运用线粒体COⅠ基因分析深圳海域石珊瑚系统发育关系
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摘要
通过COⅠ基因特异扩增测序,对深圳东部海域45种石珊瑚COⅠ基因片段序列进行了比较分析。结果表明,该片段序列的平均(A+T)含量为61.2%,所有物种的序列碱基(A+T)含量大于(G+C)含量,与其它无脊椎动物线粒体DNA序列基本一致,序列都处于高度饱和的状态。45种造礁珊瑚的平均遗传距离为0.126。采用邻位连接(NJ)、最大似然(ML)和最小进化(ME)法对本研究中45种石珊瑚COⅠ基因片段构建了系统发育树。结果显示45个石珊瑚品种分别聚为两个大的分支,木珊瑚科、滨珊瑚科、菌珊瑚科、枇杷珊瑚科、鹿角珊瑚科的18个品种聚为分支Ⅰ,蜂巢珊瑚科、铁星珊瑚科、梳状珊瑚科、裸肋珊瑚科、褶叶珊瑚科的27个品种聚为分支Ⅱ,处于进化树基部。分支Ⅱ的聚类结果与传统形态学分类存在巨大差异,提示石珊瑚表型的变异性可能对传统分类存在影响。
Sequences of COⅠ gene from 45 species of scleractinian in east water of Shenzhen were comparatively analyzed by COⅠgene specific amplification sequencing. The results indicated that the average(A+T) of this region accounted for 61.2%,(A+T) contents of COⅠ fragments were higher than(G+C), which were in accordance with the other invertebrate mt DNA sequences. The sequences of COⅠfragments had a high degree of saturation.The average genetic distance of 45 species was 0.126. According to the Neighbour-joining, Maximum-likelihood and Minimum-evolution method, trees of COⅠ from 45 species were constructed. Results showed that 45 species were composed of 2 clades. The clade Ⅰ consisted of Dendrophylliidae, Poritidae, Agariciidae, Oculinidae and Acroporidae. The clade Ⅱ as root consisted of Faviidae, Siderastreidae, Pectiniidae, Merulinidae, Mussidae. Clustering results of clade Ⅱ were significantly different from the traditional morphological classification. The result suggested that morphological classification might be limited by coral skeletons plasticity.
Sequences of COⅠ gene from 45 species of scleractinian in east water of Shenzhen were comparatively analyzed by COⅠgene specific amplification sequencing. The results indicated that the average(A+T) of this region accounted for 61.2%,(A+T) contents of COⅠ fragments were higher than(G+C), which were in accordance with the other invertebrate mt DNA sequences. The sequences of COⅠfragments had a high degree of saturation.The average genetic distance of 45 species was 0.126. According to the Neighbour-joining, Maximum-likelihood and Minimum-evolution method, trees of COⅠ from 45 species were constructed. Results showed that 45 species were composed of 2 clades. The clade Ⅰ consisted of Dendrophylliidae, Poritidae, Agariciidae, Oculinidae and Acroporidae. The clade Ⅱ as root consisted of Faviidae, Siderastreidae, Pectiniidae, Merulinidae, Mussidae. Clustering results of clade Ⅱ were significantly different from the traditional morphological classification. The result suggested that morphological classification might be limited by coral skeletons plasticity.
