陆地棉GRF基因家族的鉴定和生物信息学分析
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摘要
为了揭示陆地棉生长调控因子(growth-regulating factors, GRF)家族的功能,本研究利用全基因组信息在陆地棉基因组中鉴定了33个GRF蛋白,并对这些家族成员进行了保守结构域分析、蛋白的基本理化性质分析、进化分析、基因的结构分析、染色体定位、保守基序分析和组织表达模式分析。研究表明,陆地棉GRF均含有QLQ和WRC 2个保守结构域,系统进化分为4个亚家族,基因定位在19条染色体上,基因上有2～19个蛋白编码区域,大多数的基因在柱头、子房和20 d的种子中高量表达。本研究弄清了棉花GRF家族的基本信息,为进一步研究棉花GRF家族成员的功能提供了理论指导。
In order to reveal the function of growth-regulating factors(GRF) in Upland cotton, we used wholegenome bioinformatics to identify 33 GRF in Gossypium hirsutum, and analyzed conservative structure domain,the physicochemical properties, phylogenetic evolution, gene structure, chromosome positioning, conservative motif and gene expression pattern in different tissue. The results showed that 33 GRF genes all contained QLQ and WRC two conserved domains, and were divided into four subfamilies. These genes were locationed on 19 chromosomes, contained 2～19 protein coding regions. Many genes expressed higher in stigma, ovule and seed(20 days post anthesis [dpa]) than other tissues. This results clarify the basic information of GRF family in cotton and provide basis information for further research on the function of GRF gene family members in Gossypium hirsutum.
In order to reveal the function of growth-regulating factors(GRF) in Upland cotton, we used wholegenome bioinformatics to identify 33 GRF in Gossypium hirsutum, and analyzed conservative structure domain,the physicochemical properties, phylogenetic evolution, gene structure, chromosome positioning, conservative motif and gene expression pattern in different tissue. The results showed that 33 GRF genes all contained QLQ and WRC two conserved domains, and were divided into four subfamilies. These genes were locationed on 19 chromosomes, contained 2～19 protein coding regions. Many genes expressed higher in stigma, ovule and seed(20 days post anthesis [dpa]) than other tissues. This results clarify the basic information of GRF family in cotton and provide basis information for further research on the function of GRF gene family members in Gossypium hirsutum.
引文
Choi D.,Kim J.H.,and Kende H.,2004,Whole genome analysis of the OsGRF gene family encoding plant-specific putative transcription activators in rice(Oryza sativa L.),Plant Cell Physiol.,45(7):897-904
Debernardi J.M.,Mecchia M.A.,Vercruyssen L.,Smaczniak C.,Kaufmann K.,Inze D.,Rodriguez R.E.,and Palatnik J.F.,2014,Post-transcriptional control of GRF transcription factors by microRNA mi R396 and GIF co-activator affects leaf size and longevity,Plant J.,79(3):413-426
Horiguchi G.,Kim G.T.,and Tsukaya H.,2005,The transcription factor At GRF5 and the transcription coactivator AN3 regulate cell proliferation in leaf primordia of Arabidopsis thaliana,Plant J.,43(1):68-78
Kim J.H.,and Kende H.,2004,A transcriptional coactivator,AtGIF1,is involved in regulating leaf growth and morphology in Arabidopsis,Proc.Natl.Acad.Sci.USA,101(36):13374-13379
Kim J.H.,Chi D.,and Kenda H.,2003,The At GRF family of putative transcript ion factors is involved in leaf and cotyledon growth in Arabidopsis,Plant J.,36(1):94-104
Kim J.S.,Mizoi J.,Kidokoro S.,Maruyama K.,Nakajima J.,Nakashima K.,Mitsuda N.,Takiguchi Y.,Ohme-Takagi M.,Kondou Y.,Yoshizumi T.,Matsui M.,Shinozaki K.,and Yamaguchi-Shinozaki K.,2012,Arabidopsis growth regulating factor7 functions as a transcriptional repressor of abscisic acid-and osmotic stress-responsive genes,including DREB2A,Plant Cell,24(8):3393-3405
Knaap E.V.D.,Kim H.J.,and Kende H.,2000,A novel gibberellin-induced gene from rice and its potential regulatory role in stem growth,Plant Physiol.,122(3):695-704
