小桐子WOX基因家族全基因组鉴定与表达分析
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摘要
WOX转录因子在植物的生长发育和非生物胁迫响应中起重要的调控作用。基于全基因组和转录组测序数据,本研究首次对小桐子WOX转录因子保守域、保守基序,染色体定位和不同条件下的表达模式进行了全面的分析。总共12个WOX蛋白在小桐子基因组中被鉴定。保守域分析表明,12个小桐子WOX蛋白的结构域均含有螺旋-环-螺旋-拐角-螺旋基序。染色体定位分析表明,小桐子12个WOX蛋白不均匀地分布在7个连锁群(LGs)上,然而,没有WOX蛋白定位于LG1、LG5、LG7和LG8。系统发育树的结果表明,12个小桐子WOX蛋白被分成3个组即Ⅰ,Ⅱ,Ⅲ。在这12个WOX基因中,部分基因在被检测的组织中(根,茎皮层,叶和种子)显示出差异表达模式,如1个WOX基因(JcWOX1)在根中表达最高,3个WOX基因(JcWOX3, JcWOX7, JcWOX12)在种子中表达最高。此外,表达模式和qRT-PCR分析显示,3个小桐子WOX基因的表达在至少一个胁迫(干旱或者盐)条件下显示出至少2倍的增加或者降低。在这3个差异表达小桐子WOX基因中,2个WOX基因(JcWOX1, JcWOX6)在至少一个处理时间点表现出对干旱和盐胁迫响应,1个基因(JcWOX5)仅仅对干旱胁迫响应。该结果将为进一步研究WOX基因在调控小桐子生长发育和非生物胁迫响应中的作用提供一些有价值的信息,为小桐子WOX基因的功能研究与利用提供科学依据。
The WOX transcription factor plays an important regulatory role in plant growth and development and abiotic stress response. Based on the whole genome and transcriptome sequencing data, the conserved domain,conserved motif, chromosomal localization, and expression profiles under various growth conditions of WOX family members in physic nut were analyzed comprehensively for the first time in this study. In total of 12 WOX proteins were identified in the physic nut genome. Conserved domain analysis suggested that 12 WOX proteins of physic nut all contained helix-loop-helix motif. Chromosomal locations analysis indicated that 12 WOX proteins were inhomogeneously distributed on 7 linkage groups(LGs) of physic nut, but no WOX protein was mapped to LGs 1, 5, 7 and 8. Phylogenetic tree analysis showed that the 12 physic nut WOX proteins were clustered into 3 groups:Ⅰ,Ⅱand Ⅲ. In these 12 WOX genes, some genes showed differential expression patterns in these tissues tested(root, stem cortex, leaf, and seed), such as one WOX genes(JcWOX1) had the highest expression level in root and three WOX genes(Jc WOX3, JcWOX7, JcWOX12) had the highest expression level in seeds. In addition,expression profile and qRT-PCR analysis revealed that in roots, 3 WOX genes underwent at least a 2-fold increase or decrease in expression in response to at least one stress(drought and/or salinity). In these 3 differentially expressed WOX genes, two WOX genes(JcWOX1, JcWOX6) had response to drought and salinity stress at least one time point, and one WOX genes(JcWOX5) only responded to drought stress. The results could provide some valuable information for further studies on the roles of WOX genes in regulating the growth, development and responses to abiotic stress of physic nut, and lay the foundation for the functional identification and analysis of WOX genes in physic nut.
