十字花科开花相关基因SBP进化的基因组信息学分析
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摘要
开花是植物由营养生长转为生殖生长的一个标志,鳞状启动子结合蛋白样(squamosa promoter binding protein-like, SBP)是一类重要调控开花相关的基因。在8个十字花科基因组中对SBP进行比较分析,鉴定了每个基因组中SBP的同源拷贝,每个基因组中基因拷贝数存在显著差异,其中最多的是在甘蓝中,有30个基因;一个突出的发现是在四倍体基因组中不同亚基因组的SBP具有一定的偏性,如四倍体芥菜-A基因组SBP拷贝数(21)高于芥菜-B基因组(19),在四倍体欧洲油菜中A基因组的SBP拷贝数(23)高于芥菜-A基因组(21),但低于欧洲油菜-C基因组中拷贝数(25)。搜索SBP处于共线性区域上基因,发现不同的全基因组加倍事件都有利于家族基因拷贝数扩增,尤其是十字花科共有的古老加倍(β),拟南芥、萝卜、黑芥等6个基因组的SBP基因几乎都与β加倍关联的重复区域相关联;另外串联重复加倍对于家族基因扩增也具有重要作用。对系统发育进行分析,并对同一事件的同义核苷酸置换率(Ks)进行比较,发现甘蓝、萝卜进化速率可能比白菜快;另外一个重要的发现是四倍体亚基因组A中SBP的进化速率快于另外的B和C基因组。本研究为认识十字花科开花相关转录因子SBP进化提供了重要的基因组学基础,有助于今后的更深入研究。
Flowering is a sign that plants are transformed from vegetative growth to reproductive growth.Squamosa promoter binding protein-like(SBP) is a class of important genes involved in flowering. A comparative analysis of SBP in 8%Brassicaceae genomes identified homologous copies of SBP in each genome, and there were significant differences in gene copy number in each genome, the most of which were in Brassica oleracea, with 30 genes; The outstanding finding is that the SBP of different subgenomics in the tetraploid genome has a certain bias,such as the tetraploid Brassica juncea-A genome SBP copy number(21) is higher than the Brassica juncea-B genome(19). In tetraploid Europe the SBP copy number in the A genome of Brassica napus(23) was higher than that of the Brassica juncea-A genome(21), but lower than the copy number in the Brassica napus-C genome(25).Searching for genes in SBP in a collinear region, it was found that different genome-wide doubling events are beneficial to family gene copy number amplification, especially the ancient doubling( β) doubling common to cruciferae, Arabidopsis thaliana, Raphanus sativus L., Brassica nigra, etc. Almost all of the SBP genes of the genome are associated with a repeat region in which β is doublingly associated; in addition, tandem repeat doubling also plays an important role in family gene amplification. The phylogeny was analyzed and the synonymous nucleotide substitution rate(Ks) of the same event was compared. It was found that the evolution rate of Brassica oleracea and Raphanus sativus L. may be faster than that of Brassica rapa; another important finding is the SBP of tetraploid subgenomic A, the rate of evolution is faster than the other B and C genomes. This study provides an important genomic basis for understanding the evolution of the flowering-related transcription factor SBP of the Brassicaceae,which will be useful for further research in the future.
