大豆凝集素类受体激酶家族全基因组学分析
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摘要
植物凝集素类受体激酶(LecRLKs)是一种重要的类受体蛋白激酶,广泛参与植物激素信号转导、胁迫反应、植株生长发育、生物固氮等多种生理生化反应。本研究对大豆中的GmLecRLKs基因家族进行了全基因组水平上的分析,在大豆中共找到205个GmLecRLKs家族成员,分布在19条染色体上;根据其含有的特征结构域不同,这些成员被分为L型、G型和C型三个亚家族;每个亚家族成员在结构域类型上有其各自的特点;GmLecRLKs基因在进化过程中比较保守,但在个别位点氨基酸受到了正选择作用。该研究结果对于深入了解LecRLKs家族在大豆中的进化规律和生物学功能具有十分重要的意义。
Plant lectin-like receptor kinases(LecRLKs) are a kind of important receptor-like protein kinases,which are widely involved in many physiological and biochemical reactions of plants, such as plant hormone signal transduction, stress response, plant growth and development, and biological nitrogen fixation. In this study, the GmLecRLKs gene family in soybean was analyzed at the whole genome level, and 205 GmLecRLKs family members were found, distributing on 19 chromosomes. Aaccording to their different characteristic domains, these GmLecRLKs were divided into G, L and C subfamilies. Each subfamily had its own characteristics in domain type.GmLecRLKs were relatively conservative in the evolution process, whereas positively selection occurred on certain amino acid sites of GmLecRLKs. These results would provide a basis for further study on the evolutionary mechanism and biological function of the GmLecRLKs family in soybean.
Plant lectin-like receptor kinases(LecRLKs) are a kind of important receptor-like protein kinases,which are widely involved in many physiological and biochemical reactions of plants, such as plant hormone signal transduction, stress response, plant growth and development, and biological nitrogen fixation. In this study, the GmLecRLKs gene family in soybean was analyzed at the whole genome level, and 205 GmLecRLKs family members were found, distributing on 19 chromosomes. Aaccording to their different characteristic domains, these GmLecRLKs were divided into G, L and C subfamilies. Each subfamily had its own characteristics in domain type.GmLecRLKs were relatively conservative in the evolution process, whereas positively selection occurred on certain amino acid sites of GmLecRLKs. These results would provide a basis for further study on the evolutionary mechanism and biological function of the GmLecRLKs family in soybean.
引文
Chen X.L.,Liu S.Y.,Sun T.,Liu Z.C.,Tao J.B.,Zhao Y.X.,and Wang A.X.,2017,Bioinformatics analysis on YABBY gene family in tomoto,Dongbei Nongye Daxue Xuebao(Journal of Northeast Agricultural University),48(10):11-19(陈秀玲,刘思源,孙婷,刘智琛,陶金宝,赵迎新,王傲雪,2017,番茄YABBY基因家族的生物信息学分析,东北农业大学学报,48(10):11-19)
Cheng S.F.,Duanmu H.Z.,Chen C.,Liu A.L.,Xiao J.L.,and Zhu Y.M.,2016,Whole genome identification of soybean MYBtranscription factors and bioinformatics analysis,Dadou Kexue(Soybean Science),35(1):52-57(成舒飞,端木惠子,陈超,刘艾琳,肖家雷,朱延明,2016,大豆MYB转录因子的全基因组鉴定及生物信息学分析,大豆科学,35(1):25-57)
