枣TCP转录因子鉴定与生物信息学分析
|
摘要
TCP蛋白家族是一类植物特有的转录因子家族,在参与植物进化与发育方面起着至关重要的作用。枣基因组测序的完成为本实验提供了基础。本研究中,共鉴定到24个枣TCP基因。利用生物信息学方法对其基因分类、染色体定位、系统进化、基因结构和保守基序进行分析。系统发育表明分为3个家族:Group1、Group2和Group3,Group2和Group3位于进化树的同一分支。不同的基因在染色体上的定位呈不均匀分布。枣TCP转录因子家族在同一亚族中具有相似的基因结构和相同的保守基序。该研究初步明确了枣TCP转录因子家族成员进化关系和结构特点,为进一步研究枣TCP转录因子家族的系统发育以及生物学功能提供了理论基础,为枣的分子育种提供科学依据。
TCP prote in family is a plant-specific transcription factor family, which plays a vital role in plant evolution and development. The completion of jujube genome sequencing has provided the basis for this experiment. In this study, 24 TCP genes of Ziziphus jujuba were identified. The genetic classification, chromosome location, phylogenetic evolution, gene structure and conservative motifs were analyzed by bioinformatics. In addition, it was classed in to 3 groups, including Group 1, Group 2 and Group 3, based on the phyletic evolution,and the Group 2 and Group 3 were locate in the same branch of phylogenetic tree. The localization of different genes on the chromosome was inhomogeneous. The TCP transcription factor family of Ziziphus jujube had similar gene structure and same conserved motif in the same subgroup. This study preliminarily clarified the evolutionary relationship and structural characteristics of the members of the TCP transcription factor family of Ziziphus jujube,provided a theoretical basis for further study of the phylogenetic and biological functions of the TCP transcription factor family of Ziziphus jujube, and provided a scientific basis for molecular breeding of Ziziphus jujube.
TCP prote in family is a plant-specific transcription factor family, which plays a vital role in plant evolution and development. The completion of jujube genome sequencing has provided the basis for this experiment. In this study, 24 TCP genes of Ziziphus jujuba were identified. The genetic classification, chromosome location, phylogenetic evolution, gene structure and conservative motifs were analyzed by bioinformatics. In addition, it was classed in to 3 groups, including Group 1, Group 2 and Group 3, based on the phyletic evolution,and the Group 2 and Group 3 were locate in the same branch of phylogenetic tree. The localization of different genes on the chromosome was inhomogeneous. The TCP transcription factor family of Ziziphus jujube had similar gene structure and same conserved motif in the same subgroup. This study preliminarily clarified the evolutionary relationship and structural characteristics of the members of the TCP transcription factor family of Ziziphus jujube,provided a theoretical basis for further study of the phylogenetic and biological functions of the TCP transcription factor family of Ziziphus jujube, and provided a scientific basis for molecular breeding of Ziziphus jujube.
引文
Aguilar-M artinez J.A.,Poza-Carrion C.,and Cubas P.,2007,Arabidopsis BRANCHED1 acts as an integrator of branching signal swithin axillary buds,Plant Cell,19(2):458-472
Busch A.,and Zachgo S.,2007,Control of corolla monosymmetry in the Brassicaceae Iberis amara,Proc.Natl.Acad.Sci.USA,104(42):16714-16719
Cubas P.,Lauter N.,Doebley J.,and Coen E.,1999,The TCP domain:a motif found in proteins regulating plant growth and development,Plant J.,18(2):215-222
Doebley J.,Stec A.,and Hubbard L.,1997,The evolution of apical dominance in maize,Nature,386(6624):485-488
Efroni I.,Blum E.,Goldshmidt A.,and Eshed Y.,2008,A protracted and dynamic maturation schedule underlies Arabidopsis leaf development,Plant Cell,20(9):2293-2306