Flowering is a sign that plants are transformed from vegetative growth to reproductive growth.Squamosa promoter binding protein-like(SBP) is a class of important genes involved in flowering. A comparative analysis of SBP in 8%Brassicaceae genomes identified homologous copies of SBP in each genome, and there were significant differences in gene copy number in each genome, the most of which were in Brassica oleracea, with 30 genes; The outstanding finding is that the SBP of different subgenomics in the tetraploid genome has a certain bias,such as the tetraploid Brassica juncea-A genome SBP copy number(21) is higher than the Brassica juncea-B genome(19). In tetraploid Europe the SBP copy number in the A genome of Brassica napus(23) was higher than that of the Brassica juncea-A genome(21), but lower than the copy number in the Brassica napus-C genome(25).Searching for genes in SBP in a collinear region, it was found that different genome-wide doubling events are beneficial to family gene copy number amplification, especially the ancient doubling( β) doubling common to cruciferae, Arabidopsis thaliana, Raphanus sativus L., Brassica nigra, etc. Almost all of the SBP genes of the genome are associated with a repeat region in which β is doublingly associated; in addition, tandem repeat doubling also plays an important role in family gene amplification. The phylogeny was analyzed and the synonymous nucleotide substitution rate(Ks) of the same event was compared. It was found that the evolution rate of Brassica oleracea and Raphanus sativus L. may be faster than that of Brassica rapa; another important finding is the SBP of tetraploid subgenomic A, the rate of evolution is faster than the other B and C genomes. This study provides an important genomic basis for understanding the evolution of the flowering-related transcription factor SBP of the Brassicaceae,which will be useful for further research in the future.
引文
Cardon G.H.,Hohmann S.,Nettesheim K.,Saedler H.,and Huijser P.,1997,Functional analysis of the Arabidopsis thaliana SBP-box gene SPL3:a novel gene involved in the floral transition,Plant J.,12(2):367-377
Denoeud F.,Carretero-Paulet L.,Dereeper A.,Droc G.,Guyot R.,Pietrella M.,Zheng C.,Alberti A.,Anthony F.,Aprea G.,Aury J.M.,Bento P.,Bernard M.,Bocs S.,Campa C.,Cenci A.,Combes M.C.,Crouzillat D.,Da Silva C.,Daddiego L.,De Bellis F.,Dussert S.,Garsmeur O.,Gayraud T.,Guignon V.,Jahn K.,Jamilloux V.,Jo觕t T.,Labadie K.,Lan T.,Leclercq J.,Lepelley M.,Leroy T.,Li L.T.,Librado P.,Lopez L.,Mu觡oz A.,Noel B.,Pallavicini A.,Perrotta G.,Poncet V.,Pot D.,Priyono,Rigoreau M.,Rouard M.,Rozas J.,Tranchant-Dubreuil C.,VanBuren R.,Zhang Q.,Andrade A.C.,Argout X.,Bertrand B.,de Kochko A.,Graziosi G.,Henry R.J.,Ming R.,Nagai C.,Rounsley S.,Sankoff D.,Giuliano G.,Albert V.A.,Wincker P.,and Lashermes P.,2014,The coffee genome provides insight into the convergent evolution of caffeine biosynthesis,Science,345(6201):1181-1184
