萝卜全基因组中LBD基因家族成员的鉴定与分析
|
摘要
LBD基因家族是植物所特有的一类转录因子,在植物生长发育过程中起到非常重要的作用。本研究利用生物信息学方法,从萝卜基因组中鉴定出分布于9条染色体上的59个LBD基因。该家族成员结构比较简单,内含子数均不超过3个。萝卜LBD基因可分为两大类,分别包含50个和9个成员。它们在染色体上的分布不均匀,1号染色体上基因数目最多,有18个,而7号和8号染色体分别仅有1个LBD基因。对它们在不同组织和发育时期的表达模式研究发现,该基因家族具有一定的时空表达特异性,预测其参与萝卜不同的发育过程。本研究为萝卜LBD基因家族的功能分析奠定了基础。
LBD gene family is a plant-specific transcription factors and plays very important role in plant development.In this study,59 LBD genes were identified using bioinformatic approach and they were found on 9 chromosomes of radish genome.The radish LBD genes have simple genomic organization with the intron numbers being less than 3.These LBD genes could be classified into 2 classes according to the phylogeny relationship,including 50 and 9 members,respectively.The number of radish LBDs on chromosomes was different.For instance,eighteen members were found on chromosome 1,while only one member was found on chromosome 7 and 8.The expression patterns of radish LBD genes in different tissues and development stages showed spatial and temporal differences,implying the functional specificity.Thus,these results will become helpful for the functional characterization of the LBD genes family.
LBD gene family is a plant-specific transcription factors and plays very important role in plant development.In this study,59 LBD genes were identified using bioinformatic approach and they were found on 9 chromosomes of radish genome.The radish LBD genes have simple genomic organization with the intron numbers being less than 3.These LBD genes could be classified into 2 classes according to the phylogeny relationship,including 50 and 9 members,respectively.The number of radish LBDs on chromosomes was different.For instance,eighteen members were found on chromosome 1,while only one member was found on chromosome 7 and 8.The expression patterns of radish LBD genes in different tissues and development stages showed spatial and temporal differences,implying the functional specificity.Thus,these results will become helpful for the functional characterization of the LBD genes family.
引文
[1]Shuai B,Reynaga-Pe?a C G,Springer P S.The lateral organ boundaries gene defines a novel plant-specific gene family.Plant Physiology,2002,129(2):747-761
[2]卢寰,时振英.高等植物特有的LBD基因的分子生物学功能研究进展.植物生理学报,2013,49(9):833-846Lu H,Shi Z Y.Research progress on the molecular function of plant-specificLBDgene.PlantPhysiologyJournal,2013,49(9):833-846
[3]孙亭亭,龚达平,张磊,陈雅琼,赵维,向小华,孙玉合.普通烟草LBD基因家族的全基因组序列鉴定与表达分析.植物遗传资源学报,2016,17(2):316-325Sun T T,Gong D P,Zhang L,Chen Y Q,Zhao W,Xiang X H,Sun Y H.Genome-wide sequence identification and expression analysis of the LBD gene family in Nicotiana tabacum.Journal of Plant Genetic Resources,2016,17(2):316-325
[4]Majer C,Hochholdinger F.Defining the boundaries:structure and function of LOB domain proteins.Trends in Plant Science,2011,16(1):47-52