The WOX transcription factor plays an important regulatory role in plant growth and development and abiotic stress response. Based on the whole genome and transcriptome sequencing data, the conserved domain,conserved motif, chromosomal localization, and expression profiles under various growth conditions of WOX family members in physic nut were analyzed comprehensively for the first time in this study. In total of 12 WOX proteins were identified in the physic nut genome. Conserved domain analysis suggested that 12 WOX proteins of physic nut all contained helix-loop-helix motif. Chromosomal locations analysis indicated that 12 WOX proteins were inhomogeneously distributed on 7 linkage groups(LGs) of physic nut, but no WOX protein was mapped to LGs 1, 5, 7 and 8. Phylogenetic tree analysis showed that the 12 physic nut WOX proteins were clustered into 3 groups:Ⅰ,Ⅱand Ⅲ. In these 12 WOX genes, some genes showed differential expression patterns in these tissues tested(root, stem cortex, leaf, and seed), such as one WOX genes(JcWOX1) had the highest expression level in root and three WOX genes(Jc WOX3, JcWOX7, JcWOX12) had the highest expression level in seeds. In addition,expression profile and qRT-PCR analysis revealed that in roots, 3 WOX genes underwent at least a 2-fold increase or decrease in expression in response to at least one stress(drought and/or salinity). In these 3 differentially expressed WOX genes, two WOX genes(JcWOX1, JcWOX6) had response to drought and salinity stress at least one time point, and one WOX genes(JcWOX5) only responded to drought stress. The results could provide some valuable information for further studies on the roles of WOX genes in regulating the growth, development and responses to abiotic stress of physic nut, and lay the foundation for the functional identification and analysis of WOX genes in physic nut.
引文
Cannon S.B.,Mitra A.,Baumgarten A.,Young N.D.,and May G.,2004,The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana,BMC Plant Biol.,4(1):10
Jiang H.W.,Wu P.Z.,Zhang S.,Song C.,Chen Y.P.,Li M.R.,Jie Y.X.,Fang X.H.,Chen F.,and Wu G.J.,2012,Global analysis of gene expression profiles in developing physic nut(Jatropha curcas L.)seeds,PLoS One,7(5):36522
Jiang W.,Zhou S.L.,Zhang Q.,Song H.Z.,Zhou D.X.,and Zhao Y.,2017,Transcriptional regulatory network of WOX11 is involved in the control of crown root development,cytokinin signals,and redox in rice,J.Exp.Bot.,68(11):2787-2798
Larkin M.A.,Blackshields G.,Brown N.P.,Chenna R.,McGettigan P.A.,McWilliam H.,Valentin F.,Wallace I.M.,Thompson J.D.,Gibson T.J.,Gibson T.J.,and Higgins D.G.,2007,Clustal W and Clustal X version 2.0,Bioinformatics,23(21):2947-2948
Liu L.,White M.J.,and Macrae T.H.,1999,Transcription factors and their genes in higher plants functional domains,evolution and regulation,Eur.J.Biochem.,262(2):247-257
Pillitteri L.J.,Bemis S.M.,Shpak E.D.,and Torii K.U.,2007,Haploinsufficiency after successive loss of signaling reveals a role for ERECTA-family genes in Arabidopsis ovule development,Development,134(17):3099-3109
Romerabranchat M.,Ripoll J.J.,Yanofsky M.F.,and Pelaz S.,2013,The WOX13 homeobox gene promotes replum formation in the Arabidopsis thaliana fruit,Plant J.,73(1):37-49