He Z.,Zhang H.,Gao S.,Lercher M.J.,Chen W.H.,and Hu S.,2016,Evolview v2:an online visualization and management tool for customized and annotated phylogenetic trees,Nucleic Acids Res.,44(W1):236-241
Huang F.Y.,Liu T.K.,Wang J.,and Hou X.L.,2018,Isolation and functional characterization of a floral repressor,BcFLC2,from Pak choi(Brassica rapa ssp.chinensis),Planta,248(2):423-435
Jiao Y.,Leebens-Mack J.,Ayyampalayam S.,Bowers J.E.,McK-ain M.R.,McNeal J.,Rolf M.,Ruzicka D.R.,Wafula E.,Wickett N.J.,Wu X.,Zhang Y.,Wang J.,Zhang Y.,Carpenter E.J.,Deyholos M.K.,Kutchan T.M.,Chanderbali A.S.,Soltis P.S.,Stevenson D.W.,McCombie R.,Pires J.C.,Wong G.K.S.,Soltis D.E.,and dePamphilis C.W.,2012,Agenome triplication associated with early diversification of the core eudicots,Genome Biol.,13(1):R3
Jiao Y.,Wickett N.J.,Ayyampalayam S.,Chanderbali A.S.,Landherr L.,Ralph P.E.,Tomsho L.P.,Hu Y.,Liang H.,Soltis P.S.,Soltis D.E.,Clifton S.W.,Schlarbaum S.E.,Schuster S.C.,Ma H.,Leebens-Mack J.,and de Pamphilis C.W.,2011,Ancestral polyploidy in seed plants and angiosperms,Nature,473(7345):97-100
Kim J.J.,Lee J.H.,Kim W.,Jung H.S.,Huijser P.,and Ahn J.H.,2012,The microRNA156-SQUAMOSA PROMOTER BIN-DING PROTEIN-LIKE3 module regulates ambient temperature-responsive flowering via FLOWERING LOCUS T in Arabidopsis,Plant Physiol.,159(1):461-478
Klein J.,Saedler H.,and Huijser P.,1996,A new family of DNAbinding proteins includes putative transcriptional regulators of the Antirrhinum majus floral meristem identity gene SQUAMOSA,Mol.General Genet.,250(1):7-16
Lukens L.,Zou F.,Lydiate D.,Parkin I.,and Osborn T.,2003,Comparison of a Brassica oleracea genetic map with the genome of Arabidopsis thaliana,Genetics,164(1):359-372
Manning K.,Tor M.,Poole M.,Hong Y.G.,Thompson A.J.,King G.J.,Giovannoni J.J.,and Seymour G.B.,2006,A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening,Nat.Genet.,38(8):948-952
Murat F.,Louis A.,Maumus F.,Armero A.,Cooke R.,Quesneville H.,Crollius H.R.,and Salse J.,2016,Understanding Brassicaceae evolution through ancestral genome reconstruction,Genome Biol.,16:262
Parkin I.A.,Sharpe A.G.,and Lydiate D.J.,2003,Patterns of genome duplication within the Brassica napus genome,46(2):291
Soltis D.E.,Visger C.J.,Marchant D.B.,and Soltis P.S.,2016,Polyploidy:Pitfalls and paths to a paradigm,Am.J.Bot.,103(7):1146-1166
Srikanth A.,and Schmid M.,2011,Regulation of flowering time:all roads lead to Rome,Cell.Mol.Life Sci.,68(12):2013-2037
The Arabidopsis Genome Initiative,2000,Analysis of the genome sequence of the flowering plant Arabidopsis thaliana,Nature,408(6814):796-815
Unte U.S.,Sorensen A.M.,Pesaresi P.,Gandikota M.,Leister D.,Saedler H.,and Huijser P.,2003,SPL8,an SBP-box gene that affects pollen sac development in Arabidopsis,Plant Cell,15(4):1009-1019
Usami T.,Horiguchi G.,Yano S.,and Tsukaya H.,2009,The more and smaller cells mutants of Arabidopsis thaliana identify novel roles for SQUAMOSA PROMOTER BINDINGPROTEIN-LIKE genes in the control of heteroblasty,Development,136(6):955-964
Wang J.W.,Czech B.,and Weigel D.,2009,mi R156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana,Cell,138(4):738-749
