亚洲棉、雷蒙德棉和陆地棉NRAMP基因家族的鉴定和进化分析
|
摘要
自然抗性相关巨噬细胞蛋白(NRAMP)家族是跨膜转运蛋白家族,参与多种金属离子的转运过程。为了更好了解棉花NRAMP基因的成员和特征,二倍体和四倍体棉花之间的进化关系,本研究利用二倍体亚洲棉、雷蒙德棉和陆地棉基因组的氨基酸序列对三个棉种中的NRAMP家族成员进行鉴定,分析了NRAMP家族的种类、理化性质、进化关系、基因结构、蛋白基序、染色体定位、共线性关系和选择压力。结果显示,在二倍体亚洲棉基因组(A)中确定12个成员,在二倍体雷蒙德棉基因组(D)中确定15个成员,在四倍体陆地棉基因组(At, Dt)中确定23个成员。按照进化关系的远近将这50个成员分为3个亚类,进化关系较近的成员之间具有更为相似的理化性质、基因结构和蛋白质基序;通过和其他植物的进化关系分析发现,NRAMP基因在单子叶和双子叶植物分离前已经产生;染色体定位发现NRAMP在染色体上的分布并不规律;共线性分析和选择压力分析表明,片段复制在棉花NRAMP基因的遗传进化过程中发挥主导作用,同源基因对在进化过程中处于纯化选择。
The natural resistance-associated macrophage protein(NRAMP) family is a transmembrane transporter family, which participates in transport process of multiple metal ions. In order to better understand the members and characteristics of NRAMP gene in cotton and the evolutionary relationship between diploid and tetraploid cotton, the NRAMP family members in diploid Gossypium arboretum, Gossypium raimondii and Gossypium hirsutum were identified by amino acid sequences of the genomes of these three cotton varieties. The species, physical and chemical properties, evolutionary relationships, gene structure, protein motifs, chromosome location, collinearity and selection pressure of NRAMP family were analyzed. The results showed that 12, 15 and 23 genes were identi fied in the genomes of the diploid progenitor Gossypium arboretum(A), Gossypium raimondii(D) and the tetraploid Gossypium hirsutum(At, Dt), respectively. The 50 members were divided into three subfamilies based on the evolutionary relationship, and genes with closer relationship possessed similar physical properties, gene structure and protein motif. The analysis of evolutionary relationships with other plants showed that NRAMP gene had been produced before the isolation of monocotyledons and dicotyledons. Chromosomal localization revealed that the distribution of NRAMP on chromosomes was not regular. Colinearity analysis and selection pressure analysis indicated that fragment replication played a dominant role in the genetic evolution of NRAMP gene in cotton, and homologous genes were in the purification and selection process.
The natural resistance-associated macrophage protein(NRAMP) family is a transmembrane transporter family, which participates in transport process of multiple metal ions. In order to better understand the members and characteristics of NRAMP gene in cotton and the evolutionary relationship between diploid and tetraploid cotton, the NRAMP family members in diploid Gossypium arboretum, Gossypium raimondii and Gossypium hirsutum were identified by amino acid sequences of the genomes of these three cotton varieties. The species, physical and chemical properties, evolutionary relationships, gene structure, protein motifs, chromosome location, collinearity and selection pressure of NRAMP family were analyzed. The results showed that 12, 15 and 23 genes were identi fied in the genomes of the diploid progenitor Gossypium arboretum(A), Gossypium raimondii(D) and the tetraploid Gossypium hirsutum(At, Dt), respectively. The 50 members were divided into three subfamilies based on the evolutionary relationship, and genes with closer relationship possessed similar physical properties, gene structure and protein motif. The analysis of evolutionary relationships with other plants showed that NRAMP gene had been produced before the isolation of monocotyledons and dicotyledons. Chromosomal localization revealed that the distribution of NRAMP on chromosomes was not regular. Colinearity analysis and selection pressure analysis indicated that fragment replication played a dominant role in the genetic evolution of NRAMP gene in cotton, and homologous genes were in the purification and selection process.