引文
Arrigoni R.,Stefani F.,Pichon M.,Galli P.,and Benzoni F.2012,Molecular phylogeny of the robust clade(Faviidae Mussidae,Merulinidae,and Pectiniidae):an Indian ocean perspective,Molecular Phylogenetics and Evolution,65(1)183-193
Budd A.F.,Romano S.L.,Smith N.D.,and Barbeitos M.S.,2010Rethinking the phylogeny of scleractinian corals:a review o morphological and molecular data,Integrative&Compara tive Biology,50(3):411-427
Fukami H.,Budd A.F.,Paulay G.,Solé-Cava A.,Allen Chen C.Iwao K.,and Knowlton N.,2004,Conventional taxonomy obscures deep divergence between Pacific and Atlantic corals,Nature,427(6977):832-835
Fukami H.,Chen C.A.,Budd A.F.,Collins A.,Wallace C.Chuang Y.Y.,Chen C.,Dai C.F.,Iwao K.,Sheppard C.,and Knowlton N.,2008,Mitochondrial and nuclear genes sug gest that stony corals are monophyletic but most families o stony corals are not(Order Scleractinia,Class Anthozoa Phylum Cnidaria),PLo S One,3(9):e3222
Hebert P.D.,Ratnasingham S.,and Dewaard J.R.,2003,Barcod ing animal life:cytochrome coxidase subunit 1 divergence among closely related species,Proceedings of the Royal So ciety B Biological Sciences,270(Suppl):S96-S99
Hellberg M.E.,2006,No variation and low synonymous substitu tion rates in coral mt DNA despite high nuclear variation BMC Evolutionary Biology,6(1):24
Huang D.,Benzoni F.,Fukami H.,Knowlton N.,Smith N.D.,and Budd A.F.,2014,Taxonomic classification of the reef cora families Merulinidae,Montastraeidae,and Diploastraeida(Cnidaria:Anthozoa:Scleractinia),Zoological Journal of th Linnean Society,171(2):277-355
Huang D.W.,Hoeksema B.W.,Affendi Y.A.,Ang P.O.,Chen C.A.,Huang H.,Lane D.J.M.,Licuanan W.Y.,Vibol O.Vo S.T.,Yeemin T.,and Chou L.M.,2016,Conservation of reef corals in the South China Sea based on species and evolutionary diversity,Biodiversity&Conservation,25(2)331-344
Huang D.,Licuanan W.Y.,Baird A.H.,and Fukami H.,2011Cleaning up the'Bigmessidae':molecular phylogeny of scle ractinian corals from Faviidae,Merulinidae,Pectiniidae and Trachyphylliidae,BMC Evolutionary Biology,11(1):37
Huang D.,Meier R.,Todd P.A.,and Chou L.M.,2009,More evi dence for perv asive paraphyly in scleractinian corals:sys tematic study of Southeast Asian Faviidae(Cnidaria;Scler actinia)based on molecular and morphological data,Molec ular Phylogenetics and Evolution,50(1):102-116
Keshavmurthy S.,Yang S.Y.,Alamaru A.,Chuang Y.Y.,Pichon M.,Obura D.,Fontana S.,De Palmas S.,Stefani F.,Benzon F.,Mac Donald A.,Noreen A.M.,Chen C.,Wallace C.C.Pillay R.M.,Denis V.,Amri A.Y.,Reimer J.D.,Mezaki T.Sheppard C.,Loya Y.,Abelson A.,Mohammed M.S.,Bake A.C.,Mostafavi P.G.,Suharsono B.A.,and Chen C.A.2004,DNA barcoding reveals the coral"laboratory-rat"Stylophora pistillata encompasses multiple identities Japanese Journal of Applied Physics,43(43):1520
Kitahara M.V.,Cairns S.D.,Stolarski J.,Blair D.,and Miller D.J.2010,A comprehensive phylogenetic analysis of the sclerac tinia(Cnidaria,Anthozoa)based on mitochondrial COⅠse quence data,PLo S One,5(7):e11490
Li X.N.,2012,Phylogenic study of scleractinian corals based on mitochondrial genes,Thesis for M.S.,Guangdong Ocean University,Supervisor:Liu C.W.,pp.18(李晓娜,2012,基于线粒体基因的常见石珊瑚系统进化研究,硕士学位论文广东海洋大学,导师:刘楚吾,pp.18)
Li X.N.,Liu L.,and Liu C.W.,2012,Phylogenetic relationship in 8species of scleractinian coral based on COⅠsequences Yuye Kexue Jinzhan(Progress in Fishery Sciences),33(4)83-88(李晓娜,刘丽,刘楚吾,2012,运用线粒体COⅠ基因分析8种石珊瑚系统发育关系,渔业科学进展,33(4)83-88)
