蓖麻WOX转录因子家族成员的全基因组分析及逆境胁迫响应
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摘要
WOX是植物中特有的一类转录因子,参与植物发育和应激反应。为探究蓖麻基因组WOX转录因子信息,本研究通过生物信息学方法鉴定出11个蓖麻WOX转录因子家族成员,并对其系统发育、基因结构、保守基序及理化性质等基本信息进行鉴定与分析。结果显示,11个WOX成员被分为三个进化支,在古代进化支、中间进化支和现在进化支分别有2、2和7个成员,同一进化支成员的外显子、基因结构具有相似性,但理化性质差异较大。利用RT-qPCR检测根、茎、叶不同组织中5个蓖麻RcWOXs基因在干旱与盐胁迫下表达情况,结果表明,RcWOXs在不同组织中的表达具有特异性;除RcWOX10受干旱胁迫抑制外,RcWOX2、RcWOX4、RcWOX8和RcWOX9在干旱和盐胁迫下均被诱导表达,表明RcWOX转录因子在蓖麻逆境胁迫中起调控作用。本研究结果为进一步探究蓖麻WOX转录因子家族在逆境胁迫中的功能提供了一定的理论参考。
WOX(wuschel-related homeobox) is a transcription factor that is only expressed in plants and is involved in a variety of plant development and stress responses. In order to explore the related information of WOX transcription factor in castor bean genome, bioinformatics methods were carried out. 11 members of castor bean WOX transcription factor family were identified and their basic information including phylogeny, gene structure, conserved motif and physicochemical properties were characterized and analyzed. The results showed that 11 members were divided into three phylogenetic branches through phylogenetic relationships. The exons and gene structures shares high similar among same phylogenetic branch members, but their physicochemical properties were different. The RT-qPCR technology was used to detect the expression of 5 castor RcWOXs genes in root, stem and leaf of castor under drought and salt stress. The results showed that the expression of RcWOXs in different tissues was specific; except the expression of RcWOX10 was repressed by drought stress, the expression of RcWOX2, RcWOX4, RcWOX8 and RcWOX9 were up-regulated induced under stress, indicating that RcWOX transcription factor has a regulatory effect in castor stress. Our data provides a reference for further studies on the function of castor WOX transcription factor family in response to stress.
WOX(wuschel-related homeobox) is a transcription factor that is only expressed in plants and is involved in a variety of plant development and stress responses. In order to explore the related information of WOX transcription factor in castor bean genome, bioinformatics methods were carried out. 11 members of castor bean WOX transcription factor family were identified and their basic information including phylogeny, gene structure, conserved motif and physicochemical properties were characterized and analyzed. The results showed that 11 members were divided into three phylogenetic branches through phylogenetic relationships. The exons and gene structures shares high similar among same phylogenetic branch members, but their physicochemical properties were different. The RT-qPCR technology was used to detect the expression of 5 castor RcWOXs genes in root, stem and leaf of castor under drought and salt stress. The results showed that the expression of RcWOXs in different tissues was specific; except the expression of RcWOX10 was repressed by drought stress, the expression of RcWOX2, RcWOX4, RcWOX8 and RcWOX9 were up-regulated induced under stress, indicating that RcWOX transcription factor has a regulatory effect in castor stress. Our data provides a reference for further studies on the function of castor WOX transcription factor family in response to stress.
引文
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[3] Wu X,Dabi T,Weigel D.Requirement of homeobox gene STIMPY/WOX9 for Arabidopsis meristem growth and maintenance[J].Current Biology,2005,15(5):436-440
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[6] 丛娇娇,王晓宇,李平,李惠根,张丽雪,张继星.蓖麻耐盐基因HKT的克隆及表达载体构建[J].分子植物育种,2018,16(14):4648-4657
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[15] Sievers F,Wilm A,Dineen D,Gibson T J,Karplus K,Li W,Lopez R,McWilliam H,Remmert M,S?ding J,Thompson J D,Higgins D G.Fast,scalable generation of high-quality protein multiple sequence alignments using Clustal Omega[J].Molecular Systems Biology,2011,7(539):1-6