Dai J.Y.,and Cheng J.L.,2008,HMMEditor:a visual editing tool for profile hidden Markov model,BMC Genomics,9(S1):S8
Deng K.Q.,2009,Bioinformatic anlysis and function investigation of Arabidopsis Lectin receptor like kinase LecRK-b2,Dissertation for Ph.D.,Hunan University,Supervisors:Liu X.M.,and Lin C.T.,pp.9-11(邓克勤,2009,植物凝集素类受体蛋白激酶LecRK-b2的生物信息学分析及基因功能研究,博士学位论文,湖南大学,导师:刘选明,林辰涛,pp.9-11)
Leister D.,2004,Tandem and segmental gene duplication and recombination in the evolution of plant disease resistance gene,Trends Genet.,20(3):116-122
Liu Y.Q.,Wu H.,Chen H.,Liu Y.L.,He J.,Kang H.,Sun Z.G.,Pan G.,Wang Q.,Hu J.L.,Zhou F.,Zhou K.N.,Zheng X.M.,Ren Y.L.,Chen L.M.,Wang Y.H.,Zhao Z.G.,Lin Q.B.,Wu F.Q.,Zhang X.,Guo X.P.,Cheng X.N.,Jiang L.,Wu C.Y.,Wang H.Y.,and Wan J.M.,2015,A gene cluster encoding lectin receptor kinases confers broad-spectrum and durable insect resistance in rice,Nat.Biotechnol.,33(3):301-305
Lu X.T.,2016,Mechanism of action of lectin receptor like kinase LecRKⅢ.1 and LecRKⅢ.2 genes in Arabidopsis thaliana,Thesis for M.S.,Hunan University,Supervisor:Guo X.H.,pp.1-6(陆秀涛,2016,拟南芥凝集素类受体激酶基因LecRKⅢ.1和LecRKⅢ.2的作用机制研究,硕士学位论文,湖南大学,导师:郭新红,pp.1-6)
Lu X.T.,He Z.,Hu S.,Xiao W.J.,Zhang C.,Li J.Y.,Huang J.,and Guo X.H.,2016,A preliminary study of nine Lectin receptor like kinase genes in Arabidopsis thaliana,Jiguang Shengwu Xuebao(Acta Laser Biology Sinica),25(1):61-68(陆秀涛,何壮,胡帅,肖文君,张骋,李金燕,黄吉,郭新红,2016,9个拟南芥凝集素类受体激酶基因功能的初步研究,激光生物学报,25(1):61-68)
Shi S.C.,Zhang R.Y.,Zhao Z.T.,Yang L.,and Ge W.N.,2018,Genome-wide analysis of the DREBs subfamily in foxtail millet,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),37(2):827-835(史松昌,张如月,赵振廷,杨磊,葛伟娜,2018,谷子DREBs亚家族的全基因组学分析,基因组学与应用生物学,37(2):827-835)
Shiu S.H.,and Bleecker A.B.,2003,Expansion of the receptor-like kinase/Pelle gene family and receptor-like proteins in Arabidopsis,Plant Physiol.,132(2):530-543
Singh P.,and Zimmerli L.,2013,Lectin receptor kinases in plant innate immunity,Front.Plant Sci.,4(4):124
Vaid N.,Macovei A.,and Tuteja N.,2013,Knights in action:lectin receptor-like kinases in plant development and stress responses,Mol.Plant,6(5):1405-1418
Vaid N.,Pandey P.K.,and Tuteja N.,2012,Genome-wide analysis of lectin receptor-like kinase family from Arabidopsis and rice,Plant Mol.Biol.,80(4-5):365-388
Wang J.P.,Sun P.C.,Li Y.X.,Liu Y.Z.,Yu J.G.,Ma X.L.,Sun S.R.,Yang N.S.,Xia R.X.,Lei T.Y.,Liu X.J.,Jiao B.B.,Xing Y.,Ge W.,Wang L.,Wang Z.Y.,Song X.M.,Yuan M.,Guo D.,Zhang L.,Zhang J.Q.,Jin D.C.,Chen W.,Pan Y.X.,Liu T.,Jin L.,Sun J.X.,Yu J.X.,Cheng R.,Duan X.Q.,Shen S.Q.,Qin J.,Zhang M.C.,Paterson A.H.,and Wang X.Y.,2017,Hierarchically aligning 10 legume genomes establishes a family-level genomics platform,Plant Physiol.,174(1):284-300