Giraud E.,Ng S.,Carrie C.,Duncan O.,Low J.,and Lee C.P.,Aken O.V.,Millar A.H.,Murcha M.,and Whelan J.,2010,TCP transcription factors link the regulation of genes encoding mitochondrial proteins with the circadian clock in Arabidopsis thaliana,Plant Cell,22(12):3921-3934
James E.R.,Michael F.F.,Quentin C.B.C.,Diane B.,and Mark W.C.,2000,A phylogenetic analysis of Rhamnaceae using rbcL and trnL-F plastid DNA sequences,Am.J.Bot.,87(9):1309-1324
Kosugi S.,and Ohashi Y.,1997,PCF1 and PCF2 specifically bind tocis elements in the rice proliferating cell nuclear antigen gene,Plant Cell,9(9):1607-1619
Koyama T.,Furutani M.,Tasaka M.,and Ohme-Takagi M.,2007,TCP transcription factors control the morphology of shoot lateral organs via negative regulation of the expression of boundary-specific genes in Arabidopsis,Plant Cell,19(2):473-484
Li C.,Potuschak T.,Colon-Carmona A.,Gutierrez R.A.,and Doerner P.,2005,Arabidopsis TCP20 links regulation of growth and cell division control pathways,Proc.Natl.Acad.Sci.USA,102(36):12978-12983
Liu Y.,Guan X.,Liu S.,Yang M.,Ren J.,Guo M.,Huang Z.,and Zhang Y.,2018,Genome-wide identification and analysis of TCP transcription factors involved in the formation of leafy head in Chinese cabbage,Int.J.Mol.Sci.,19(3):847-862
Luo D.,Carpenter R.,Copsey L.,Vincent C.,Clark J.,and Coen E.,1999,Control of organ asymmetry in flowers of Antirrhinum,Cell,99(5):367-376
Ma J.,Wang Q.,Sun R.,Xie F.,Jones D.C.,and Zhang B.,2014,Genome-wide identification and expression analysis of TCPtranscription factors in Gossypium raimondii,Sci.Rep.,4(8):6645-6655
Manassero N.G.,Viola I.L.,Welchen E.,and Gonzalez D.H.,2013,TCP transcription factors:architetures of plant from,Biomol.Concepts,4(2):111-127
Nag A.,King S.,and Jack T.,2009,mi R319a targeting of TCP4is critical forpetal growth and development in Arabidopsis,Proc.Natl.Acad.Sci.USA,106(52):22534-22539
Palatnik J.F.,Allen E.,Wu X.,Schommer C.,Schwab R.,and Carrington J.C.,2003,Control of leaf morphogenesis by microRNAs,Nature,428(6955):257-263
Poza-Carrion C.,Aguilar-Martinez J.A.,and Cubas P.,2007,Role of TCP gene BRANCHED1 in the control of shoot branching in Arabidopsis,Plant Signal.Behav.,2(6):551-552
Sarvepalli K.,and Nath U.,2011,Hyper-activation of the TCP4transcription factor in Arabidopsis thaliana accelerates multiple aspects of plant maturation,Plant J.,67(4):595-607
Schommer C.,Palatnik J.F.,Aggarwal P.,Chetelat A.,Cubas P.,and Farmer E.E.,2008,Control of jasmonate biosynthe sis and senescence by mi R319 targets,PLoS Biol.,6(9):e230
Takeda T.,Amano K.,Ohto M.A.,Nakamura K.,Sato S.,Kato T.,Tabata S.,and Uequchi C.,2006,RNA interference of the Arabidopsis putative transcription factor TCP16 gene results in abortion of early pollendevelopment,Plant Mol.Biol.,61(1-2):165-177
Xu R.,Sun P.,Jia F.,Lu L.,Li Y.,Zhang S.,and Huang J.,2014,Genomewide analysis of TCP transcription factor gene family in Malus domestica,J.Genet.,93(3):733-746
Yao Y.X.,Li M.,Zhai H.,You C.X.,and Hao Y.J.,2007,Isolationand characterization of an apple cytosolic malate dehydrogenase gene reveal its function in malate synthesis,J.Plant Physiol.,168(5):474-480
Zhou Y.,Xu Z.,Zhao K.,Yang W.,Cheng T.,Wang J.,and Zhang Q.,2016,Genome-wide identification,characterization and expression analysis of the TCP gene family in Prunus mume,Front.Plant Sci.,7:1301-1316
Busch A.,and Zachgo S.,2007,Control of corolla monosymmetry in the Brassicaceae Iberis amara,Proc.Natl.Acad.Sci.USA,104(42):16714-16719
Cubas P.,Lauter N.,Doebley J.,and Coen E.,1999,The TCP domain:a motif found in proteins regulating plant growth and development,Plant J.,18(2):215-222