引文
Bian B.,Kage shima S.,Yano K.,Fujiwara T.,and Kamiya T.,2018,Screening for low-Mn-sensitive Arabidopsis thaliana mutants identified novel alleles of nramp1 and pgsip6,J.Exp.Bot.,69(7):1795-1803
Cailliatte R.,Lapeyre B.,Briat J.F.,Mari S.,and Curie C.,2009,The NRAMP6 metal transporter contributes to cadmium toxicity,Biochem.J.,422(2):217-228
Cailliatte R.,Schikora A.,Briat J.F.,Mari S.,and Curie C.,2010,High-affinity manganese uptake by the metal transporter NRAMP1 is essential for Arabidopsis growth in low manganese conditions,Plant Cell,22(3):904-917
Cannon S.B.,Mitra A.,Baumgarten A.,Young N.D.,and May G.,2004,The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana,BMC Plant Biol.,4:10
Curie C.,Alonso J.M.,Jean M.L.,Ecker J.R.,and Briat J.F.,2000,Involvement of NRAMP1 from Arabidopsis thaliana in iron transport,Biochem.J.,3(3):749
Feng J.,Li Y.,Hashad M.,Schurr E.,Gros P.,Adams L.G.,and Templeton J.W.,1996,Bovine natural resistance associated macrophage protein 1(Nramp1)gene,Genome Res.,6(10):956-964
Hu R.F.,Lin G.Q.,Zhang G.Q.,Teng Z.Y.,and Chen Z.X.,2011,Analysis on soybean Nramp gene family sequence features and phylogeny,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),9(2):245-250(胡润芳,林国强,张广庆,滕振勇,陈志雄,2011,大豆Nramp基因家族的序列特征与亲缘关系分析,分子植物育种,9(2):245-250)
Lanquar V.,Lelièvre F.,Bolte S.,Hames C.,Alcon C.,Neumann D.,Vansuyt G.,Curie C.,Schroder A.,Kramer U.,Barbier-Brygoo H.,and Thomine S.,2014,Mobilization of vacuolar iron by AtNRAMP3 and AtNRAMP4 is essential for seed germination on low iron,EMBO J.,24(23):4041-4051
Larkin M.A.,Blackshields G.,Brown N.P.,Chenna R.,McGettigan P.A.,McWilliam H.,Valentin F.,Wallace I.M.,Wilm A.,Lopez R.,Thompson J.D.,Gibson T.J.,and Higgins D.G.,2007,Clustal W and Clustal X version 2.0,Bioinformatics,23(21):2947-2948
Mser P.,Thomine S.,Schroeder J.I.,Ward J.M.,Hirschi K.,Sze H.,Talke I.N.,Amtmann A.,Maathuis F.J.,Sanders D.,Harper J.F.,Tchieu J.,Gribskov M.,Persans M.W.,Salt D.E.,Kim S.A.,and Guerinot M.L.,2001,Phylogenetic relationships within cation transporter families of Arabidopsis,Plant Physiol.,126(4):1646-1667
Nevo Y.,and Nelson N.,2006,The NRAMP family of metal-ion transporters,Biochimica Et Biochim.Biophys.Acta,1763(7):609-620
Qin L.,Han P.,Chen L.,Walk T.C.,Li Y.,Hu X.,Xie L.,Liao H.,and Liao X.,2017,Genome-wide identification and expression analysis of NRAMP family genes in soybean(Glycine Max L.),Front.Plant Sci.,8:1436
Vacca G.M.,Pazzola M.,Pisano C.,Carcanqiu V.,Diaz M.L.,Nieddu M.,Robledo R.,Mezzanotte R.,and Dettori M.L.,2011,Chromosomal localisation and genetic variation of the SLC11A1 gene in goats(Capra hircus),Vet.J.,190(1):60-65
Vatansever R.,Filiz E.,and Ozyigit I.I.,2016,In silico analysis of Mn transporters(NRAMP1)in various plant species,Mol.Biol.Rep.,43(3):151-163
Vidal S.M.,Malo D.,Vogan K.,Skamene E.,and Gros P.,1993,Natural resistance to infection with intracellular parasites:isolation of a candidate for Bcg,Cell,73(3):469-485
West A.H.,Clark D.J.,Martin J.,Neupert W.,Hartl F.U.,and Horwich A.L.,1992,Two related genes encoding extremely hydrophobic proteins suppress a lethal mutation in the yeast mitochondrial processing enhancing protein,J.Biol.Chem.,267(34):24625-24633
Zhang B.J.,Zhang X.X.,and Luo L.G.,2013,The major gene families related to cadmium absorption and transportation in plants,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),32(1):127-134(张标金,张祥喜,罗林广,2013,与植物镉吸收转运相关的主要基因家族,基因组学与应用生物学,32(1):127-134)