Wang Y.,Weide R.,Govers F.,and Bouwmeester K.,2015,L-type lectin receptor kinases in Nicotiana benthamiana and tomato and their role in phytophthora resistance,J.Exp.Bot.,66(21):6731-6743
Wang Y.,Ye J.Z.,Chang H.P.,Yuan C.Y.,Hu S.,Yue J.M.,and Guo X.H.,2012,Progresses on lectin receptor like kinase,Shengming Kexue Yanjiu(Life Science Research),16(3):266-271(王育,叶佳卓,常洪平,袁聪颖,胡帅,岳敬梅,郭新红,2012,植物凝集素类受体激酶的研究进展,生命科学研究,16(3):266-271)
Wu D.,2016,Adaptive evolution of soybean oil synthesis gene family,Thesis for M.S.,North China University of Technology,Supervisors:Wang W.J.,and Wang J.P.,pp.8-10(吴丹,2016,大豆油脂合成基因家族的适应性进化研究,硕士学位论文,华北理工大学,导师:王巍杰,王金鹏,pp.8-10)
Xu B.,and Yang Z.H.,2013,PAMLX:A graphical user interface for PAML,Mol.Biol.Evol.,30(12):2723-2724
Yang Y.,LabbéJ.,Muchero W.,Yang X.,Jawdy S.S.,Kennedy M.,Johnson J.,Sreedasyam A.,Schmutz J.,and Tuskan G.A.,2016,Genome-wide analysis of lectin receptor-like kinases in Populus,BMC Genomics,17:699
Zhu Y.M.,Zhu Y.,Duanmu H.Z.,Xiao J.L.,Yu Y.,and Liu A.L.,2015,Bioinformatics analysis of GmUGD gene family in soybean genome,Dongbei Nongye Daxue Xuebao(Journal of Northeast Agricultural University),46(9):23-29(朱延明,朱毅,端木慧子,肖佳雷,于洋,刘艾林,2015,大豆GmUGD基因家族生物信息学分析,东北农业大学学报,46(9):23-29)
Cheng S.F.,Duanmu H.Z.,Chen C.,Liu A.L.,Xiao J.L.,and Zhu Y.M.,2016,Whole genome identification of soybean MYBtranscription factors and bioinformatics analysis,Dadou Kexue(Soybean Science),35(1):52-57(成舒飞,端木惠子,陈超,刘艾琳,肖家雷,朱延明,2016,大豆MYB转录因子的全基因组鉴定及生物信息学分析,大豆科学,35(1):25-57)
Dai J.Y.,and Cheng J.L.,2008,HMMEditor:a visual editing tool for profile hidden Markov model,BMC Genomics,9(S1):S8
Deng K.Q.,2009,Bioinformatic anlysis and function investigation of Arabidopsis Lectin receptor like kinase LecRK-b2,Dissertation for Ph.D.,Hunan University,Supervisors:Liu X.M.,and Lin C.T.,pp.9-11(邓克勤,2009,植物凝集素类受体蛋白激酶LecRK-b2的生物信息学分析及基因功能研究,博士学位论文,湖南大学,导师:刘选明,林辰涛,pp.9-11)
Leister D.,2004,Tandem and segmental gene duplication and recombination in the evolution of plant disease resistance gene,Trends Genet.,20(3):116-122
Liu Y.Q.,Wu H.,Chen H.,Liu Y.L.,He J.,Kang H.,Sun Z.G.,Pan G.,Wang Q.,Hu J.L.,Zhou F.,Zhou K.N.,Zheng X.M.,Ren Y.L.,Chen L.M.,Wang Y.H.,Zhao Z.G.,Lin Q.B.,Wu F.Q.,Zhang X.,Guo X.P.,Cheng X.N.,Jiang L.,Wu C.Y.,Wang H.Y.,and Wan J.M.,2015,A gene cluster encoding lectin receptor kinases confers broad-spectrum and durable insect resistance in rice,Nat.Biotechnol.,33(3):301-305
Lu X.T.,2016,Mechanism of action of lectin receptor like kinase LecRKⅢ.1 and LecRKⅢ.2 genes in Arabidopsis thaliana,Thesis for M.S.,Hunan University,Supervisor:Guo X.H.,pp.1-6(陆秀涛,2016,拟南芥凝集素类受体激酶基因LecRKⅢ.1和LecRKⅢ.2的作用机制研究,硕士学位论文,湖南大学,导师:郭新红,pp.1-6)
