斑点叉尾鮰Cbx基因家族的全基因组鉴定与进化分析
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摘要
利用Cbx家族基因高度保守的Chromo结构域氨基酸序列作为种子序列,检索斑点叉尾鮰(Ictalurus punetaus)基因组注释的蛋白数据库,共鉴定分离出14个Cbx基因。并在全基因组水平对斑点叉尾鮰Cbx基因家族进行了保守结构域序列、进化、基因结构、染色体定位的系统分析。本研究中鉴定出的斑点叉尾鮰Cbx家族基因蛋白序列与已知的人类、小鼠、鸡、斑马鱼等物种Cbx蛋白序列构建系统进化树。根据系统进化树分析结果,14个斑点叉尾鮰Cbx基因分成两个亚族,5个隶属于Hp1s亚族,9个隶属于PcGs亚族。Cbx基因主要分布于斑点叉尾鮰7条染色体中,且呈不均匀分布。本研究对于后续斑点叉尾鮰Cbx基因家族深入的功能验证及分子作用机制研究具有重要的意义,也为日益丰富的水产基因组资源的挖掘利用提供了参考。
Chromobox(Cbx) family proteins are transcriptional repressors that play diverse regulatory roles in epigenetic and developmental processes. In the study, we aimed to identify the Cbx family members in the channel catfish genome and analyze their phylogenetic patterns. Cbx genes were identified from the whole genome of channel catfish(Ictalurus punetaus) by bioinformatics methods. A total of 14 Cbx genes were identified. The obtained amino acid sequences were analyzed with DNAMAN 5.0, WebLogo 3, MEGA 5.1, MapInspect and MEME bioinformatics softwares. A phylogenetic analysis was conducted based on the alignment of the Cbx proteins from Ictalurus punetaus, Homo sapiens, Mus musculus, Gallus gallus, Danio rerio and so on. 14 Cbx genes divided into two subgroups based on phylogenetic analyses, five members in Hp1s subgroup and nine members in Pc Gs subgroup, and distributed on seven chromosomes. This study puts forward a comprehensive overview of the Cbx gene family in channel catfish and provides new insights into the formation of this gene family.
Chromobox(Cbx) family proteins are transcriptional repressors that play diverse regulatory roles in epigenetic and developmental processes. In the study, we aimed to identify the Cbx family members in the channel catfish genome and analyze their phylogenetic patterns. Cbx genes were identified from the whole genome of channel catfish(Ictalurus punetaus) by bioinformatics methods. A total of 14 Cbx genes were identified. The obtained amino acid sequences were analyzed with DNAMAN 5.0, WebLogo 3, MEGA 5.1, MapInspect and MEME bioinformatics softwares. A phylogenetic analysis was conducted based on the alignment of the Cbx proteins from Ictalurus punetaus, Homo sapiens, Mus musculus, Gallus gallus, Danio rerio and so on. 14 Cbx genes divided into two subgroups based on phylogenetic analyses, five members in Hp1s subgroup and nine members in Pc Gs subgroup, and distributed on seven chromosomes. This study puts forward a comprehensive overview of the Cbx gene family in channel catfish and provides new insights into the formation of this gene family.
引文
Aloia L.,Di Stefano B.,and Di Croce L.,2013,Polycomb complexes in stem cells and embryonic development,Dev.,140(12):2525-2534
Bailey T.L.,Boden M.,Buske F.A.,Frith M.,Grant C.E.,Clementi L.,Ren J.,Li W.W.,and Noble W.S.,2009,MEME SUITE:tools for motif discovery and searching,Nucleic Acids Res.,37(Web Server issue):W202-208
Bernstein B.E.,Mikkelsen T.S.,Xie X.,Kamal M.,Huebert D.J.,Cuff J.,Fry B.,Meissner A.,Wernig M.,Plath K.,Jaenisch R.,Wagschal A.,Feil R.,Schreiber S.L.,and Lander E.S.,2006,A bivalent chromatin structure marks key developmental genes in embryonic stem cells,Cell,125(2):315-326
Biason-Lauber A.,Konrad D.,Meyer M.,DeBeaufort C.,and Schoenle E.J.,2009,Ovaries and female phenotype in a girl with 46,XY karyotype and mutations in the CBX2 gene,Am.J.Hum.Genet.,84(5):658-663