[5]Semiarti N U A J,Ueno Y,Tsukaya H,Iwakawa H,Machida C,Machida Y.The ASYMMETRIC LEAVES2 gene of Arabidopsis thalianaregulatesformationofasymmetriclamina,establishmentofvenationandrepressionofmeristem-related homeobox genes in leaves.Development,2001,128(10):1771
[6]Iwakawa H,Iwasaki M,Kojima S,Ueno Y,Soma T,Tanaka H,SemiartiE,MachidaY,MachidaC.Expressionofthe ASYMMETRICLEAVES2geneintheadaxialdomainof Arabidopsisleavesrepressescellproliferationinthisdomain and is critical for the development of properly expanded leaves.Plant Journal,2010,51(2):173-184
[7]Kim M J,Kim M,Kim J.Combinatorial interactions between LBD10andLBD27areessentialformalegametophyte development in Arabidopsis.Plant Signaling&Behavior,2015,10(8):e1044193
[8]Sun X D,Feng Z H,Meng L S,Zhu J,Geitmann A.Arabidopsis A S L 11/L B D 1 5i si n v o l v e di ns h o o ta p i c a lm e r i s t e m development;and regulates WUS expression.Planta,2013,237(5):1367-1378
[9]Fan M,Xu C,Xu K,Hu Y.LATERAL ORGAN BOUNDARIES DOMAINtranscriptionfactorsdirectcallusformationin Arabidopsis regeneration.Cell Research,2012,22(7):1169
[10]HanWL,Nan YK,DongJL,KimJ.LBD18/ASL20regulateslateralrootformationincombinationwithLBD16/ASL18 downstream of ARF7 and ARF19 in Arabidopsis.Plant Physiology,2009,151(3):1377-1389
[11]Okushima Y,Fukaki H,Onoda M,Theologis A,Tasaka M.ARF7and ARF19 regulate lateral root formation via direct activation ofLBD/ASLgenesin Arabidopsis.PlantCell,2007,19(1):118-130
[12]Thatcher L F,Powell J J,Aitken E A,Kazan K,Manners J M.Thelateralorganboundariesdomaintranscriptionfactor LBD20 functions in Fusarium wilt susceptibility and jasmonate signalingin Arabidopsis.PlantPhysiology,2012,160(12):407-418
[13]Kim M J,Kim M,Lee M R,Park S K,Kim J.LATERAL ORGANBOUNDARIESDOMAIN(LBD)10interactswith SIDECAR POLLEN/LBD27 to control pollen development in Arabidopsis.Plant Journal for Cell&Molecular Biology,2015,81(5):794-809
[14]Kim M,Kim M J,Pandey S,Kim J.Expression and protein interactionanalysesrevealcombinatorialinteractionsofLBD transcriptionfactorsduring Arabidopsispollendevelopment.Plant&Cell Physiology,2016,57(11):2291-2299
[15]Rast M I,Simon R.Arabidopsis JAGGED LATERAL ORGANS acts with ASYMMETRIC LEAVES2 to coordinate KNOX and PIN expression in shoot and root meristems.Plant Cell,2012,24(7):2917-2933
[16]Chalfun-Junior A,Franken J,Mes J J,Marsch-Martinez N,Pereira A,AngenentGC.ASYMMETRICLEAVES2-LIKE1gene,amemberofthe AS2/LOBfamily,controlsproximaldistal patterning in Arabidopsis petals.Plant Molecular Biology,2005,57(4):559-575
[17]RubinG,TohgeT,MatsudaF,SaitoK,ScheibleW R.Members of the LBD family of transcription factors repress anthocyanin synthesis and affect additional nitrogen responses in Arabidopsis.Plant Cell,2009,21(11):3567-3584
[18]Li H H,Liu X,An J P,Hao Y J,Wang X F,You C X.Cloning andelucidationofthefunctionalroleofappleMdLBD13,in anthocyaninbiosynthesisandnitrateassimilation.PlantCell Tissue&Organ Culture,2017(4):1-13
[19]Zhang J,Tang W,Huang Y,Niu X L,Zhao Y,Han Y,Liu YS.Down-regulationofaLBD-likegene,OsIG1,leads tooccurrenceofunusualdoubleovulesanddevelopmental abnormalities of various floral organs and megagametophyte in rice.2015,66(1):99-112