[16] 石晓雯,贺立恒,焦晋华,刘霞宇,王婷,刘世芳,贾小云,李润植.甘薯二倍体近缘野生种三裂叶薯MYB转录因子全基因组分析及逆境胁迫响应[J].核农学报,2018,32(7):1338-1348
[17] Bailey T L,Johnson J,Grant C E,Noble W S.The MEME suite[J].Nucleic Acids Research,2015,43(W1):W39-W49
[18] 陈红霖,胡亮亮,王丽侠,王素华,程须珍.绿豆bHLH转录因子家族的鉴定与生物信息学分析[J].植物遗传资源学报,2017,18(6):1159-1167
[19] Ji J,Shimizu R,Sinha N,Scanlon M J.Analyses of WOX4 transgenics provide further evidence for the evolution of the WOX gene family during the regulation of diverse stem cell functions[J].Plant Signaling & Behavior,2010,5:916-920
[20] Haecker A.Expression dynamics of WOX genes mark cell fate decisions during early embryonic patterning in Arabidopsis thaliana[J].Development,2004,131(3):657-668
[21] Zhang Y,Wu R,Qin G,Chen Z,Gu H,Qu L J.Over-expresion of WOX1 leads to defects in meristem development and polyamine homeostasis in Arabidopsis[J].Journal of Integrative Plant Biology,2011,53(6):493-506
[22] 李晓旭,刘成,李伟,张增林,高晓明,周慧,郭永峰.番茄WOX转录因子家族的鉴定及其进化、表达分析[J].遗传,2016,38(5):444-460
[23] 黄玉兰.WOX同源异型盒基因在水稻生长发育中的功能鉴定和分析[D].武汉:华中农业大学,2015:30-32
[24] Ramkumar T R,Madhvi K,Kumar U S,Sembi J K.Identification and characterization of,WUSCHEL-related homeobox,(WOX) gene family in economically important orchid species Phalaenopsis equestris and Dendrobium catenatum[J].Plant Gene,2018,14:37-45
[25] Wang X L,Bi C W,Wang C Y,Ye Q L,Yin T M,Ye N.Genome-wide identification and characterization of WUSCHEL-related homeobox (WOX) genes in Salix suchowensis[J].Journal of Forestry Research,2018.DOI:10.1007/s11676-018-0734-2
[26] Zhao Y,Hu Y,Dai M,Huang L,Zhou D X.The wuschel-related homeobox gene wox11 is required to activate shoot-borne crown root development in rice[J].Plant Cell,2009,21(3):736-748
[27] Maida R J,Juan J R,Yanofsky M F,Pelaz S.The WOX13 homeobox gene promotes replum formation in the Arabidopsis thaliana fruit[J].The Plant Journal,2013,73(1):13-49
[28] Jiang W,Zhou S,Zhang Q,Song H,Zhou D X,Zhao Y.Transcriptional regulatory network of WOX11 is involved in the control of crown root development,cytokinin signals,and redox in rice[J].Journal of Experimental Botany Journal,2017,68(11):2787-2798
[29] 张洪涛.鹰嘴豆WOX转录因子基因家族全基因组分析[J].分子植物育种,2018,16(10):3113-3120
[30] Li J,Zhang J,Jia H,Liu B,Sun P,Hu J,Wang L,Lu M.The WUSCHEL-related homeobox 5a (PtoWOX5a) is involved in adventitious root development in poplar[J].Tree Physiology,2018,38(1):139-153
[31] Cheng S,Huang Y,Zhu N,Zhao Y.The rice WUSCHEL-related homeobox genes are involved in reproductive organ development,hormone signaling and abiotic stress response[J].Gene,2014,549(2):266-274
[32] Tang F,Chen N Z,Zhao M L,Wang Y C,He R P,Peng X J,Shen S H.Identification and functional divergence analysis of WOX gene family in paper mulberry[J].International Journal of Molecular Sciences,2017,18(8):1782
[2] Sarkar A K,Luijten M,Miyashima S,Lenhard M,Hashimoto T,Nakajima K,Scheres B,Heidstra R,Laux T.Conserved factors regulate signalling in arabidopsis thaliana shoot and root stem cell organizers[J].Nature,2007,446(7137):811-814
[3] Wu X,Dabi T,Weigel D.Requirement of homeobox gene STIMPY/WOX9 for Arabidopsis meristem growth and maintenance[J].Current Biology,2005,15(5):436-440
[4] Etchells J P,Provost C M,Mishra L,Turner S R.Wox4 and wox14 act downstream of the pxy receptor kinase to regulate plant vascular proliferation independently of any role in vascular organisation[J].Development,2013,140(10):2224-2234
[5] Ramkumar T R,Kanchan M,Upadhyay S K,Sembi J K.Identification and characterization of WUSCHEL-related homeobox (WOX) gene family in economically important orchid species Phalaenopsis equestris and Dendrobium catenatum[J].Plant Gene,2018,14:37-45
[6] 丛娇娇,王晓宇,李平,李惠根,张丽雪,张继星.蓖麻耐盐基因HKT的克隆及表达载体构建[J].分子植物育种,2018,16(14):4648-4657
[7] 李威,李国瑞,黄凤兰,丛安琪,李晓晨,白英俊,李孟建,陈永胜.蓖麻RcDELLA基因的克隆及序列分析[J].华北农学报,2018,33(1):14-19
[8] 杨丽凤,常如慧,李国瑞,狄建军,徐雅楠,梁塔娜,张艳欣,李丽丽,孙洪玲,隋久香,黄凤兰.喷施草铵膦与草甘膦对蓖麻叶片生理生化的影响研究[J].内蒙古民族大学学报(自然科学版),2018,33(5):411-416