Cailliatte R.,Lapeyre B.,Briat J.F.,Mari S.,and Curie C.,2009,The NRAMP6 metal transporter contributes to cadmium toxicity,Biochem.J.,422(2):217-228
Cailliatte R.,Schikora A.,Briat J.F.,Mari S.,and Curie C.,2010,High-affinity manganese uptake by the metal transporter NRAMP1 is essential for Arabidopsis growth in low manganese conditions,Plant Cell,22(3):904-917
Cannon S.B.,Mitra A.,Baumgarten A.,Young N.D.,and May G.,2004,The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana,BMC Plant Biol.,4:10
Curie C.,Alonso J.M.,Jean M.L.,Ecker J.R.,and Briat J.F.,2000,Involvement of NRAMP1 from Arabidopsis thaliana in iron transport,Biochem.J.,3(3):749
Feng J.,Li Y.,Hashad M.,Schurr E.,Gros P.,Adams L.G.,and Templeton J.W.,1996,Bovine natural resistance associated macrophage protein 1(Nramp1)gene,Genome Res.,6(10):956-964
Hu R.F.,Lin G.Q.,Zhang G.Q.,Teng Z.Y.,and Chen Z.X.,2011,Analysis on soybean Nramp gene family sequence features and phylogeny,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),9(2):245-250(胡润芳,林国强,张广庆,滕振勇,陈志雄,2011,大豆Nramp基因家族的序列特征与亲缘关系分析,分子植物育种,9(2):245-250)
Lanquar V.,Lelièvre F.,Bolte S.,Hames C.,Alcon C.,Neumann D.,Vansuyt G.,Curie C.,Schroder A.,Kramer U.,Barbier-Brygoo H.,and Thomine S.,2014,Mobilization of vacuolar iron by AtNRAMP3 and AtNRAMP4 is essential for seed germination on low iron,EMBO J.,24(23):4041-4051
Larkin M.A.,Blackshields G.,Brown N.P.,Chenna R.,McGettigan P.A.,McWilliam H.,Valentin F.,Wallace I.M.,Wilm A.,Lopez R.,Thompson J.D.,Gibson T.J.,and Higgins D.G.,2007,Clustal W and Clustal X version 2.0,Bioinformatics,23(21):2947-2948
Mser P.,Thomine S.,Schroeder J.I.,Ward J.M.,Hirschi K.,Sze H.,Talke I.N.,Amtmann A.,Maathuis F.J.,Sanders D.,Harper J.F.,Tchieu J.,Gribskov M.,Persans M.W.,Salt D.E.,Kim S.A.,and Guerinot M.L.,2001,Phylogenetic relationships within cation transporter families of Arabidopsis,Plant Physiol.,126(4):1646-1667
Nevo Y.,and Nelson N.,2006,The NRAMP family of metal-ion transporters,Biochimica Et Biochim.Biophys.Acta,1763(7):609-620
Qin L.,Han P.,Chen L.,Walk T.C.,Li Y.,Hu X.,Xie L.,Liao H.,and Liao X.,2017,Genome-wide identification and expression analysis of NRAMP family genes in soybean(Glycine Max L.),Front.Plant Sci.,8:1436
Vacca G.M.,Pazzola M.,Pisano C.,Carcanqiu V.,Diaz M.L.,Nieddu M.,Robledo R.,Mezzanotte R.,and Dettori M.L.,2011,Chromosomal localisation and genetic variation of the SLC11A1 gene in goats(Capra hircus),Vet.J.,190(1):60-65
Vatansever R.,Filiz E.,and Ozyigit I.I.,2016,In silico analysis of Mn transporters(NRAMP1)in various plant species,Mol.Biol.Rep.,43(3):151-163
Vidal S.M.,Malo D.,Vogan K.,Skamene E.,and Gros P.,1993,Natural resistance to infection with intracellular parasites:isolation of a candidate for Bcg,Cell,73(3):469-485
West A.H.,Clark D.J.,Martin J.,Neupert W.,Hartl F.U.,and Horwich A.L.,1992,Two related genes encoding extremely hydrophobic proteins suppress a lethal mutation in the yeast mitochondrial processing enhancing protein,J.Biol.Chem.,267(34):24625-24633
Zhang B.J.,Zhang X.X.,and Luo L.G.,2013,The major gene families related to cadmium absorption and transportation in plants,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),32(1):127-134(张标金,张祥喜,罗林广,2013,与植物镉吸收转运相关的主要基因家族,基因组学与应用生物学,32(1):127-134)