[20]Ma W W,Wu F Q,Sheng P,Wang X L,Zhang Z,Zhou K N,ZhangH,HuJL,LinQB,ChengZJ,WangJL,ZhuSS,Zhang X,Guo X P,Wang H Y,Wu C Y,Zhai H Q,Wan J M.The LBD12-1transcriptionfactorsuppressesapicalmeristemsize by repressing Argonaute 10 expression.Plant Physiology,2016,173(1):801-811
[21]Inukai Y,Sakamoto T,Uequchi-Tanaka M,Shibata Y,Gomi K,Umemura I,Hasegawa Y,Ashikari M,Kitano H,Matsuoka M.Crown rootless1,which is essential for crown root formation in rice,is a target of an AUXIN RESPONSE FACTOR in auxin signaling.Plant Cell,2005,17(5):1387-1396
[22]Li C,Zou X,Zhang C,Shao Q,Liu J,Liu B,Li H,Zhao T.OsLBD3-7 overexpression induced adaxially rolled leaves in rice.PLoS One,2016,11(6):e0156413
[23]Li C,Zhu S,Zhang H,Chen L,Cai M,Wang J,Chai J,Wu F,Cheng Z,Guo X,Zhang X,Wan J.OsLBD37 and OsLBD38,two class II type LBD proteins,are involved in the regulation of heading date by controlling the expression of Ehd1 in rice.Biochemical and biophysical research communications,2017,486(3):720-725
[24]Liu H,Wang S,Yu X J,Yu J,He X,Zhang S,Shou H,Wu P.ARL1,a LOB-domain protein required for adventitious root formation in rice.Plant Journal,2010,43(1):47-56
[25]Evans M M S.The indeterminate gamethophyte1 gene of maize encodes a LOB domain protein required for embryo sac and leaf development.Plant Cell,2007,19(1):46-62
[26]MatsumuraY,IwakawaH,MachidaY,MachidaC.Characterizationofgenesinthe ASYMMETRICLEAVES2/LATERALORGANBOUNDARIES(AS2/LOB)familyin Arabidopsis thaliana,and functional and molecular comparisons between AS2 and other family members.Plant Journal,2010,58(3):525-537
[27]Yang Y,Yu X,Wu P.Comparison and evolution analysis of two ricesubspeciesLATERALORGANBOUNDARIESdomain genefamilyandtheirevolutionarycharacterizationfrom Arabidopsis.MolecularPhylogenetics&Evolution,2006,39(1):248-262
[28]Zhang Y M,Zhang S Z,Zheng C C.Genomewide analysis of LATERALORGANBOUNDARIESDomaingenefamilyin Zea mays.Journal of Genetics,2014,93(1):79-91
[29]Zhu Q H,Guo A Y,Gao G,Zhong Y F,Xu M,Huang M,LuoJ.DPTF:adatabaseofpoplartranscriptionfactors.Bioinformatics,2007,23(10):1307-1308
[30]王小非,刘鑫,苏玲,孙永江,张世忠,郝玉金,由春香.番茄LBD基因家族的全基因组序列鉴定及其进化和表达分析.中国农业科学,2013,46(12):2501-2513Wang X F,Liu X,Su L,Sun Y J,Zhang S Z,Hao Y J,You C X.Identification,evolution and expression analysis of the LBD genefamilyintomato.Scientia AgriculturaSinica,2013,46(12):2501-2513
[31]郑忠凡,张亚利,胡灿,戴雄泽,刘峰,袁祖华.辣椒全基因组中LBD转录因子的鉴定与表达分析.园艺学报,2016,43(4):683-694ZhengZF,ZhangYL,HuC,DaiXZ,LiuF,YuanZ H.Genome-wide identification and expression analysis of LBD transcription factor in pepper.Acta Horticulturae Sinica,2016,43(4):683-694
[32]Cao H,Liu C Y,Liu C X,Zhao Y L,Xu R R.Genomewide analysis of the lateral organ boundaries domain gene family in Vitis vinifera.Journal of Genetics,2016,95(3):515-526
