龙眼Hsf基因家族密码子使用模式分析
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摘要
为了解龙眼热激转录因子(heat shock transcription factor, Hsf)基因家族密码子使用偏性特征,本研究利用CodonW程序和EMBOSS在线软件对龙眼Hsf (DlHsf)基因家族密码子偏好性进行数据的提取及分析,运用SPSS、Origin和GraphPad软件对密码子偏好性参数进行统计、分析与图表制作。结果显示:(1) DlHsf基因家族密码子A/T (U)选择偏性较G/C更强,且更偏好以A/T (U)结尾。(2)最优密码子有CUU等12个。(3)密码子组成成分分析、中性绘图分析、ENC-plot分析及PR2-plot分析表明,DlHsf基因家族密码子偏好性主要受到突变压力影响。(4)与模式生物基因组密码子使用偏性使用频率比较显示,酵母菌真核表达系统更适合作为该家族基因异源表达系统,拟南芥、烟草、番茄均可作为该家族遗传转化的受体,但为提高表达效率,可能仍需在实验过程中对家族基因密码子进行改造优化。本研究为DlHsf基因家族密码子优化及转基因功能尤其是在异源表达上的研究提供一定的理论基础。
In order to understand the bias characteristics of codon usage of heat transcription factor(Hsf) gene family in%Dimocarpus longan Lour. this study used CodonW program and EMBOSS online software to extract and analyze the codon preference of Dimocarpus longan Lour. Hsf(DlHsf) gene family. Statistics, analysis and charting of codon preference parameters have been used by the software of SPSS, Origin and GraphPad. The results showed four points:(1) The DlHsf gene family codons A/T(U) selection bias were stronger than G/C, and it was more preferred to end with A or T(U);(2) There were 12 optimal codons of CUU;(3) Codon composition analysis, neutral mapping analysis, ENc-plot analysis, and PR2-plot analysis indicated that the DlHsf gene family codons preference was mainly due to mutational stress;(4) Compared with the pattern bio-genome codon usage bias, the yeast eukaryotic expression system was more suitable for heterologous expression system of this family. Arabidopsis, Nicotiana sylvestris and Solanum lycopersicum always can be used as a better receptor for genetic transformation of this family members, but during the experiment, the modification and optimization of codons is necessary. The results of this study provide a theoretical basis for the study of transgenic functions and codon optimization of DlHsf gene family.
In order to understand the bias characteristics of codon usage of heat transcription factor(Hsf) gene family in%Dimocarpus longan Lour. this study used CodonW program and EMBOSS online software to extract and analyze the codon preference of Dimocarpus longan Lour. Hsf(DlHsf) gene family. Statistics, analysis and charting of codon preference parameters have been used by the software of SPSS, Origin and GraphPad. The results showed four points:(1) The DlHsf gene family codons A/T(U) selection bias were stronger than G/C, and it was more preferred to end with A or T(U);(2) There were 12 optimal codons of CUU;(3) Codon composition analysis, neutral mapping analysis, ENc-plot analysis, and PR2-plot analysis indicated that the DlHsf gene family codons preference was mainly due to mutational stress;(4) Compared with the pattern bio-genome codon usage bias, the yeast eukaryotic expression system was more suitable for heterologous expression system of this family. Arabidopsis, Nicotiana sylvestris and Solanum lycopersicum always can be used as a better receptor for genetic transformation of this family members, but during the experiment, the modification and optimization of codons is necessary. The results of this study provide a theoretical basis for the study of transgenic functions and codon optimization of DlHsf gene family.