Liao B.L.,Xiao B.H.,Yang X.D.,and Xie Z.Q.,2016,Phyloge netic analysis for 14 species of reef-building corals based on16S r RNA genes,Guangdong Haiyang Daxue Xuebao(Journal of Guangdong Ocean University),36(4):23-29(廖宝林,肖宝华,杨小东,谢子强,2016,基于线粒体16Sr RNA基因的14种造礁石珊瑚系统发育关系分析,广东海洋大学学报,36(4):23-29)
Medina M.,Weil E.,and Szmant A.M.,1999,Examination of the montastraea annularis species complex(Cnidaria:Sclerac tinia)using ITS and COⅠsequences,Marine Biotechnolo gy,1(1):89-97
Romano S.L.,and Palumbi S.R.,1996,Evolution of scleractinian corals inferred from molecular systematics,Science,271(5249):640-642
Shearer T.L.,Van Oppen M.J.,Romano S.L.,and Wrheide G.2002,Slow mitochondrial DNA sequence evolution in th Anthozoa(Cnidaria),Molecular Ecology,11(12):2475-2487
Song C.J.,Zhao H.T.,and Wang L.R.,2007,Characteristics o the coral reefs along continental coast of South China,Reda Dili(Tropical Geography),27(4):294-299(宋朝景,赵焕庭,王丽荣,2007,华南大陆沿岸珊瑚礁的特点与分析,热带地理,27(4):294-299)
Stolarski J.,Kitahara M.V.,Miller D.J.,Cairns S.D.,Mazur M.and Meibom A.,2011,The ancient evolutionary origins o Scleractinia revealed by azooxanthellate corals,BMC Evo lutionary Biology,11(1):316
Veron J.E.N.,ed.,1995,Corals in space and time:the bio geography and evolution of the Scleractinia,Com stock/Cornell,New York,Ithaca,pp.634
Yamauchi M.M.,Miya M.U.,and Nishida M.,2003,Complet mitochondrial DNA sequence of the swimming crab,Por tunus trituberculatus(Crustacea:De capoda:Brachyura)Gene,311:129-135
You F.,Huang H.,Dong Z.J.,and Zhou G.W.,2010,Progress in taxonomy and genetic diversity of Scleratinia corals Haiyang Tongbao(Marine Science Bulletin),29(4):459-465(尤丰,黄晖,董志军,周国伟,2010,造礁石珊瑚的分子系统学研究进展,海洋通报,29(4):459-465)
Zhang S.,Sun X.L.,Wang W.,Huang R.H.,Lai Y.X.,Liu Y.Zhu L.,Song T.,Jin X.X.,Zhang H.H.,and Tian X.L.,2013Features of coastal landforms in Dapeng Peninsula of Shenzhen,China,Redai Dili(Tropical Geography),33(6):647-658(张崧,孙现领,王为,黄日辉,赖宜迅,刘韫,朱雷,宋婷,金杏杏,张欢欢,田雪莲,2013,广东深圳大鹏半岛海岸地貌特征,热带地理,33(6):647-658)
Zhou R.L.,ed.,2001,Coelenterata anthozoa scleractinia-Her matypic coral,Science Press,Beijing,China,pp.8-18(邹仁林,主编,2001,中国动物志-石珊瑚,科学出版杜,中国北京,pp.8-18)
Budd A.F.,Romano S.L.,Smith N.D.,and Barbeitos M.S.,2010Rethinking the phylogeny of scleractinian corals:a review o morphological and molecular data,Integrative&Compara tive Biology,50(3):411-427
Fukami H.,Budd A.F.,Paulay G.,Solé-Cava A.,Allen Chen C.Iwao K.,and Knowlton N.,2004,Conventional taxonomy obscures deep divergence between Pacific and Atlantic corals,Nature,427(6977):832-835
Fukami H.,Chen C.A.,Budd A.F.,Collins A.,Wallace C.Chuang Y.Y.,Chen C.,Dai C.F.,Iwao K.,Sheppard C.,and Knowlton N.,2008,Mitochondrial and nuclear genes sug gest that stony corals are monophyletic but most families o stony corals are not(Order Scleractinia,Class Anthozoa Phylum Cnidaria),PLo S One,3(9):e3222
Hebert P.D.,Ratnasingham S.,and Dewaard J.R.,2003,Barcod ing animal life:cytochrome coxidase subunit 1 divergence among closely related species,Proceedings of the Royal So ciety B Biological Sciences,270(Suppl):S96-S99
Hellberg M.E.,2006,No variation and low synonymous substitu tion rates in coral mt DNA despite high nuclear variation BMC Evolutionary Biology,6(1):24
Huang D.,Benzoni F.,Fukami H.,Knowlton N.,Smith N.D.,and Budd A.F.,2014,Taxonomic classification of the reef cora families Merulinidae,Montastraeidae,and Diploastraeida(Cnidaria:Anthozoa:Scleractinia),Zoological Journal of th Linnean Society,171(2):277-355
Huang D.W.,Hoeksema B.W.,Affendi Y.A.,Ang P.O.,Chen C.A.,Huang H.,Lane D.J.M.,Licuanan W.Y.,Vibol O.Vo S.T.,Yeemin T.,and Chou L.M.,2016,Conservation of reef corals in the South China Sea based on species and evolutionary diversity,Biodiversity&Conservation,25(2)331-344