Doebley J.,Stec A.,and Hubbard L.,1997,The evolution of apical dominance in maize,Nature,386(6624):485-488
Efroni I.,Blum E.,Goldshmidt A.,and Eshed Y.,2008,A protracted and dynamic maturation schedule underlies Arabidopsis leaf development,Plant Cell,20(9):2293-2306
Giraud E.,Ng S.,Carrie C.,Duncan O.,Low J.,and Lee C.P.,Aken O.V.,Millar A.H.,Murcha M.,and Whelan J.,2010,TCP transcription factors link the regulation of genes encoding mitochondrial proteins with the circadian clock in Arabidopsis thaliana,Plant Cell,22(12):3921-3934
James E.R.,Michael F.F.,Quentin C.B.C.,Diane B.,and Mark W.C.,2000,A phylogenetic analysis of Rhamnaceae using rbcL and trnL-F plastid DNA sequences,Am.J.Bot.,87(9):1309-1324
Kosugi S.,and Ohashi Y.,1997,PCF1 and PCF2 specifically bind tocis elements in the rice proliferating cell nuclear antigen gene,Plant Cell,9(9):1607-1619
Koyama T.,Furutani M.,Tasaka M.,and Ohme-Takagi M.,2007,TCP transcription factors control the morphology of shoot lateral organs via negative regulation of the expression of boundary-specific genes in Arabidopsis,Plant Cell,19(2):473-484
Li C.,Potuschak T.,Colon-Carmona A.,Gutierrez R.A.,and Doerner P.,2005,Arabidopsis TCP20 links regulation of growth and cell division control pathways,Proc.Natl.Acad.Sci.USA,102(36):12978-12983
Liu Y.,Guan X.,Liu S.,Yang M.,Ren J.,Guo M.,Huang Z.,and Zhang Y.,2018,Genome-wide identification and analysis of TCP transcription factors involved in the formation of leafy head in Chinese cabbage,Int.J.Mol.Sci.,19(3):847-862
Luo D.,Carpenter R.,Copsey L.,Vincent C.,Clark J.,and Coen E.,1999,Control of organ asymmetry in flowers of Antirrhinum,Cell,99(5):367-376
Ma J.,Wang Q.,Sun R.,Xie F.,Jones D.C.,and Zhang B.,2014,Genome-wide identification and expression analysis of TCPtranscription factors in Gossypium raimondii,Sci.Rep.,4(8):6645-6655
Manassero N.G.,Viola I.L.,Welchen E.,and Gonzalez D.H.,2013,TCP transcription factors:architetures of plant from,Biomol.Concepts,4(2):111-127
Nag A.,King S.,and Jack T.,2009,mi R319a targeting of TCP4is critical forpetal growth and development in Arabidopsis,Proc.Natl.Acad.Sci.USA,106(52):22534-22539
Palatnik J.F.,Allen E.,Wu X.,Schommer C.,Schwab R.,and Carrington J.C.,2003,Control of leaf morphogenesis by microRNAs,Nature,428(6955):257-263
Poza-Carrion C.,Aguilar-Martinez J.A.,and Cubas P.,2007,Role of TCP gene BRANCHED1 in the control of shoot branching in Arabidopsis,Plant Signal.Behav.,2(6):551-552
Sarvepalli K.,and Nath U.,2011,Hyper-activation of the TCP4transcription factor in Arabidopsis thaliana accelerates multiple aspects of plant maturation,Plant J.,67(4):595-607
Schommer C.,Palatnik J.F.,Aggarwal P.,Chetelat A.,Cubas P.,and Farmer E.E.,2008,Control of jasmonate biosynthe sis and senescence by mi R319 targets,PLoS Biol.,6(9):e230
Takeda T.,Amano K.,Ohto M.A.,Nakamura K.,Sato S.,Kato T.,Tabata S.,and Uequchi C.,2006,RNA interference of the Arabidopsis putative transcription factor TCP16 gene results in abortion of early pollendevelopment,Plant Mol.Biol.,61(1-2):165-177
Xu R.,Sun P.,Jia F.,Lu L.,Li Y.,Zhang S.,and Huang J.,2014,Genomewide analysis of TCP transcription factor gene family in Malus domestica,J.Genet.,93(3):733-746
Yao Y.X.,Li M.,Zhai H.,You C.X.,and Hao Y.J.,2007,Isolationand characterization of an apple cytosolic malate dehydrogenase gene reveal its function in malate synthesis,J.Plant Physiol.,168(5):474-480
Zhou Y.,Xu Z.,Zhao K.,Yang W.,Cheng T.,Wang J.,and Zhang Q.,2016,Genome-wide identification,characterization and expression analysis of the TCP gene family in Prunus mume,Front.Plant Sci.,7:1301-1316