Chen X.H.,Zhong L.Q.,Bian C.,Xu P.,Qiu Y.,You X.X.,Zhang S.Y.,Huang Y.,Li J.,Wang M.H.,Qin Q.,Zhu X.H.,Peng C.,Wong A.,Zhu Z.F.,Wang M.,Gu R.B.,Xu J.M.,Shi Q.,and Bian W.J.,2016,High-quality genome assembly of channel catfish,Ictalurus punctatus,Giga Science,5:39
Crooks G.E.,Hon G.,Chandonia J.M.,and Brenner S.E.,2004,WebLogo:A sequence logo generator,Genome Res.,14(6):1188-1190
Dehal P.,and Boore J.L.,2005,Two rounds of whole genome duplication in the ancestral vertebrate,PLoS Biol.,3:e314
Dihazi G.H.,Jahn O.,Tampe B.,Zeisberg M.,Müller C.,Müller G.A.,and Dihazi H.,2015,Proteomic analysis of embryonic kidney development:heterochromatin proteins as epigenetic regulators of nephrogenesis,Sci.Rep.,5:13951
Fischle W.,Wang Y.,Jacobs S.A.,Kim Y.C.,Allis C.D.,and Khorasanizadeh S.,2003,Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3by Polycomb and HP1 chromodomains,Gene Dev.,17(15):1870-1881
Guan S.L.,Wang J.,Xie Y.,and Cheng B.,2017,Structural and functional diversity of mammalian CBX proteins,Zhongguo Kexue:Shengming Kexue(Scientia Sinica(Vitae)),47(8):847-862(关珊丽,王健,谢忆,程博,2017,多梳蛋白CBX家族在哺乳动物中结构与功能多样性的研究进展,中国科学:生命科学,47(8):847-862)
Guo A.Y.,Zhu Q.H.,Chen X.,and Luo J.C.,2007,GSDS:a gene structure display server,Hereditas,29(8):1023-1026
Gwen L.,Lori W.,and Raul U.,2006,The heterochromatin protein 1 family,Genome Bio.,7:228
Le F.P.,Volkel P.,and Angrand P.O.,2011,The zebrafish genes encoding the Polycomb repressive complex(PRC)1,Gene,475(1):10-21
Liu X.Y.,Zhang X.B.,Li M.H.,Zheng S.Q.,Liu Z.L.,Cheng Y.Y.,and Wang D.S.,2017,Genome-wide identification,evolution of chromobox family genes and their expression in Nile tilapia,Comp.Biochem.Physiol.B Biochem.Mol.Biol.,203:25-34
Liu Z.J.,Liu S.K.,Yao J.,Bao L.S.,Zhang J.R.,Li Y.,Jiang C.,Sun L.Y.,Wang R.J.,Zhang Y.,Zhou T.,Zeng Q.F.,Fu Q.,Gao S.,Li N.,Koren S.,Jiang Y.L.,Zimin A.,Xu P.,Phillippy A.M.,Geng X.,Song L.,Sun F.Y.,Li C.,Wang X.Z.,Chen A.,Jin Y.L.,Yuan Z.H.,Yang Y.J.,Tan S.X.,Peatman E.,Lu J.G.,Qin Z.K.,Dunham R.,Li Z.X.,Sonstegard T.,Feng J.B.,Danzmann R.G.,Schroeder S.,Scheffler B.,Duke M.V.,Ballard L.,Kucuktas H.,Kaltenboeck L.,Liu H.X.,Armbruster J.,Xie Y.J.,Kirby M.L.,Tian Y.,Flanagan M.E.,Mu W.J.,and Waldbieser G.C.,2016,The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts,Nat.Commun.,7:11757
Ma R.G.,Zhang Y.,Sun T.T,and Cheng B.,2014,Epigenetic regulation by polycomb group complexes:focus on roles of CBX proteins,J.Zhejiang Univ.Sci.B,15(5):412-428
Ren X.,and Kerppola T.K.,2011,REST interacts with Cbx proteins and regulates polycomb repressive complex 1 occupancy at RE1 elements,Mol.Cell.Bio.,31(10):2100-2110
Spring J.,1997,Vertebrate evolution by interspecific hybridization-are we polyploid,FEBS Lett,400(1):2-8
Tamura K.,Stecher G.,Peterson D.,Filipski A.,and Kumar S.,2013,Mega 6:molecular evolutionary genetics analysis version6.0,Mol.Biol.Evol.,30(12):2725-2729
Taylor J.S,Braasch I.,Frickey T.,Meyer A.,and Van de Peer Y.,2003,Genome duplication,a trait shared by 22 000 species of ray-finned fish,Genome Res.,13(3):382-390
Wotton D.,and Merrill J.C.,2007,Pc2 and SUMOylation,Biochem.Soc.Trans.,35(6):1401-1404
Bailey T.L.,Boden M.,Buske F.A.,Frith M.,Grant C.E.,Clementi L.,Ren J.,Li W.W.,and Noble W.S.,2009,MEME SUITE:tools for motif discovery and searching,Nucleic Acids Res.,37(Web Server issue):W202-208
Bernstein B.E.,Mikkelsen T.S.,Xie X.,Kamal M.,Huebert D.J.,Cuff J.,Fry B.,Meissner A.,Wernig M.,Plath K.,Jaenisch R.,Wagschal A.,Feil R.,Schreiber S.L.,and Lander E.S.,2006,A bivalent chromatin structure marks key developmental genes in embryonic stem cells,Cell,125(2):315-326