[33]Zhang X H,Yue Z,Mei S Y,Qiu Y,Yang X H,Chen X H,Cheng F,Wu Z Y,Sun Y Y,Jing Y,Liu B,Shen D,Wang H P,Cui N,Duan Y D,Wu J,Wang J L,Gan C X,Wang J,Wang X W,Li X X.A de novo genome of a Chinese radish cultivar.Horticultural Plant Journal,2015,1(3):155-164
[34]Hu B,Jin J,Guo A Y,Zhang H,Luo J,Gao G.GSDS 2.0:an upgraded gene feature visualization server.Bioinformatics,2015,31(8):1296
[35]Deng W,Wang Y,Liu Z,Cheng H,Xue Y.HemI:A toolkit for illustrating heatmaps.PLoS One,2014,9(11):e111988
[36]Karanja B K,Fan L,Xu L,Wang Y,Zhu X,Tang M,Wang R,Zhang F,Muleke E M,Liu L.Genome-wide characterization of the WRKY gene family in radish(Raphanus sativus L.)reveals its critical functions under different abiotic stresses.Plant Cell Reports,2017,36(11):1757-1773
[37]Karanja B K,Xu L,Wang Y,Muleke E M,Jabir B M,Xie Y,ZhuX,Cheng W,LiuL.Genome-widecharacterizationand expressionprofilingofNACtranscriptionfactorgenesunder abiotic stresses in radish(Raphanus sativus L.).Peer Journal,2017,5:e4172
[38]Li C,Wang Y,Xu L,Nie S,Chen Y,Liang D,Sun X,Karanja BK,LuoX,LiuL.Genome-widecharacterizationofthe MADS-Box gene family in Radish(Raphanus sativus L.)and assessmentofitsrolesinfloweringandfloralorganogenesis.Frontiers in Plant Science,2016,7:1390
[2]卢寰,时振英.高等植物特有的LBD基因的分子生物学功能研究进展.植物生理学报,2013,49(9):833-846Lu H,Shi Z Y.Research progress on the molecular function of plant-specificLBDgene.PlantPhysiologyJournal,2013,49(9):833-846
[3]孙亭亭,龚达平,张磊,陈雅琼,赵维,向小华,孙玉合.普通烟草LBD基因家族的全基因组序列鉴定与表达分析.植物遗传资源学报,2016,17(2):316-325Sun T T,Gong D P,Zhang L,Chen Y Q,Zhao W,Xiang X H,Sun Y H.Genome-wide sequence identification and expression analysis of the LBD gene family in Nicotiana tabacum.Journal of Plant Genetic Resources,2016,17(2):316-325
[4]Majer C,Hochholdinger F.Defining the boundaries:structure and function of LOB domain proteins.Trends in Plant Science,2011,16(1):47-52
[5]Semiarti N U A J,Ueno Y,Tsukaya H,Iwakawa H,Machida C,Machida Y.The ASYMMETRIC LEAVES2 gene of Arabidopsis thalianaregulatesformationofasymmetriclamina,establishmentofvenationandrepressionofmeristem-related homeobox genes in leaves.Development,2001,128(10):1771
[6]Iwakawa H,Iwasaki M,Kojima S,Ueno Y,Soma T,Tanaka H,SemiartiE,MachidaY,MachidaC.Expressionofthe ASYMMETRICLEAVES2geneintheadaxialdomainof Arabidopsisleavesrepressescellproliferationinthisdomain and is critical for the development of properly expanded leaves.Plant Journal,2010,51(2):173-184
[7]Kim M J,Kim M,Kim J.Combinatorial interactions between LBD10andLBD27areessentialformalegametophyte development in Arabidopsis.Plant Signaling&Behavior,2015,10(8):e1044193
[8]Sun X D,Feng Z H,Meng L S,Zhu J,Geitmann A.Arabidopsis A S L 11/L B D 1 5i si n v o l v e di ns h o o ta p i c a lm e r i s t e m development;and regulates WUS expression.Planta,2013,237(5):1367-1378
[9]Fan M,Xu C,Xu K,Hu Y.LATERAL ORGAN BOUNDARIES DOMAINtranscriptionfactorsdirectcallusformationin Arabidopsis regeneration.Cell Research,2012,22(7):1169
[10]HanWL,Nan YK,DongJL,KimJ.LBD18/ASL20regulateslateralrootformationincombinationwithLBD16/ASL18 downstream of ARF7 and ARF19 in Arabidopsis.Plant Physiology,2009,151(3):1377-1389