Xu M.L.,Hu T.Q.,Zhao J.F.,Park M.Y.,Earley K.W.,Wu G.,Yang L.,and Poethig R.S.,2016,Developmental functions of mi R156-Regulated SQUAMOSA PROMOTER BINDINGPROTEIN-LIKE(SPL)genes in Arabidopsis thaliana,PLoSGenet.,12(8):e1006263
Yang N.S.,Wang J.P.,and Wang X.Y.,2017,Research progress on evolution of cotton genome structure,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),36(3):1090-1095(杨南山,王金朋,王希胤,2017,棉花基因组结构进化研究进展,基因组学与应用生物学,36(3):1090-1095)
Yuan M.,Xing C.B.,Ge W.N.,Wang L.,and Guo D.,2017,Protein expression and purification of flowering inducer gene FT in Arabidopsis thaliana,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),36(8):3053-3056(袁敏,邢朝斌,葛伟娜,王莉,郭棣,2017,拟南芥开花诱导基因FT的蛋白表达及纯化,基因组学与应用生物学,36(8):3053-3056)
Zhang J.,Ping A.M.,Wang X.T.,Li G.Z.,Zhu Z.J.,Li M.L.,Xing G.M.,and Hou L.P.,2017,Cloning and expression analysis of SPL8 homolog from pak choi(Brassica rapa subsp.chinensis),Biotechnol.Biotec.Eq.,31(6):1132-1138
Zhang X.,and Wessler S.R.,2004,Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea,Proc.Natl.A-cad.Sci.USA,101(15):5589-5594
Denoeud F.,Carretero-Paulet L.,Dereeper A.,Droc G.,Guyot R.,Pietrella M.,Zheng C.,Alberti A.,Anthony F.,Aprea G.,Aury J.M.,Bento P.,Bernard M.,Bocs S.,Campa C.,Cenci A.,Combes M.C.,Crouzillat D.,Da Silva C.,Daddiego L.,De Bellis F.,Dussert S.,Garsmeur O.,Gayraud T.,Guignon V.,Jahn K.,Jamilloux V.,Jo觕t T.,Labadie K.,Lan T.,Leclercq J.,Lepelley M.,Leroy T.,Li L.T.,Librado P.,Lopez L.,Mu觡oz A.,Noel B.,Pallavicini A.,Perrotta G.,Poncet V.,Pot D.,Priyono,Rigoreau M.,Rouard M.,Rozas J.,Tranchant-Dubreuil C.,VanBuren R.,Zhang Q.,Andrade A.C.,Argout X.,Bertrand B.,de Kochko A.,Graziosi G.,Henry R.J.,Ming R.,Nagai C.,Rounsley S.,Sankoff D.,Giuliano G.,Albert V.A.,Wincker P.,and Lashermes P.,2014,The coffee genome provides insight into the convergent evolution of caffeine biosynthesis,Science,345(6201):1181-1184
He Z.,Zhang H.,Gao S.,Lercher M.J.,Chen W.H.,and Hu S.,2016,Evolview v2:an online visualization and management tool for customized and annotated phylogenetic trees,Nucleic Acids Res.,44(W1):236-241
Huang F.Y.,Liu T.K.,Wang J.,and Hou X.L.,2018,Isolation and functional characterization of a floral repressor,BcFLC2,from Pak choi(Brassica rapa ssp.chinensis),Planta,248(2):423-435
Jiao Y.,Leebens-Mack J.,Ayyampalayam S.,Bowers J.E.,McK-ain M.R.,McNeal J.,Rolf M.,Ruzicka D.R.,Wafula E.,Wickett N.J.,Wu X.,Zhang Y.,Wang J.,Zhang Y.,Carpenter E.J.,Deyholos M.K.,Kutchan T.M.,Chanderbali A.S.,Soltis P.S.,Stevenson D.W.,McCombie R.,Pires J.C.,Wong G.K.S.,Soltis D.E.,and dePamphilis C.W.,2012,Agenome triplication associated with early diversification of the core eudicots,Genome Biol.,13(1):R3
Jiao Y.,Wickett N.J.,Ayyampalayam S.,Chanderbali A.S.,Landherr L.,Ralph P.E.,Tomsho L.P.,Hu Y.,Liang H.,Soltis P.S.,Soltis D.E.,Clifton S.W.,Schlarbaum S.E.,Schuster S.C.,Ma H.,Leebens-Mack J.,and de Pamphilis C.W.,2011,Ancestral polyploidy in seed plants and angiosperms,Nature,473(7345):97-100