Sarkar A.K.,Luijten M.,Miyashima S.,Lenhard M.,Hashimoto T.,Nakajima K.,Scheres B.,Heidstra R.,and Laux T.,2007,Conserved factors regulate signalling in Arabidopsis thaliana shoot and root stem cell organizers,Nature.,446(7137):811-814
Tamura K.,Peterson D.,Peterson N.,Stechere G.,Nei M.,and Kumar S.,2011,MEGA5:molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance,and maximum parsimony methods,Mol.Bio.Evol.,28(10):2731-2739
Tang F.,Chen N.Z.,Zhao M.L.,Wang Y.C.,He R.P.,Peng X.J.,and Shen S.H.,2017,Identification and functional divergence analysis of WOX gene family in paper mulberry,Int.J.Mol.Sci.,18(8):1782
Tang Y.H.,Qin S.S.,Guo Y.L.,Chen Y.B.,Wu P.Z.,Chen Y.P.,Li M.R.,Jiang H.W.,and Wu G.J.,2016,Genome-wide analysis of the AP2/ERF gene family in physic nut and overexpression of the JcERF011 gene in rice increased its sensitivity to salinity stress,PLoS One,11(3):150879
Wang H.,Niu L.F.,Fu C.X.,Meng Y.Y.,Sang D.J.,Yin P.C.,Wu J.X.,Tang Y.H.,Lu T.G.,Wang Z.Y.,Tadege M.,and Lin H.,2017,Overexpression of the WOX gene STENOFO-LIA improves biomass yield and sugar release in transgenic grasses and display altered cytokinin homeostasis,PLo SGenet.,13(3):1006649
Wu P.Z.,Zhou C.P.,Cheng S.F.,Wu P.Z.,Lu W.J.,Han J.L.,Chen Y.B.,Chen Y.,Ni P.X.,Wang Y.,Xu X.,Huang Y.,Song C.,Wang Z.W.,Shi N.,Zhang X.D.,Fang X.H.,Yang Q.,Jiang H.W.,Chen Y.P.,Li M.R.,Wang Y.,Chen F.,and Wang G.J.,2015,Integrated genome sequence and linkage map of physic nut(Jatropha curcas L.),a biodiesel plant,Plant J.,81(5):810-821
Yamaguchi Y.L.,Suzuki R.,Cabrera J.,Nakagami S.,Sagara T.,Ejima C.,Sano R.,Aoki Y.,Olmo R.,Kurata T.,Obayashi T.,Demura T.,Ishida T.,Escobar C.,and Sawa S.,2017,Root-knot and cyst nematodes activate procambium-associated genes in Arabidopsis roots,Front.Plant Sci.,8:1195
Yang Z.E.,Gong Q.,Qin W.Q.,Yang Z.R.,Cheng Y.,Lu L.L.,Ge X.Y.,Zhang C.J.,Wu Z.X.,and Li F.G.,2017,Genome-wide analysis of WOX genes in upland cotton and their expression pattern under different stresses,BMC Plant Biol.,17(1):113
Zhang L.,Zhang C.,Wu P.Z.,Chen Y.P.,Li M.R.,Jiang H.W.,and Wu G.J.,2014,Global analysis of gene expression profiles in physic nut(Jatropha curcas L.)seedlings exposed to salt stress,PLoS One,9(5):97878
Zhang X.,Zong J.,Liu J.H.,Yin J.Y.,and Zhang D.B.,2010,Genome-wide analysis of WOX gene family in rice,sorghum,maize,Arabidopsis and poplar,J.Integ.Plant Biol.,52(11):1016-1026
Zhao Y.,Hu Y.F.,Dai M.Q.,Huang L.M.,and Zhou D.X.,2009,The WUSCHEL-related homeobox gene WOX11 is required to activate shoot-borne crown root development in rice,Plant Cell,21(3):736-748
Jiang H.W.,Wu P.Z.,Zhang S.,Song C.,Chen Y.P.,Li M.R.,Jie Y.X.,Fang X.H.,Chen F.,and Wu G.J.,2012,Global analysis of gene expression profiles in developing physic nut(Jatropha curcas L.)seeds,PLoS One,7(5):36522
Jiang W.,Zhou S.L.,Zhang Q.,Song H.Z.,Zhou D.X.,and Zhao Y.,2017,Transcriptional regulatory network of WOX11 is involved in the control of crown root development,cytokinin signals,and redox in rice,J.Exp.Bot.,68(11):2787-2798
Larkin M.A.,Blackshields G.,Brown N.P.,Chenna R.,McGettigan P.A.,McWilliam H.,Valentin F.,Wallace I.M.,Thompson J.D.,Gibson T.J.,Gibson T.J.,and Higgins D.G.,2007,Clustal W and Clustal X version 2.0,Bioinformatics,23(21):2947-2948