Biason-Lauber A.,Konrad D.,Meyer M.,DeBeaufort C.,and Schoenle E.J.,2009,Ovaries and female phenotype in a girl with 46,XY karyotype and mutations in the CBX2 gene,Am.J.Hum.Genet.,84(5):658-663
Chen X.H.,Zhong L.Q.,Bian C.,Xu P.,Qiu Y.,You X.X.,Zhang S.Y.,Huang Y.,Li J.,Wang M.H.,Qin Q.,Zhu X.H.,Peng C.,Wong A.,Zhu Z.F.,Wang M.,Gu R.B.,Xu J.M.,Shi Q.,and Bian W.J.,2016,High-quality genome assembly of channel catfish,Ictalurus punctatus,Giga Science,5:39
Crooks G.E.,Hon G.,Chandonia J.M.,and Brenner S.E.,2004,WebLogo:A sequence logo generator,Genome Res.,14(6):1188-1190
Dehal P.,and Boore J.L.,2005,Two rounds of whole genome duplication in the ancestral vertebrate,PLoS Biol.,3:e314
Dihazi G.H.,Jahn O.,Tampe B.,Zeisberg M.,Müller C.,Müller G.A.,and Dihazi H.,2015,Proteomic analysis of embryonic kidney development:heterochromatin proteins as epigenetic regulators of nephrogenesis,Sci.Rep.,5:13951
Fischle W.,Wang Y.,Jacobs S.A.,Kim Y.C.,Allis C.D.,and Khorasanizadeh S.,2003,Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3by Polycomb and HP1 chromodomains,Gene Dev.,17(15):1870-1881
Guan S.L.,Wang J.,Xie Y.,and Cheng B.,2017,Structural and functional diversity of mammalian CBX proteins,Zhongguo Kexue:Shengming Kexue(Scientia Sinica(Vitae)),47(8):847-862(关珊丽,王健,谢忆,程博,2017,多梳蛋白CBX家族在哺乳动物中结构与功能多样性的研究进展,中国科学:生命科学,47(8):847-862)
Guo A.Y.,Zhu Q.H.,Chen X.,and Luo J.C.,2007,GSDS:a gene structure display server,Hereditas,29(8):1023-1026
Gwen L.,Lori W.,and Raul U.,2006,The heterochromatin protein 1 family,Genome Bio.,7:228
Le F.P.,Volkel P.,and Angrand P.O.,2011,The zebrafish genes encoding the Polycomb repressive complex(PRC)1,Gene,475(1):10-21
Liu X.Y.,Zhang X.B.,Li M.H.,Zheng S.Q.,Liu Z.L.,Cheng Y.Y.,and Wang D.S.,2017,Genome-wide identification,evolution of chromobox family genes and their expression in Nile tilapia,Comp.Biochem.Physiol.B Biochem.Mol.Biol.,203:25-34
Liu Z.J.,Liu S.K.,Yao J.,Bao L.S.,Zhang J.R.,Li Y.,Jiang C.,Sun L.Y.,Wang R.J.,Zhang Y.,Zhou T.,Zeng Q.F.,Fu Q.,Gao S.,Li N.,Koren S.,Jiang Y.L.,Zimin A.,Xu P.,Phillippy A.M.,Geng X.,Song L.,Sun F.Y.,Li C.,Wang X.Z.,Chen A.,Jin Y.L.,Yuan Z.H.,Yang Y.J.,Tan S.X.,Peatman E.,Lu J.G.,Qin Z.K.,Dunham R.,Li Z.X.,Sonstegard T.,Feng J.B.,Danzmann R.G.,Schroeder S.,Scheffler B.,Duke M.V.,Ballard L.,Kucuktas H.,Kaltenboeck L.,Liu H.X.,Armbruster J.,Xie Y.J.,Kirby M.L.,Tian Y.,Flanagan M.E.,Mu W.J.,and Waldbieser G.C.,2016,The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts,Nat.Commun.,7:11757
Ma R.G.,Zhang Y.,Sun T.T,and Cheng B.,2014,Epigenetic regulation by polycomb group complexes:focus on roles of CBX proteins,J.Zhejiang Univ.Sci.B,15(5):412-428
Ren X.,and Kerppola T.K.,2011,REST interacts with Cbx proteins and regulates polycomb repressive complex 1 occupancy at RE1 elements,Mol.Cell.Bio.,31(10):2100-2110
Spring J.,1997,Vertebrate evolution by interspecific hybridization-are we polyploid,FEBS Lett,400(1):2-8
Tamura K.,Stecher G.,Peterson D.,Filipski A.,and Kumar S.,2013,Mega 6:molecular evolutionary genetics analysis version6.0,Mol.Biol.Evol.,30(12):2725-2729
Taylor J.S,Braasch I.,Frickey T.,Meyer A.,and Van de Peer Y.,2003,Genome duplication,a trait shared by 22 000 species of ray-finned fish,Genome Res.,13(3):382-390
Wotton D.,and Merrill J.C.,2007,Pc2 and SUMOylation,Biochem.Soc.Trans.,35(6):1401-1404