[11]Okushima Y,Fukaki H,Onoda M,Theologis A,Tasaka M.ARF7and ARF19 regulate lateral root formation via direct activation ofLBD/ASLgenesin Arabidopsis.PlantCell,2007,19(1):118-130
[12]Thatcher L F,Powell J J,Aitken E A,Kazan K,Manners J M.Thelateralorganboundariesdomaintranscriptionfactor LBD20 functions in Fusarium wilt susceptibility and jasmonate signalingin Arabidopsis.PlantPhysiology,2012,160(12):407-418
[13]Kim M J,Kim M,Lee M R,Park S K,Kim J.LATERAL ORGANBOUNDARIESDOMAIN(LBD)10interactswith SIDECAR POLLEN/LBD27 to control pollen development in Arabidopsis.Plant Journal for Cell&Molecular Biology,2015,81(5):794-809
[14]Kim M,Kim M J,Pandey S,Kim J.Expression and protein interactionanalysesrevealcombinatorialinteractionsofLBD transcriptionfactorsduring Arabidopsispollendevelopment.Plant&Cell Physiology,2016,57(11):2291-2299
[15]Rast M I,Simon R.Arabidopsis JAGGED LATERAL ORGANS acts with ASYMMETRIC LEAVES2 to coordinate KNOX and PIN expression in shoot and root meristems.Plant Cell,2012,24(7):2917-2933
[16]Chalfun-Junior A,Franken J,Mes J J,Marsch-Martinez N,Pereira A,AngenentGC.ASYMMETRICLEAVES2-LIKE1gene,amemberofthe AS2/LOBfamily,controlsproximaldistal patterning in Arabidopsis petals.Plant Molecular Biology,2005,57(4):559-575
[17]RubinG,TohgeT,MatsudaF,SaitoK,ScheibleW R.Members of the LBD family of transcription factors repress anthocyanin synthesis and affect additional nitrogen responses in Arabidopsis.Plant Cell,2009,21(11):3567-3584
[18]Li H H,Liu X,An J P,Hao Y J,Wang X F,You C X.Cloning andelucidationofthefunctionalroleofappleMdLBD13,in anthocyaninbiosynthesisandnitrateassimilation.PlantCell Tissue&Organ Culture,2017(4):1-13
[19]Zhang J,Tang W,Huang Y,Niu X L,Zhao Y,Han Y,Liu YS.Down-regulationofaLBD-likegene,OsIG1,leads tooccurrenceofunusualdoubleovulesanddevelopmental abnormalities of various floral organs and megagametophyte in rice.2015,66(1):99-112
[20]Ma W W,Wu F Q,Sheng P,Wang X L,Zhang Z,Zhou K N,ZhangH,HuJL,LinQB,ChengZJ,WangJL,ZhuSS,Zhang X,Guo X P,Wang H Y,Wu C Y,Zhai H Q,Wan J M.The LBD12-1transcriptionfactorsuppressesapicalmeristemsize by repressing Argonaute 10 expression.Plant Physiology,2016,173(1):801-811
[21]Inukai Y,Sakamoto T,Uequchi-Tanaka M,Shibata Y,Gomi K,Umemura I,Hasegawa Y,Ashikari M,Kitano H,Matsuoka M.Crown rootless1,which is essential for crown root formation in rice,is a target of an AUXIN RESPONSE FACTOR in auxin signaling.Plant Cell,2005,17(5):1387-1396
[22]Li C,Zou X,Zhang C,Shao Q,Liu J,Liu B,Li H,Zhao T.OsLBD3-7 overexpression induced adaxially rolled leaves in rice.PLoS One,2016,11(6):e0156413
[23]Li C,Zhu S,Zhang H,Chen L,Cai M,Wang J,Chai J,Wu F,Cheng Z,Guo X,Zhang X,Wan J.OsLBD37 and OsLBD38,two class II type LBD proteins,are involved in the regulation of heading date by controlling the expression of Ehd1 in rice.Biochemical and biophysical research communications,2017,486(3):720-725