Kuijt S.J.H.,Greco R.,Agalou A.,Shao J.,Hoen C.C.J.,Overnas E.,Osnato M.,Curiale S.,Meynard D.,van Gulik R.,de Faria Maraschin S.,Atallah M.,De Kam R.J.,Lamers G.E.M.,Guiderdoni E.,Rossini L.,Meijer A.H.,and Ouwerkerk P.B.F.,2014,Interaction between the GROWTH-REGU-LA-TING FACTOR and KNOTTED1-LIKE HOMEOBOX families of transcription factors,Plant Physiol.,164(4):1952-1966
Lee B.H.,Ko J.H.,Lee S.,Lee Y.,Pak J.H.,and Kim J.H.,2009,The Arabidopsis GRF-INTERACTING FACTOR gene family performs an overlapping function in determining organ size as well as multiple developmental properties,Plant Physiol.,151(2):655-668
Lee B.H.,Wynn A.N.,Franks R.G.,Hwang Y.,Lim J.,and Kim J.H.,2014,The Arabidopsis thaliana GRF-INTERACTINGFACTOR gene family plays an essential role in control of male and female reproductive development,Develop.Biol.,386(1):12-24
Li S.C.,Gao F.Y.,Xie K.L.,Zeng X.H.,Cao Y.,Zeng J.,He Z.S.,Ren Y.,Li W.B.,Deng Q.M.,Wang S.Q.,Zheng A.P.,Zhu J.,Liu H.N.,Wang L.X.,and Li P.,2016,The Osmi R396cOs GRF4-Os GIF1 regulatory module determines grain size and yield in rice,Plant Biotechnol.J.,14(11):2134-2146
Lu X.R.,Jia X.Y.,and Niu J.H.,2018,The present situation and prospects of cotton industry development in China,Zhongguo Nongye Kexue(Scientia Agricultura Sinica),51(1):26-36(卢秀茹,贾肖月,牛佳慧,2018,中国棉花产业发展现状及展望,中国农业科学,51(1):26-36)
Omidbakhshfard M.A.,Proost S.,Fujikura U.,and Mueller-Roeber B.,2015,Growth-regulating factors(GRFs):a small transcription factor family with important functions in plant biology,Molecular Plant,8(7):998-1010
Ruan X.L.,Wang J.S.,Liu H.Z.,and Zhao J.H.,2018,Identification and basic characteristic analysis of GRF gene family in Brassica napus L.,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),16(8):2420-2428(阮先乐,王俊生,刘红占,赵锦慧,2018,油菜GRF基因家族的鉴定和基本特征分析,分子植物育种,16(8):2420-2428)
Sun P.Y.,Zhang W.H.,Wang Y.H.,He Q.,Shu F.,Liu H.,Wang J.,Wang J.M.,Yuan L.P.,and Deng H.F.,2016,Os GRF4controls grain shape,panicle length and seed shattering in rice,J.Integr.Plant Biol.,58(10):836-847
Yang Y.H.,Wang S.N.,Xu H.,Sun H.Y.,Zhao H.S.,Chen D.F.,and Gao Z.M.,2018,Genome-wide identification of the enzyme genes involved in gibberellin biosynthesis and their expression analyses in moso bamboo,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),37(9):3966-3977(杨意宏,王思宁,徐浩,孙化雨,赵韩生,陈段芬,高志民,2018,毛竹赤霉素合成相关酶基因的全基因组鉴定和表达分析,基因组学与应用生物学,37(9):3966-3977)
Zhai J.M.,Luan Y.S.,and Cui J.J.,2013,Evolution and function analysis of mi R396 gene family,Zhiwu Yanjiu(Bulletin of Botanical Research),33(4):421-428(翟俊淼,栾雨时,崔娟娟,2013,mi R396基因家族的进化及功能分析,植物研究,33(4):421-428)
Zhang D.,Sun W.,Singh R.,Zheng Y.Y.,Cao Z.,Li M.F.,Lunde C.,Hake S.,and Zhang Z.X.,2018,GRF-interacting factor1regulates shoot architecture and meristem determinacy in Maize,Plant Cell,30(2):360-374
Zhou H.J.,2016,Genome wide analysis of PtGRF gene family and functional characterization of Pt GRF1/2d,Dissertation for Ph.D.,Chinese Academy of Forestry,Supervisor:Lu M.Z.,pp.1-10(周厚君,2016,杨树GRF基因家族分析及PtGRF1/2dd功能研究,博士学位论文,中国林业科学研究院,导师:卢孟柱,pp.1-10)
Debernardi J.M.,Mecchia M.A.,Vercruyssen L.,Smaczniak C.,Kaufmann K.,Inze D.,Rodriguez R.E.,and Palatnik J.F.,2014,Post-transcriptional control of GRF transcription factors by microRNA mi R396 and GIF co-activator affects leaf size and longevity,Plant J.,79(3):413-426
Horiguchi G.,Kim G.T.,and Tsukaya H.,2005,The transcription factor At GRF5 and the transcription coactivator AN3 regulate cell proliferation in leaf primordia of Arabidopsis thaliana,Plant J.,43(1):68-78
Kim J.H.,and Kende H.,2004,A transcriptional coactivator,AtGIF1,is involved in regulating leaf growth and morphology in Arabidopsis,Proc.Natl.Acad.Sci.USA,101(36):13374-13379