Liu L.,White M.J.,and Macrae T.H.,1999,Transcription factors and their genes in higher plants functional domains,evolution and regulation,Eur.J.Biochem.,262(2):247-257
Pillitteri L.J.,Bemis S.M.,Shpak E.D.,and Torii K.U.,2007,Haploinsufficiency after successive loss of signaling reveals a role for ERECTA-family genes in Arabidopsis ovule development,Development,134(17):3099-3109
Romerabranchat M.,Ripoll J.J.,Yanofsky M.F.,and Pelaz S.,2013,The WOX13 homeobox gene promotes replum formation in the Arabidopsis thaliana fruit,Plant J.,73(1):37-49
Sarkar A.K.,Luijten M.,Miyashima S.,Lenhard M.,Hashimoto T.,Nakajima K.,Scheres B.,Heidstra R.,and Laux T.,2007,Conserved factors regulate signalling in Arabidopsis thaliana shoot and root stem cell organizers,Nature.,446(7137):811-814
Tamura K.,Peterson D.,Peterson N.,Stechere G.,Nei M.,and Kumar S.,2011,MEGA5:molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance,and maximum parsimony methods,Mol.Bio.Evol.,28(10):2731-2739
Tang F.,Chen N.Z.,Zhao M.L.,Wang Y.C.,He R.P.,Peng X.J.,and Shen S.H.,2017,Identification and functional divergence analysis of WOX gene family in paper mulberry,Int.J.Mol.Sci.,18(8):1782
Tang Y.H.,Qin S.S.,Guo Y.L.,Chen Y.B.,Wu P.Z.,Chen Y.P.,Li M.R.,Jiang H.W.,and Wu G.J.,2016,Genome-wide analysis of the AP2/ERF gene family in physic nut and overexpression of the JcERF011 gene in rice increased its sensitivity to salinity stress,PLoS One,11(3):150879
Wang H.,Niu L.F.,Fu C.X.,Meng Y.Y.,Sang D.J.,Yin P.C.,Wu J.X.,Tang Y.H.,Lu T.G.,Wang Z.Y.,Tadege M.,and Lin H.,2017,Overexpression of the WOX gene STENOFO-LIA improves biomass yield and sugar release in transgenic grasses and display altered cytokinin homeostasis,PLo SGenet.,13(3):1006649
Wu P.Z.,Zhou C.P.,Cheng S.F.,Wu P.Z.,Lu W.J.,Han J.L.,Chen Y.B.,Chen Y.,Ni P.X.,Wang Y.,Xu X.,Huang Y.,Song C.,Wang Z.W.,Shi N.,Zhang X.D.,Fang X.H.,Yang Q.,Jiang H.W.,Chen Y.P.,Li M.R.,Wang Y.,Chen F.,and Wang G.J.,2015,Integrated genome sequence and linkage map of physic nut(Jatropha curcas L.),a biodiesel plant,Plant J.,81(5):810-821
Yamaguchi Y.L.,Suzuki R.,Cabrera J.,Nakagami S.,Sagara T.,Ejima C.,Sano R.,Aoki Y.,Olmo R.,Kurata T.,Obayashi T.,Demura T.,Ishida T.,Escobar C.,and Sawa S.,2017,Root-knot and cyst nematodes activate procambium-associated genes in Arabidopsis roots,Front.Plant Sci.,8:1195
Yang Z.E.,Gong Q.,Qin W.Q.,Yang Z.R.,Cheng Y.,Lu L.L.,Ge X.Y.,Zhang C.J.,Wu Z.X.,and Li F.G.,2017,Genome-wide analysis of WOX genes in upland cotton and their expression pattern under different stresses,BMC Plant Biol.,17(1):113
Zhang L.,Zhang C.,Wu P.Z.,Chen Y.P.,Li M.R.,Jiang H.W.,and Wu G.J.,2014,Global analysis of gene expression profiles in physic nut(Jatropha curcas L.)seedlings exposed to salt stress,PLoS One,9(5):97878
Zhang X.,Zong J.,Liu J.H.,Yin J.Y.,and Zhang D.B.,2010,Genome-wide analysis of WOX gene family in rice,sorghum,maize,Arabidopsis and poplar,J.Integ.Plant Biol.,52(11):1016-1026
Zhao Y.,Hu Y.F.,Dai M.Q.,Huang L.M.,and Zhou D.X.,2009,The WUSCHEL-related homeobox gene WOX11 is required to activate shoot-borne crown root development in rice,Plant Cell,21(3):736-748