[9] 郑鹭.蓖麻种质资源鉴定评价及遗传多样性ISSR与SRAP分析[D].泉州:福建农林大学,2007:3-6
[10] Ogunniyi D S.Castor oil:A vital industrial raw material[J].Bioresour Technol,2006,97(9):1086-1091
[11] 丛安琪,李国瑞,王月,李威,李晓晨,黄凤兰,陈永胜.蓖麻RcGA20ox1基因克隆及生物信息学分析[J].分子植物育种,2018,16(10):3121-3126
[12] Robert D F,Alex B,Jody C,Penelope C,Ruth Y E,Sean R E,Andreas H,Kirstie H,Liisa H,Jaina M,Erik L L S,John T,Marco P.Pfam:the protein families database[J].Nucleic acids research,2014,42(Database issue):D222-D230
[13] Letunic Ⅰ,Doerks T,Bork P.SMART 7:Recent updates to the protein domain annotation resource[J].Nucleic Acids Research,2012,40 (Database issue):D302-D305
[14] Gasteiger E,Gattiker A,Hoogland C,Ivanyi Ⅰ,Appel R D,Bairoch A.ExPASy:The proteomics server for indepth protein knowledge and analysis[J].Nucleic Acids Resarch,2003,31(13):3784-3788
[15] Sievers F,Wilm A,Dineen D,Gibson T J,Karplus K,Li W,Lopez R,McWilliam H,Remmert M,S?ding J,Thompson J D,Higgins D G.Fast,scalable generation of high-quality protein multiple sequence alignments using Clustal Omega[J].Molecular Systems Biology,2011,7(539):1-6
[16] 石晓雯,贺立恒,焦晋华,刘霞宇,王婷,刘世芳,贾小云,李润植.甘薯二倍体近缘野生种三裂叶薯MYB转录因子全基因组分析及逆境胁迫响应[J].核农学报,2018,32(7):1338-1348
[17] Bailey T L,Johnson J,Grant C E,Noble W S.The MEME suite[J].Nucleic Acids Research,2015,43(W1):W39-W49
[18] 陈红霖,胡亮亮,王丽侠,王素华,程须珍.绿豆bHLH转录因子家族的鉴定与生物信息学分析[J].植物遗传资源学报,2017,18(6):1159-1167
[19] Ji J,Shimizu R,Sinha N,Scanlon M J.Analyses of WOX4 transgenics provide further evidence for the evolution of the WOX gene family during the regulation of diverse stem cell functions[J].Plant Signaling & Behavior,2010,5:916-920
[20] Haecker A.Expression dynamics of WOX genes mark cell fate decisions during early embryonic patterning in Arabidopsis thaliana[J].Development,2004,131(3):657-668
[21] Zhang Y,Wu R,Qin G,Chen Z,Gu H,Qu L J.Over-expresion of WOX1 leads to defects in meristem development and polyamine homeostasis in Arabidopsis[J].Journal of Integrative Plant Biology,2011,53(6):493-506
[22] 李晓旭,刘成,李伟,张增林,高晓明,周慧,郭永峰.番茄WOX转录因子家族的鉴定及其进化、表达分析[J].遗传,2016,38(5):444-460
[23] 黄玉兰.WOX同源异型盒基因在水稻生长发育中的功能鉴定和分析[D].武汉:华中农业大学,2015:30-32
[24] Ramkumar T R,Madhvi K,Kumar U S,Sembi J K.Identification and characterization of,WUSCHEL-related homeobox,(WOX) gene family in economically important orchid species Phalaenopsis equestris and Dendrobium catenatum[J].Plant Gene,2018,14:37-45
[25] Wang X L,Bi C W,Wang C Y,Ye Q L,Yin T M,Ye N.Genome-wide identification and characterization of WUSCHEL-related homeobox (WOX) genes in Salix suchowensis[J].Journal of Forestry Research,2018.DOI:10.1007/s11676-018-0734-2
[26] Zhao Y,Hu Y,Dai M,Huang L,Zhou D X.The wuschel-related homeobox gene wox11 is required to activate shoot-borne crown root development in rice[J].Plant Cell,2009,21(3):736-748
[27] Maida R J,Juan J R,Yanofsky M F,Pelaz S.The WOX13 homeobox gene promotes replum formation in the Arabidopsis thaliana fruit[J].The Plant Journal,2013,73(1):13-49
[28] Jiang W,Zhou S,Zhang Q,Song H,Zhou D X,Zhao Y.Transcriptional regulatory network of WOX11 is involved in the control of crown root development,cytokinin signals,and redox in rice[J].Journal of Experimental Botany Journal,2017,68(11):2787-2798
[29] 张洪涛.鹰嘴豆WOX转录因子基因家族全基因组分析[J].分子植物育种,2018,16(10):3113-3120
[30] Li J,Zhang J,Jia H,Liu B,Sun P,Hu J,Wang L,Lu M.The WUSCHEL-related homeobox 5a (PtoWOX5a) is involved in adventitious root development in poplar[J].Tree Physiology,2018,38(1):139-153
[31] Cheng S,Huang Y,Zhu N,Zhao Y.The rice WUSCHEL-related homeobox genes are involved in reproductive organ development,hormone signaling and abiotic stress response[J].Gene,2014,549(2):266-274
[32] Tang F,Chen N Z,Zhao M L,Wang Y C,He R P,Peng X J,Shen S H.Identification and functional divergence analysis of WOX gene family in paper mulberry[J].International Journal of Molecular Sciences,2017,18(8):1782
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