Lu X.T.,He Z.,Hu S.,Xiao W.J.,Zhang C.,Li J.Y.,Huang J.,and Guo X.H.,2016,A preliminary study of nine Lectin receptor like kinase genes in Arabidopsis thaliana,Jiguang Shengwu Xuebao(Acta Laser Biology Sinica),25(1):61-68(陆秀涛,何壮,胡帅,肖文君,张骋,李金燕,黄吉,郭新红,2016,9个拟南芥凝集素类受体激酶基因功能的初步研究,激光生物学报,25(1):61-68)
Shi S.C.,Zhang R.Y.,Zhao Z.T.,Yang L.,and Ge W.N.,2018,Genome-wide analysis of the DREBs subfamily in foxtail millet,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),37(2):827-835(史松昌,张如月,赵振廷,杨磊,葛伟娜,2018,谷子DREBs亚家族的全基因组学分析,基因组学与应用生物学,37(2):827-835)
Shiu S.H.,and Bleecker A.B.,2003,Expansion of the receptor-like kinase/Pelle gene family and receptor-like proteins in Arabidopsis,Plant Physiol.,132(2):530-543
Singh P.,and Zimmerli L.,2013,Lectin receptor kinases in plant innate immunity,Front.Plant Sci.,4(4):124
Vaid N.,Macovei A.,and Tuteja N.,2013,Knights in action:lectin receptor-like kinases in plant development and stress responses,Mol.Plant,6(5):1405-1418
Vaid N.,Pandey P.K.,and Tuteja N.,2012,Genome-wide analysis of lectin receptor-like kinase family from Arabidopsis and rice,Plant Mol.Biol.,80(4-5):365-388
Wang J.P.,Sun P.C.,Li Y.X.,Liu Y.Z.,Yu J.G.,Ma X.L.,Sun S.R.,Yang N.S.,Xia R.X.,Lei T.Y.,Liu X.J.,Jiao B.B.,Xing Y.,Ge W.,Wang L.,Wang Z.Y.,Song X.M.,Yuan M.,Guo D.,Zhang L.,Zhang J.Q.,Jin D.C.,Chen W.,Pan Y.X.,Liu T.,Jin L.,Sun J.X.,Yu J.X.,Cheng R.,Duan X.Q.,Shen S.Q.,Qin J.,Zhang M.C.,Paterson A.H.,and Wang X.Y.,2017,Hierarchically aligning 10 legume genomes establishes a family-level genomics platform,Plant Physiol.,174(1):284-300
Wang Y.,Weide R.,Govers F.,and Bouwmeester K.,2015,L-type lectin receptor kinases in Nicotiana benthamiana and tomato and their role in phytophthora resistance,J.Exp.Bot.,66(21):6731-6743
Wang Y.,Ye J.Z.,Chang H.P.,Yuan C.Y.,Hu S.,Yue J.M.,and Guo X.H.,2012,Progresses on lectin receptor like kinase,Shengming Kexue Yanjiu(Life Science Research),16(3):266-271(王育,叶佳卓,常洪平,袁聪颖,胡帅,岳敬梅,郭新红,2012,植物凝集素类受体激酶的研究进展,生命科学研究,16(3):266-271)
Wu D.,2016,Adaptive evolution of soybean oil synthesis gene family,Thesis for M.S.,North China University of Technology,Supervisors:Wang W.J.,and Wang J.P.,pp.8-10(吴丹,2016,大豆油脂合成基因家族的适应性进化研究,硕士学位论文,华北理工大学,导师:王巍杰,王金鹏,pp.8-10)
Xu B.,and Yang Z.H.,2013,PAMLX:A graphical user interface for PAML,Mol.Biol.Evol.,30(12):2723-2724
Yang Y.,LabbéJ.,Muchero W.,Yang X.,Jawdy S.S.,Kennedy M.,Johnson J.,Sreedasyam A.,Schmutz J.,and Tuskan G.A.,2016,Genome-wide analysis of lectin receptor-like kinases in Populus,BMC Genomics,17:699
Zhu Y.M.,Zhu Y.,Duanmu H.Z.,Xiao J.L.,Yu Y.,and Liu A.L.,2015,Bioinformatics analysis of GmUGD gene family in soybean genome,Dongbei Nongye Daxue Xuebao(Journal of Northeast Agricultural University),46(9):23-29(朱延明,朱毅,端木慧子,肖佳雷,于洋,刘艾林,2015,大豆GmUGD基因家族生物信息学分析,东北农业大学学报,46(9):23-29)
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