Kim J.H.,Chi D.,and Kenda H.,2003,The At GRF family of putative transcript ion factors is involved in leaf and cotyledon growth in Arabidopsis,Plant J.,36(1):94-104
Kim J.S.,Mizoi J.,Kidokoro S.,Maruyama K.,Nakajima J.,Nakashima K.,Mitsuda N.,Takiguchi Y.,Ohme-Takagi M.,Kondou Y.,Yoshizumi T.,Matsui M.,Shinozaki K.,and Yamaguchi-Shinozaki K.,2012,Arabidopsis growth regulating factor7 functions as a transcriptional repressor of abscisic acid-and osmotic stress-responsive genes,including DREB2A,Plant Cell,24(8):3393-3405
Knaap E.V.D.,Kim H.J.,and Kende H.,2000,A novel gibberellin-induced gene from rice and its potential regulatory role in stem growth,Plant Physiol.,122(3):695-704
Kuijt S.J.H.,Greco R.,Agalou A.,Shao J.,Hoen C.C.J.,Overnas E.,Osnato M.,Curiale S.,Meynard D.,van Gulik R.,de Faria Maraschin S.,Atallah M.,De Kam R.J.,Lamers G.E.M.,Guiderdoni E.,Rossini L.,Meijer A.H.,and Ouwerkerk P.B.F.,2014,Interaction between the GROWTH-REGU-LA-TING FACTOR and KNOTTED1-LIKE HOMEOBOX families of transcription factors,Plant Physiol.,164(4):1952-1966
Lee B.H.,Ko J.H.,Lee S.,Lee Y.,Pak J.H.,and Kim J.H.,2009,The Arabidopsis GRF-INTERACTING FACTOR gene family performs an overlapping function in determining organ size as well as multiple developmental properties,Plant Physiol.,151(2):655-668
Lee B.H.,Wynn A.N.,Franks R.G.,Hwang Y.,Lim J.,and Kim J.H.,2014,The Arabidopsis thaliana GRF-INTERACTINGFACTOR gene family plays an essential role in control of male and female reproductive development,Develop.Biol.,386(1):12-24
Li S.C.,Gao F.Y.,Xie K.L.,Zeng X.H.,Cao Y.,Zeng J.,He Z.S.,Ren Y.,Li W.B.,Deng Q.M.,Wang S.Q.,Zheng A.P.,Zhu J.,Liu H.N.,Wang L.X.,and Li P.,2016,The Osmi R396cOs GRF4-Os GIF1 regulatory module determines grain size and yield in rice,Plant Biotechnol.J.,14(11):2134-2146
Lu X.R.,Jia X.Y.,and Niu J.H.,2018,The present situation and prospects of cotton industry development in China,Zhongguo Nongye Kexue(Scientia Agricultura Sinica),51(1):26-36(卢秀茹,贾肖月,牛佳慧,2018,中国棉花产业发展现状及展望,中国农业科学,51(1):26-36)
Omidbakhshfard M.A.,Proost S.,Fujikura U.,and Mueller-Roeber B.,2015,Growth-regulating factors(GRFs):a small transcription factor family with important functions in plant biology,Molecular Plant,8(7):998-1010
Ruan X.L.,Wang J.S.,Liu H.Z.,and Zhao J.H.,2018,Identification and basic characteristic analysis of GRF gene family in Brassica napus L.,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),16(8):2420-2428(阮先乐,王俊生,刘红占,赵锦慧,2018,油菜GRF基因家族的鉴定和基本特征分析,分子植物育种,16(8):2420-2428)
Sun P.Y.,Zhang W.H.,Wang Y.H.,He Q.,Shu F.,Liu H.,Wang J.,Wang J.M.,Yuan L.P.,and Deng H.F.,2016,Os GRF4controls grain shape,panicle length and seed shattering in rice,J.Integr.Plant Biol.,58(10):836-847
Yang Y.H.,Wang S.N.,Xu H.,Sun H.Y.,Zhao H.S.,Chen D.F.,and Gao Z.M.,2018,Genome-wide identification of the enzyme genes involved in gibberellin biosynthesis and their expression analyses in moso bamboo,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),37(9):3966-3977(杨意宏,王思宁,徐浩,孙化雨,赵韩生,陈段芬,高志民,2018,毛竹赤霉素合成相关酶基因的全基因组鉴定和表达分析,基因组学与应用生物学,37(9):3966-3977)
Zhai J.M.,Luan Y.S.,and Cui J.J.,2013,Evolution and function analysis of mi R396 gene family,Zhiwu Yanjiu(Bulletin of Botanical Research),33(4):421-428(翟俊淼,栾雨时,崔娟娟,2013,mi R396基因家族的进化及功能分析,植物研究,33(4):421-428)
Zhang D.,Sun W.,Singh R.,Zheng Y.Y.,Cao Z.,Li M.F.,Lunde C.,Hake S.,and Zhang Z.X.,2018,GRF-interacting factor1regulates shoot architecture and meristem determinacy in Maize,Plant Cell,30(2):360-374
Zhou H.J.,2016,Genome wide analysis of PtGRF gene family and functional characterization of Pt GRF1/2d,Dissertation for Ph.D.,Chinese Academy of Forestry,Supervisor:Lu M.Z.,pp.1-10(周厚君,2016,杨树GRF基因家族分析及PtGRF1/2dd功能研究,博士学位论文,中国林业科学研究院,导师:卢孟柱,pp.1-10)