant Sci.,167(1):101-105
Luo H.,Hu S.S.,Wu Q.,and Yao H.P.,2015,Analysis of buckwheat chloroplast gene codon bias,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(11):2457-2464(罗洪,胡莎莎,吴琦,姚慧鹏,2015,甜荞叶绿体基因密码子偏爱性分析,基因组学与应用生物学,35(11):2457-2464)
Mizoi J.,Shinozaki K.,and Yamaguchi-Shinozaki K.,2012,AP2/ERF family transcription factors in plant abiotic stress responses,Biochimica et Biophysica Acta,1819(2):86-96
Moriyama E.N.,and Powell J.R.,1997,Codon usage bias and t R-NA abundance in Drosophila,J.Mol.Evol.,45(5):514-523
Qu J.J.,Huang Y.,Lu J.,Wei Z.,and Yin L.,2017,Codon usage bias of banana genome,Nanfang Nongye Xuebao(Journal of Southern Agriculture),48(1):14-19(曲俊杰,黄羽,卢江,魏征,尹玲,2017,香蕉基因组密码子使用偏好性分析,南方农业学报,48(1):14-19)
Wu Y.Q.,Li Z.Y.,Zhao D.Q.,and Tao J.,2017,Comparative analysis of codon usage patterns in APETALA1 gene across several plant species,Yuanyi Xuebao(Acta Horticulturae Sinica),44(3):504-514(吴彦庆,李志远,赵大球,陶俊,2017,几种植物花分生组织决定基因APETALA1密码子使用模式比较,园艺学报,44(3):504-514)
Xiao Z.A.,ed.,2005,Plant biotechnology,Chemical Industry Press,Beijing,China,pp.219-226(肖尊安,编著,2005,植物生物技术,化学工业出版社,中国,北京,pp.219-226)
Xu C.,Cai X.N.,Qian B.L.,and Ben A.L.,2012,Codon usage bias in Vitis vinifera,Xibei Zhiwu Xuebao(Acta Botanica Boreali-Occidentalia Sinica),32(2):409-415(续晨,蔡小宁钱保俐,贲爱玲,2012,葡萄基因组密码子使用偏好模式研究,西北植物学报,32(2):409-415)
Zhang L.,Jin L.G.,Luo L.,Wang Y.P.,Dong Z.M.,Sun S.H.and Qiu L.J.,2011,Analysis of nuclear gene codon bias on soybean genome and transcriptome,Zuowu Xuebao(Acta Agronomica Sinica),37(6):965-974(张乐,金龙国,罗玲王跃平,董志敏,孙守红,邱丽娟,2011,大豆基因组和转录组的核基因密码子使用偏好性分析,作物学报,37(6):965-974)
Zhang T.K.,Qi G.H.,Ye H.L.,Zhang M.W.,Xiao W.,and Yuan Z.H.,2017,Codon usage bias in pomegranate transcriptome,Yuanyi Xuebao(Acta Horticulturae Sinica),44(4):675-690(张太奎,起国海,叶红莲,张孟伟,肖巍,苑兆和,2017,石榴转录组密码子使用偏向性,园艺学报,44(4):675-690)
Zheng W.W.,Chen J.H.,Hao Z.D.,and Shi J.S.,2016,Analysis on codon usage bias of chloroplast genes from five conifers including Cunninghamia lanceolata,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),14(5):1091-1097(郑薇玮,陈金慧,郝兆东,施季森,2016,杉木等5种针叶树叶绿体密码子偏好性分析,分子植物育种,14(5):1091-1097)