Kim J.J.,Lee J.H.,Kim W.,Jung H.S.,Huijser P.,and Ahn J.H.,2012,The microRNA156-SQUAMOSA PROMOTER BIN-DING PROTEIN-LIKE3 module regulates ambient temperature-responsive flowering via FLOWERING LOCUS T in Arabidopsis,Plant Physiol.,159(1):461-478
Klein J.,Saedler H.,and Huijser P.,1996,A new family of DNAbinding proteins includes putative transcriptional regulators of the Antirrhinum majus floral meristem identity gene SQUAMOSA,Mol.General Genet.,250(1):7-16
Lukens L.,Zou F.,Lydiate D.,Parkin I.,and Osborn T.,2003,Comparison of a Brassica oleracea genetic map with the genome of Arabidopsis thaliana,Genetics,164(1):359-372
Manning K.,Tor M.,Poole M.,Hong Y.G.,Thompson A.J.,King G.J.,Giovannoni J.J.,and Seymour G.B.,2006,A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening,Nat.Genet.,38(8):948-952
Murat F.,Louis A.,Maumus F.,Armero A.,Cooke R.,Quesneville H.,Crollius H.R.,and Salse J.,2016,Understanding Brassicaceae evolution through ancestral genome reconstruction,Genome Biol.,16:262
Parkin I.A.,Sharpe A.G.,and Lydiate D.J.,2003,Patterns of genome duplication within the Brassica napus genome,46(2):291
Soltis D.E.,Visger C.J.,Marchant D.B.,and Soltis P.S.,2016,Polyploidy:Pitfalls and paths to a paradigm,Am.J.Bot.,103(7):1146-1166
Srikanth A.,and Schmid M.,2011,Regulation of flowering time:all roads lead to Rome,Cell.Mol.Life Sci.,68(12):2013-2037
The Arabidopsis Genome Initiative,2000,Analysis of the genome sequence of the flowering plant Arabidopsis thaliana,Nature,408(6814):796-815
Unte U.S.,Sorensen A.M.,Pesaresi P.,Gandikota M.,Leister D.,Saedler H.,and Huijser P.,2003,SPL8,an SBP-box gene that affects pollen sac development in Arabidopsis,Plant Cell,15(4):1009-1019
Usami T.,Horiguchi G.,Yano S.,and Tsukaya H.,2009,The more and smaller cells mutants of Arabidopsis thaliana identify novel roles for SQUAMOSA PROMOTER BINDINGPROTEIN-LIKE genes in the control of heteroblasty,Development,136(6):955-964
Wang J.W.,Czech B.,and Weigel D.,2009,mi R156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana,Cell,138(4):738-749
Xu M.L.,Hu T.Q.,Zhao J.F.,Park M.Y.,Earley K.W.,Wu G.,Yang L.,and Poethig R.S.,2016,Developmental functions of mi R156-Regulated SQUAMOSA PROMOTER BINDINGPROTEIN-LIKE(SPL)genes in Arabidopsis thaliana,PLoSGenet.,12(8):e1006263
Yang N.S.,Wang J.P.,and Wang X.Y.,2017,Research progress on evolution of cotton genome structure,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),36(3):1090-1095(杨南山,王金朋,王希胤,2017,棉花基因组结构进化研究进展,基因组学与应用生物学,36(3):1090-1095)
Yuan M.,Xing C.B.,Ge W.N.,Wang L.,and Guo D.,2017,Protein expression and purification of flowering inducer gene FT in Arabidopsis thaliana,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),36(8):3053-3056(袁敏,邢朝斌,葛伟娜,王莉,郭棣,2017,拟南芥开花诱导基因FT的蛋白表达及纯化,基因组学与应用生物学,36(8):3053-3056)
Zhang J.,Ping A.M.,Wang X.T.,Li G.Z.,Zhu Z.J.,Li M.L.,Xing G.M.,and Hou L.P.,2017,Cloning and expression analysis of SPL8 homolog from pak choi(Brassica rapa subsp.chinensis),Biotechnol.Biotec.Eq.,31(6):1132-1138
Zhang X.,and Wessler S.R.,2004,Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea,Proc.Natl.A-cad.Sci.USA,101(15):5589-5594