引文
Bla zej P.,Mackiewicz D.,Wnetrz ak M.,and Mackiewicz P.,2017,The impact of selection at the amino acid level on the usage of synonymous codons,G3,7(3):967-981
Chen Y.T.,Lai R.L.,Feng X.,Gao M.X.,Zhang C.H.,and Wu R.J.,2017,Preliminary analysis of CHS codon preference of kiwifruit chalcone synthase gene,Fujian Nongye Xuebao(Fujian Journal of Agricultural Sciences),(11):1213-1217(陈义挺,赖瑞联,冯新,高敏霞,张长和,吴如健,2017,猕猴桃查尔酮合成酶基因CHS密码子偏好性分析,福建农业学报,(11):1213-1217)
Fang H.,Qu J.J.,Sun J.M.,Yin L.,and Huang Y.,2017,The codon usage bias of NBS disease resistance genes in whole genome of banana,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),15(3):883-889(方辉,曲俊杰,孙嘉曼,尹玲,黄羽,2017,香蕉全基因组NBS抗病基因密码子使用偏好性分析,分子植物育种,15(3):883-889)
Feng C.,Xu C.,Wang Y.,Liu W.,Yin X.,and Chen K.S.,2013,Codon usage patterns in Chinese bayberry(Myrica rubra)based on RNA-Seq data,BMC Genomics,14(1):1-14
Feng C.,Zhang Y.T.,Xiao J.,and Tang H.R.,2016,Analysis of codon usage bias of%RuTT12-1 gene in blackberry,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(8):2133-2144(冯琛,张云婷,肖婕,汤浩茹,2016,黑莓RuTT12-1基因密码子偏好性分析,基因组学与应用生物学,35(8):2133-2144)
Lai R.L.,Feng X.,Chen J.,Wei X.X.,Chen Y.T.,and Wu R.J.,2017,Codon usage pattern of chalcone isomerase gene(CHI)in Canarium album(Lour.)raeusch,Yingyong Yu Huanjing Shengwu Xuebao(Chinese Journal of Applied Environmental Biology),23(5):945-951(赖瑞联,冯新,陈瑾,韦晓霞,陈义挺,吴如健,2017,橄榄查尔酮异构酶基因CHI的密码子偏好模式,应用与环境生物学报,23(5):945-951)
Lai R.L.,Lin Y.L.,Zhong C.S.,and Lai Z.X.,2016,Analysis of codon bias of auxin receptor gene TIR1 in dimocarpus lon-%gan,Yuanyi Xuebao(Acta Horticulturae Sinica),43(4):771-780(赖瑞联,林玉玲,钟春水,赖钟雄,2016,龙眼生长素受体基因TIR1密码子偏好性分析,园艺学报,43(4):771-780)
Li Z.,Li Y.G.,Bo L.,Wang D.H.,and Li W.B.,2014,Comparison of the use of synonymous codons between soybean and Arabidopsis NFYB gene families,Zuowu Zazhi(Crop Journal),(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)
Lin Y.L.,Min J.,Lai R.L.,Wu Z.Y.,Chen Y.K.,Lu L.L.,Cheng C.Z.,Jin Y.C.,Tian Q.L.,Liu Q.F.,Liu W.H.,Zhang C.G.,Lin L.X.,Hu Y.,Zhang D.M.,Thu M.K.,Zhang Z.H.,Liu S.C.,Zhong C.S.,Fang X.D.,Wang J.,Yang H.M.,Yin Y.,and Lai Z.X.,2017,Genome-wide sequencing of longan(Dimocarpus longan Lour.)provides insights into molecular basis of its polyphenol-rich characteristics,Giga Science,6(5):1-14
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)
Niu Y.,Xu Q.,Wang Y.D.,Dai L.L.,Zhuang J.,and Zhao Y.L.,2018,An analysis on codon usage bias of chloroplast genome of Rosa odorata var.gigantea,Xibei Linxueyuan Xuebao(Journal of Northwest Forestry University),(3):12(牛元,徐琼,王嵛德,代立兰,庄健,赵亚兰,2018,大花香水月季叶绿体基因组密码子使用偏性分析,西北林学院学报,(3):12)
Ohama N.,Sato H.,Shinozaki K.,and Yamaguchi-shinozaki K.,2017,Transcriptional regulatory network of plant heat stress response,Trends Plant Sci.,22(1):53
Prabha R.,Singh D.P.,Sinha S.,Khurshid A.,and Rai A.,2017,Genome-wide comparative analysis of codon usage bias and codon context patterns among cyanobacterial genomes,Marine Genomics,32:31
Qi W.H.,Chen H.B.,Peng D.F.,and Yan F.F.,2016,Current status,problems and countermeasures of China's longan industry development,Guangdong Nongye Kexue(Guangdong Agricultural Sciences),43(8):169-174(齐文娥,陈厚彬,彭朵芬宴发发,2016,中国龙眼产业发展现状,问题与对策建议,广东农业科学,43(8):169-174)
