香蕉Aux/IAA基因家族密码子偏好性分析
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摘要
通过对香蕉Aux/IAA (auxin/indole-3-acetic acid)基因家族密码子使用偏好性进行研究为进一步的功能研究尤其是异源表达验证提供参考。本研究采用CodonW、EMBOSS在线程序、SPSS和Origin软件分析了香蕉Aux/IAA基因家族的密码子使用偏好性参数,并和香蕉基因组以及几种遗传转化再生体系成熟的模式植物基因组做了比较。结果表明:家族基因密码子偏好性较弱,偏好使用G或C,且以G或C结尾,与单子叶植物密码子偏好特性较为一致,UUG、GCA、GAC、GGA是该家族的最优密码子,具有偏好性的密码子和最优密码子与香蕉基因组差异较大。香蕉Aux/IAA基因家族密码子偏好性主要受突变压力影响。在密码子改造和优化的基础上,大肠杆菌原核表达系统适合作为该家族成员的异源表达系统,烟草可作为该家族基因遗传转化的受体。本研究结果有助于开展香蕉Aux/IAA基因家族的功能研究。
Research on the codon usage bias of the banana Aux/IAA(auxin/indole-3-acetic acid) gene family could provide reference for further functional studies, especially for verification of heterologous expression. In this study,CodonW, EMBOSS online programs, SPSS and Origin software were used to analyze the codon usage bias of the banana Aux/IAA gene family, and compared with the banana genome and several mature model plant genomes of the genetic transformation and regeneration system. The results showed that the genetic codon bias of the family was weak, preferring to use G or C, and ending with G or C, which was consistent with monocotyledon codon preference characteristics. UUG, GCA, GAC, GGA were the family's optimal codons. Preferred codons and optimal codons differed greatly from the banana genome. Codon bias of banana Aux/IAA gene family was mainly affected by mutation pressure. On the basis of codon modification and optimization, the E. coli prokaryotic expression system was suitable as a heterologous expression system for the family members, and tobacco could be used as a genetic transformation receptor for the family. This study could lay a foundation for the study of the function of banana Aux/IAA gene family.
Research on the codon usage bias of the banana Aux/IAA(auxin/indole-3-acetic acid) gene family could provide reference for further functional studies, especially for verification of heterologous expression. In this study,CodonW, EMBOSS online programs, SPSS and Origin software were used to analyze the codon usage bias of the banana Aux/IAA gene family, and compared with the banana genome and several mature model plant genomes of the genetic transformation and regeneration system. The results showed that the genetic codon bias of the family was weak, preferring to use G or C, and ending with G or C, which was consistent with monocotyledon codon preference characteristics. UUG, GCA, GAC, GGA were the family's optimal codons. Preferred codons and optimal codons differed greatly from the banana genome. Codon bias of banana Aux/IAA gene family was mainly affected by mutation pressure. On the basis of codon modification and optimization, the E. coli prokaryotic expression system was suitable as a heterologous expression system for the family members, and tobacco could be used as a genetic transformation receptor for the family. This study could lay a foundation for the study of the function of banana Aux/IAA gene family.
引文
Abel S.,Oeller P.W.,and Theologis A.,1994,Early auxin-induced genes encode short-lived nuclear proteins,Proc.Natl.Acad.Sci.USA,91(1):326
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)
Gao J.P.,Cao X.L.,Shi S.D.,Ma Y.L.,Wang K.,Liu S.J.,Chen D.,Chen Q.,and Ma H.L.,2016,Genome-wide survey of Aux/IAA gene family members in potato(Solanum tuberosum):identification,expression analysis,and evaluation of their roles in tuber development,Biochem.Biophys.Res.Commun.,471(2):320-327
Grantham R.,Gautier C.,and Gouy M.,1980,Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type,Nucleic Acids Res.,8(9):1893-1912
Hayashi K.I.,2012,The interaction and integration of auxin signaling components,Plant Cell Physiol.,53(6):965-975