[24]Liu H,Wang S,Yu X J,Yu J,He X,Zhang S,Shou H,Wu P.ARL1,a LOB-domain protein required for adventitious root formation in rice.Plant Journal,2010,43(1):47-56
[25]Evans M M S.The indeterminate gamethophyte1 gene of maize encodes a LOB domain protein required for embryo sac and leaf development.Plant Cell,2007,19(1):46-62
[26]MatsumuraY,IwakawaH,MachidaY,MachidaC.Characterizationofgenesinthe ASYMMETRICLEAVES2/LATERALORGANBOUNDARIES(AS2/LOB)familyin Arabidopsis thaliana,and functional and molecular comparisons between AS2 and other family members.Plant Journal,2010,58(3):525-537
[27]Yang Y,Yu X,Wu P.Comparison and evolution analysis of two ricesubspeciesLATERALORGANBOUNDARIESdomain genefamilyandtheirevolutionarycharacterizationfrom Arabidopsis.MolecularPhylogenetics&Evolution,2006,39(1):248-262
[28]Zhang Y M,Zhang S Z,Zheng C C.Genomewide analysis of LATERALORGANBOUNDARIESDomaingenefamilyin Zea mays.Journal of Genetics,2014,93(1):79-91
[29]Zhu Q H,Guo A Y,Gao G,Zhong Y F,Xu M,Huang M,LuoJ.DPTF:adatabaseofpoplartranscriptionfactors.Bioinformatics,2007,23(10):1307-1308
[30]王小非,刘鑫,苏玲,孙永江,张世忠,郝玉金,由春香.番茄LBD基因家族的全基因组序列鉴定及其进化和表达分析.中国农业科学,2013,46(12):2501-2513Wang X F,Liu X,Su L,Sun Y J,Zhang S Z,Hao Y J,You C X.Identification,evolution and expression analysis of the LBD genefamilyintomato.Scientia AgriculturaSinica,2013,46(12):2501-2513
[31]郑忠凡,张亚利,胡灿,戴雄泽,刘峰,袁祖华.辣椒全基因组中LBD转录因子的鉴定与表达分析.园艺学报,2016,43(4):683-694ZhengZF,ZhangYL,HuC,DaiXZ,LiuF,YuanZ H.Genome-wide identification and expression analysis of LBD transcription factor in pepper.Acta Horticulturae Sinica,2016,43(4):683-694
[32]Cao H,Liu C Y,Liu C X,Zhao Y L,Xu R R.Genomewide analysis of the lateral organ boundaries domain gene family in Vitis vinifera.Journal of Genetics,2016,95(3):515-526
[33]Zhang X H,Yue Z,Mei S Y,Qiu Y,Yang X H,Chen X H,Cheng F,Wu Z Y,Sun Y Y,Jing Y,Liu B,Shen D,Wang H P,Cui N,Duan Y D,Wu J,Wang J L,Gan C X,Wang J,Wang X W,Li X X.A de novo genome of a Chinese radish cultivar.Horticultural Plant Journal,2015,1(3):155-164
[34]Hu B,Jin J,Guo A Y,Zhang H,Luo J,Gao G.GSDS 2.0:an upgraded gene feature visualization server.Bioinformatics,2015,31(8):1296
[35]Deng W,Wang Y,Liu Z,Cheng H,Xue Y.HemI:A toolkit for illustrating heatmaps.PLoS One,2014,9(11):e111988
[36]Karanja B K,Fan L,Xu L,Wang Y,Zhu X,Tang M,Wang R,Zhang F,Muleke E M,Liu L.Genome-wide characterization of the WRKY gene family in radish(Raphanus sativus L.)reveals its critical functions under different abiotic stresses.Plant Cell Reports,2017,36(11):1757-1773
[37]Karanja B K,Xu L,Wang Y,Muleke E M,Jabir B M,Xie Y,ZhuX,Cheng W,LiuL.Genome-widecharacterizationand expressionprofilingofNACtranscriptionfactorgenesunder abiotic stresses in radish(Raphanus sativus L.).Peer Journal,2017,5:e4172
[38]Li C,Wang Y,Xu L,Nie S,Chen Y,Liang D,Sun X,Karanja BK,LuoX,LiuL.Genome-widecharacterizationofthe MADS-Box gene family in Radish(Raphanus sativus L.)and assessmentofitsrolesinfloweringandfloralorganogenesis.Frontiers in Plant Science,2016,7:1390