Su H.,Li Y.G.,Tan W.Y.,Teng W.Y.,and Li W.B.,2015,Codon preference analysis and optimization of escherichia coli gdhA gene,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),34(3):521-529(苏惠,李永光,谭文雍,滕卫丽,李文滨,2015,大肠杆菌gdhA基因的密码子偏好性分析及优化,基因组学与应用生物学,34(3):521-529)
Tao P.,Dai L.,Luo M.,Tang F.,Tien P.,and Pan Z.S.,2009,Analysis of synonymous codon usage in classical swine fever virus,Virus Genes,38(1):104-112
Taylor T.L.,Dimitrov K.M.,and Afonso C.L.,2017,Genomewide analysis reveals class and gene specific codon usage adaptation in avian paramyxoviruses 1,Infection Genetics&Evolution,50:28-37
Wang L.,Xing H.,Yuan Y.,Wang X.,Saeed M.,Tao J.,Feng W.,Zhang G.,Song X.,and Sun X.,2018,Genome-wide analysis of codon usage bias in four sequenced cotton species,PLoS One,13(3):e0194372
Wu Y.Q.,Li Z.Y.,Zhao D.Q.,and Tao J.,2018,Comparative analysis of flower-meristem-identity gene APETALA2(AP2)codon in different plant species,Journal of Integrative Agriculture,17(4):867-877
Zaidi M.A.,Ye G.Y.,Yao H.W.,You T.H.,Loit E.,Dean D.H.,Riazuddin S.,and Altosaar I.,2009,Transgenic rice plants expressing a modified cry1Ca1 gene are resistant to Spodop-%tera litura,and Chilo suppressalis,Mol.Biotechnol.,43(3):232-242
Zhang J.,Liu B.B.,Li J.B.,Zhang L.,Wang Y.,Zheng H.Q.,Lu M.Z.,and Chen J.,2015,Hsf and Hsp gene families in Pop-%ulus:genome-wide identification,organization and correlated expression during development and in stress responses,BMC Genomics,16(1):181
Zhou Z.W.,Chang X.J.,You F.N.,Deng T.T.,Sun Y.,and Lai Z.X.,2017,Analysis of molecular evolution and codon bias of Lipoxygenase(LOX)gene family in tea tree,Zhongguo Nongye Keji Daobao(Journal of Agricultural Science and Technology),19(12):43-51(周子维,常笑君,游芳宁,邓婷婷,孙云,赖钟雄,2017,茶树脂肪氧合酶(LOX)基因家族成员的分子进化及密码子偏好性分析,中国农业科技导报,19(12):43-51)
Chen Y.T.,Lai R.L.,Feng X.,Gao M.X.,Zhang C.H.,and Wu R.J.,2017,Preliminary analysis of CHS codon preference of kiwifruit chalcone synthase gene,Fujian Nongye Xuebao(Fujian Journal of Agricultural Sciences),(11):1213-1217(陈义挺,赖瑞联,冯新,高敏霞,张长和,吴如健,2017,猕猴桃查尔酮合成酶基因CHS密码子偏好性分析,福建农业学报,(11):1213-1217)
Fang H.,Qu J.J.,Sun J.M.,Yin L.,and Huang Y.,2017,The codon usage bias of NBS disease resistance genes in whole genome of banana,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),15(3):883-889(方辉,曲俊杰,孙嘉曼,尹玲,黄羽,2017,香蕉全基因组NBS抗病基因密码子使用偏好性分析,分子植物育种,15(3):883-889)
Feng C.,Xu C.,Wang Y.,Liu W.,Yin X.,and Chen K.S.,2013,Codon usage patterns in Chinese bayberry(Myrica rubra)based on RNA-Seq data,BMC Genomics,14(1):1-14
Feng C.,Zhang Y.T.,Xiao J.,and Tang H.R.,2016,Analysis of codon usage bias of%RuTT12-1 gene in blackberry,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(8):2133-2144(冯琛,张云婷,肖婕,汤浩茹,2016,黑莓RuTT12-1基因密码子偏好性分析,基因组学与应用生物学,35(8):2133-2144)
Lai R.L.,Feng X.,Chen J.,Wei X.X.,Chen Y.T.,and Wu R.J.,2017,Codon usage pattern of chalcone isomerase gene(CHI)in Canarium album(Lour.)raeusch,Yingyong Yu Huanjing Shengwu Xuebao(Chinese Journal of Applied Environmental Biology),23(5):945-951(赖瑞联,冯新,陈瑾,韦晓霞,陈义挺,吴如健,2017,橄榄查尔酮异构酶基因CHI的密码子偏好模式,应用与环境生物学报,23(5):945-951)
Lai R.L.,Lin Y.L.,Zhong C.S.,and Lai Z.X.,2016,Analysis of codon bias of auxin receptor gene TIR1 in dimocarpus lon-%gan,Yuanyi Xuebao(Acta Horticulturae Sinica),43(4):771-780(赖瑞联,林玉玲,钟春水,赖钟雄,2016,龙眼生长素受体基因TIR1密码子偏好性分析,园艺学报,43(4):771-780)