Huang X.,Bao Y.N.,Wang B.,Liu L.J.,Chen J.,Dai L.J.,and Peng D.X.,2016,Identification and expression of Aux/IAA,ARF,and LBD family transcription factors in Boehmeria nivea,Biologia Plantarum,60(2):244-250
Ikemura T.,1985,Codon usage and t RNA content in unicellular and multicellular organisms,Molecular Biology and Evolution,2(1):13-34
Ingvarsson P.K.,2010,Natural selection on synonymous and nonsynonymous mutations shapes patterns of polymorphism in populus tremula,Molecular Biology and Evolution,27(3):650-660
Jiang Y.,Deng F.,Wang H.,and Hu Z.,2008,An extensive analysis on the global codon usage pattern of baculoviruses,Arch.Virol.,153(12):2273-2282
Jung H.,Lee D.K.,Choi Y.D.,and Kim J.K.,2015,OsIAA6,a member of the rice Aux/IAA gene family,is involved in drought tolerance and tiller outgrowth,Plant Science,236:304-312
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 longan,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 W.M.,Chen J.J.,Duan Y.J.,Pang Z.C.,Sun D.Q.,Hu Y.L.,Hu H.G.,and Xie J.H.,2018,The pathogenicity of Fusarium oxysporum f.sp.cubense tropical race 4 on three model plants,Yuanyi Xuebao(Acta Horticulturae Sinica),45(4):743-752(李伟明,陈晶晶,段雅婕,庞振才,孙德权,胡玉林,胡会刚,谢江辉,2018,香蕉枯萎病菌热带4号小种对番茄等3种模式植物的致病性分析,园艺学报,45(4):743-752)
Liscum E.,and Reed J.W.,2002,Genetics of Aux/IAA and ARFaction in plant growth and development,Plant Mol.Biol.,49(3-4):387-400
Liu H.,He R.,Zhang H.,Huang Y.,Tian M.,and Zhang J.,2010,Analysis of synonymous codon usage in zea mays,Mol.Biol.Rep.,37(2):677-684
Lv J.,and Yu J.Q.,2004,Mechanism of auxin action,Zhiwu Shenglixue Tongxun(Plant Physiology Communications),40(5):624-628(吕剑,喻景权,2004,植物生长素的作用机制,植物生理学通讯,40(5):624-628)
Nie X.J.,Deng P.C.,Feng K.W.,Liu P.X.,Du X.H.,Frank Y.,and Song W.N.,2014,Comparative analysis of codon usage patterns in chloroplast genomes of the asteraceae family,Plant Mol.Biol.Rep.,32(4):828-840
Peden J.F.,2011,Analysis of codon usage,University of Nottingham,90(1):73-74
Plotkin J.B.,and Kudla G.,2011,Synonymous but not the same:the causes and consequences of codon bias,Nature Reviews Genetics,12(1):32-42
Qiu S.,Zeng K.,Slotte T.,Wright S.,and Charlesworth D.,2011,Reduced efficacy of natural selection on codon usage bias in selfing arabidopsis and capsella species,Genome Biol.Evol.,3(3):868-880
Rice P.,Longden I.,and Bleasby A.,2000,EMBOSS:the european molecular biology open software suite,Trends in Genetics,16(6):276-277
Sharp P.M.,and Li W.H.,1986,Codon usage in regulatory genes in Escherichia coli does not reflect selection for'rare'codons,Nucleic Acids Res.,14(19):7737-7749
Wu X.M.,Wu S.F.,Ren D.M.,Zhu Y.P.,and He F.C.,2007,The analysis method and progress in the study of codon bias,Yichuan(Hereditas),29(4):420-426(吴宪明,吴松锋,任大明,朱云平,贺福初,2007,密码子偏性的分析方法及相关研究进展,遗传,29(4):420-426)
Yu H.,Soler M.,Clemente H.S.,Mila I.,Paiva J.A.,Myburg A.A.,Bouzayen M.,Grimapettenati J.,and Cassan-wang H.,2015,Comprehensive genome-wide analysis of the Aux/IAA gene family in eucalyptus:evidence for the role of egrIAA4 in wood formation,Plant and Cell Physiology,56(4):700-714
Zeng W.F.,Wang X.B.,Pan L.,Niu L.,Lu Z.H.,Cui G.C.,and Wang Z.Q.,2017,Identification and expression profiling of Aux/IAA family gene during peach fruit ripening,Yuanyi Xuebao(Acta Horticulturae Sinica),44(2):233-244(曾文芳,王小贝,潘磊,牛良,鲁振华,崔国朝,王志强,2017,桃Aux/IAA家族基因鉴定及在果实成熟过程中的表达分析,园艺学报,44(2):233-244)
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)
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)
Gao J.P.,Cao X.L.,Shi S.D.,Ma Y.L.,Wang K.,Liu S.J.,Chen D.,Chen Q.,and Ma H.L.,2016,Genome-wide survey of Aux/IAA gene family members in potato(Solanum tuberosum):identification,expression analysis,and evaluation of their roles in tuber development,Biochem.Biophys.Res.Commun.,471(2):320-327
Grantham R.,Gautier C.,and Gouy M.,1980,Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type,Nucleic Acids Res.,8(9):1893-1912
Hayashi K.I.,2012,The interaction and integration of auxin signaling components,Plant Cell Physiol.,53(6):965-975
Huang X.,Bao Y.N.,Wang B.,Liu L.J.,Chen J.,Dai L.J.,and Peng D.X.,2016,Identification and expression of Aux/IAA,ARF,and LBD family transcription factors in Boehmeria nivea,Biologia Plantarum,60(2):244-250
Ikemura T.,1985,Codon usage and t RNA content in unicellular and multicellular organisms,Molecular Biology and Evolution,2(1):13-34
Ingvarsson P.K.,2010,Natural selection on synonymous and nonsynonymous mutations shapes patterns of polymorphism in populus tremula,Molecular Biology and Evolution,27(3):650-660
Jiang Y.,Deng F.,Wang H.,and Hu Z.,2008,An extensive analysis on the global codon usage pattern of baculoviruses,Arch.Virol.,153(12):2273-2282
Jung H.,Lee D.K.,Choi Y.D.,and Kim J.K.,2015,OsIAA6,a member of the rice Aux/IAA gene family,is involved in drought tolerance and tiller outgrowth,Plant Science,236:304-312
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 longan,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 W.M.,Chen J.J.,Duan Y.J.,Pang Z.C.,Sun D.Q.,Hu Y.L.,Hu H.G.,and Xie J.H.,2018,The pathogenicity of Fusarium oxysporum f.sp.cubense tropical race 4 on three model plants,Yuanyi Xuebao(Acta Horticulturae Sinica),45(4):743-752(李伟明,陈晶晶,段雅婕,庞振才,孙德权,胡玉林,胡会刚,谢江辉,2018,香蕉枯萎病菌热带4号小种对番茄等3种模式植物的致病性分析,园艺学报,45(4):743-752)
Liscum E.,and Reed J.W.,2002,Genetics of Aux/IAA and ARFaction in plant growth and development,Plant Mol.Biol.,49(3-4):387-400
Liu H.,He R.,Zhang H.,Huang Y.,Tian M.,and Zhang J.,2010,Analysis of synonymous codon usage in zea mays,Mol.Biol.Rep.,37(2):677-684
Lv J.,and Yu J.Q.,2004,Mechanism of auxin action,Zhiwu Shenglixue Tongxun(Plant Physiology Communications),40(5):624-628(吕剑,喻景权,2004,植物生长素的作用机制,植物生理学通讯,40(5):624-628)
Nie X.J.,Deng P.C.,Feng K.W.,Liu P.X.,Du X.H.,Frank Y.,and Song W.N.,2014,Comparative analysis of codon usage patterns in chloroplast genomes of the asteraceae family,Plant Mol.Biol.Rep.,32(4):828-840
Peden J.F.,2011,Analysis of codon usage,University of Nottingham,90(1):73-74
Plotkin J.B.,and Kudla G.,2011,Synonymous but not the same:the causes and consequences of codon bias,Nature Reviews Genetics,12(1):32-42
Qiu S.,Zeng K.,Slotte T.,Wright S.,and Charlesworth D.,2011,Reduced efficacy of natural selection on codon usage bias in selfing arabidopsis and capsella species,Genome Biol.Evol.,3(3):868-880
Rice P.,Longden I.,and Bleasby A.,2000,EMBOSS:the european molecular biology open software suite,Trends in Genetics,16(6):276-277
Sharp P.M.,and Li W.H.,1986,Codon usage in regulatory genes in Escherichia coli does not reflect selection for'rare'codons,Nucleic Acids Res.,14(19):7737-7749
Wu X.M.,Wu S.F.,Ren D.M.,Zhu Y.P.,and He F.C.,2007,The analysis method and progress in the study of codon bias,Yichuan(Hereditas),29(4):420-426(吴宪明,吴松锋,任大明,朱云平,贺福初,2007,密码子偏性的分析方法及相关研究进展,遗传,29(4):420-426)
Yu H.,Soler M.,Clemente H.S.,Mila I.,Paiva J.A.,Myburg A.A.,Bouzayen M.,Grimapettenati J.,and Cassan-wang H.,2015,Comprehensive genome-wide analysis of the Aux/IAA gene family in eucalyptus:evidence for the role of egrIAA4 in wood formation,Plant and Cell Physiology,56(4):700-714
Zeng W.F.,Wang X.B.,Pan L.,Niu L.,Lu Z.H.,Cui G.C.,and Wang Z.Q.,2017,Identification and expression profiling of Aux/IAA family gene during peach fruit ripening,Yuanyi Xuebao(Acta Horticulturae Sinica),44(2):233-244(曾文芳,王小贝,潘磊,牛良,鲁振华,崔国朝,王志强,2017,桃Aux/IAA家族基因鉴定及在果实成熟过程中的表达分析,园艺学报,44(2):233-244)
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)