Li Z.,Li Y.G.,Bo L.,Wang D.H.,and Li W.B.,2014,Comparison of the use of synonymous codons between soybean and Arabidopsis NFYB gene families,Zuowu Zazhi(Crop Journal),(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)
Lin Y.L.,Min J.,Lai R.L.,Wu Z.Y.,Chen Y.K.,Lu L.L.,Cheng C.Z.,Jin Y.C.,Tian Q.L.,Liu Q.F.,Liu W.H.,Zhang C.G.,Lin L.X.,Hu Y.,Zhang D.M.,Thu M.K.,Zhang Z.H.,Liu S.C.,Zhong C.S.,Fang X.D.,Wang J.,Yang H.M.,Yin Y.,and Lai Z.X.,2017,Genome-wide sequencing of longan(Dimocarpus longan Lour.)provides insights into molecular basis of its polyphenol-rich characteristics,Giga Science,6(5):1-14
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)
Niu Y.,Xu Q.,Wang Y.D.,Dai L.L.,Zhuang J.,and Zhao Y.L.,2018,An analysis on codon usage bias of chloroplast genome of Rosa odorata var.gigantea,Xibei Linxueyuan Xuebao(Journal of Northwest Forestry University),(3):12(牛元,徐琼,王嵛德,代立兰,庄健,赵亚兰,2018,大花香水月季叶绿体基因组密码子使用偏性分析,西北林学院学报,(3):12)
Ohama N.,Sato H.,Shinozaki K.,and Yamaguchi-shinozaki K.,2017,Transcriptional regulatory network of plant heat stress response,Trends Plant Sci.,22(1):53
Prabha R.,Singh D.P.,Sinha S.,Khurshid A.,and Rai A.,2017,Genome-wide comparative analysis of codon usage bias and codon context patterns among cyanobacterial genomes,Marine Genomics,32:31
Qi W.H.,Chen H.B.,Peng D.F.,and Yan F.F.,2016,Current status,problems and countermeasures of China's longan industry development,Guangdong Nongye Kexue(Guangdong Agricultural Sciences),43(8):169-174(齐文娥,陈厚彬,彭朵芬宴发发,2016,中国龙眼产业发展现状,问题与对策建议,广东农业科学,43(8):169-174)
Su H.,Li Y.G.,Tan W.Y.,Teng W.Y.,and Li W.B.,2015,Codon preference analysis and optimization of escherichia coli gdhA gene,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),34(3):521-529(苏惠,李永光,谭文雍,滕卫丽,李文滨,2015,大肠杆菌gdhA基因的密码子偏好性分析及优化,基因组学与应用生物学,34(3):521-529)
Tao P.,Dai L.,Luo M.,Tang F.,Tien P.,and Pan Z.S.,2009,Analysis of synonymous codon usage in classical swine fever virus,Virus Genes,38(1):104-112
Taylor T.L.,Dimitrov K.M.,and Afonso C.L.,2017,Genomewide analysis reveals class and gene specific codon usage adaptation in avian paramyxoviruses 1,Infection Genetics&Evolution,50:28-37
Wang L.,Xing H.,Yuan Y.,Wang X.,Saeed M.,Tao J.,Feng W.,Zhang G.,Song X.,and Sun X.,2018,Genome-wide analysis of codon usage bias in four sequenced cotton species,PLoS One,13(3):e0194372
Wu Y.Q.,Li Z.Y.,Zhao D.Q.,and Tao J.,2018,Comparative analysis of flower-meristem-identity gene APETALA2(AP2)codon in different plant species,Journal of Integrative Agriculture,17(4):867-877
Zaidi M.A.,Ye G.Y.,Yao H.W.,You T.H.,Loit E.,Dean D.H.,Riazuddin S.,and Altosaar I.,2009,Transgenic rice plants expressing a modified cry1Ca1 gene are resistant to Spodop-%tera litura,and Chilo suppressalis,Mol.Biotechnol.,43(3):232-242
Zhang J.,Liu B.B.,Li J.B.,Zhang L.,Wang Y.,Zheng H.Q.,Lu M.Z.,and Chen J.,2015,Hsf and Hsp gene families in Pop-%ulus:genome-wide identification,organization and correlated expression during development and in stress responses,BMC Genomics,16(1):181
Zhou Z.W.,Chang X.J.,You F.N.,Deng T.T.,Sun Y.,and Lai Z.X.,2017,Analysis of molecular evolution and codon bias of Lipoxygenase(LOX)gene family in tea tree,Zhongguo Nongye Keji Daobao(Journal of Agricultural Science and Technology),19(12):43-51(周子维,常笑君,游芳宁,邓婷婷,孙云,赖钟雄,2017,茶树脂肪氧合酶(LOX)基因家族成员的分子进化及密码子偏好性分析,中国农业科技导报,19(12):43-51)