Huang D.,Licuanan W.Y.,Baird A.H.,and Fukami H.,2011Cleaning up the'Bigmessidae':molecular phylogeny of scle ractinian corals from Faviidae,Merulinidae,Pectiniidae and Trachyphylliidae,BMC Evolutionary Biology,11(1):37
Huang D.,Meier R.,Todd P.A.,and Chou L.M.,2009,More evi dence for perv asive paraphyly in scleractinian corals:sys tematic study of Southeast Asian Faviidae(Cnidaria;Scler actinia)based on molecular and morphological data,Molec ular Phylogenetics and Evolution,50(1):102-116
Keshavmurthy S.,Yang S.Y.,Alamaru A.,Chuang Y.Y.,Pichon M.,Obura D.,Fontana S.,De Palmas S.,Stefani F.,Benzon F.,Mac Donald A.,Noreen A.M.,Chen C.,Wallace C.C.Pillay R.M.,Denis V.,Amri A.Y.,Reimer J.D.,Mezaki T.Sheppard C.,Loya Y.,Abelson A.,Mohammed M.S.,Bake A.C.,Mostafavi P.G.,Suharsono B.A.,and Chen C.A.2004,DNA barcoding reveals the coral"laboratory-rat"Stylophora pistillata encompasses multiple identities Japanese Journal of Applied Physics,43(43):1520
Kitahara M.V.,Cairns S.D.,Stolarski J.,Blair D.,and Miller D.J.2010,A comprehensive phylogenetic analysis of the sclerac tinia(Cnidaria,Anthozoa)based on mitochondrial COⅠse quence data,PLo S One,5(7):e11490
Li X.N.,2012,Phylogenic study of scleractinian corals based on mitochondrial genes,Thesis for M.S.,Guangdong Ocean University,Supervisor:Liu C.W.,pp.18(李晓娜,2012,基于线粒体基因的常见石珊瑚系统进化研究,硕士学位论文广东海洋大学,导师:刘楚吾,pp.18)
Li X.N.,Liu L.,and Liu C.W.,2012,Phylogenetic relationship in 8species of scleractinian coral based on COⅠsequences Yuye Kexue Jinzhan(Progress in Fishery Sciences),33(4)83-88(李晓娜,刘丽,刘楚吾,2012,运用线粒体COⅠ基因分析8种石珊瑚系统发育关系,渔业科学进展,33(4)83-88)
Liao B.L.,Xiao B.H.,Yang X.D.,and Xie Z.Q.,2016,Phyloge netic analysis for 14 species of reef-building corals based on16S r RNA genes,Guangdong Haiyang Daxue Xuebao(Journal of Guangdong Ocean University),36(4):23-29(廖宝林,肖宝华,杨小东,谢子强,2016,基于线粒体16Sr RNA基因的14种造礁石珊瑚系统发育关系分析,广东海洋大学学报,36(4):23-29)
Medina M.,Weil E.,and Szmant A.M.,1999,Examination of the montastraea annularis species complex(Cnidaria:Sclerac tinia)using ITS and COⅠsequences,Marine Biotechnolo gy,1(1):89-97
Romano S.L.,and Palumbi S.R.,1996,Evolution of scleractinian corals inferred from molecular systematics,Science,271(5249):640-642
Shearer T.L.,Van Oppen M.J.,Romano S.L.,and Wrheide G.2002,Slow mitochondrial DNA sequence evolution in th Anthozoa(Cnidaria),Molecular Ecology,11(12):2475-2487
Song C.J.,Zhao H.T.,and Wang L.R.,2007,Characteristics o the coral reefs along continental coast of South China,Reda Dili(Tropical Geography),27(4):294-299(宋朝景,赵焕庭,王丽荣,2007,华南大陆沿岸珊瑚礁的特点与分析,热带地理,27(4):294-299)
Stolarski J.,Kitahara M.V.,Miller D.J.,Cairns S.D.,Mazur M.and Meibom A.,2011,The ancient evolutionary origins o Scleractinia revealed by azooxanthellate corals,BMC Evo lutionary Biology,11(1):316
Veron J.E.N.,ed.,1995,Corals in space and time:the bio geography and evolution of the Scleractinia,Com stock/Cornell,New York,Ithaca,pp.634
Yamauchi M.M.,Miya M.U.,and Nishida M.,2003,Complet mitochondrial DNA sequence of the swimming crab,Por tunus trituberculatus(Crustacea:De capoda:Brachyura)Gene,311:129-135
You F.,Huang H.,Dong Z.J.,and Zhou G.W.,2010,Progress in taxonomy and genetic diversity of Scleratinia corals Haiyang Tongbao(Marine Science Bulletin),29(4):459-465(尤丰,黄晖,董志军,周国伟,2010,造礁石珊瑚的分子系统学研究进展,海洋通报,29(4):459-465)
Zhang S.,Sun X.L.,Wang W.,Huang R.H.,Lai Y.X.,Liu Y.Zhu L.,Song T.,Jin X.X.,Zhang H.H.,and Tian X.L.,2013Features of coastal landforms in Dapeng Peninsula of Shenzhen,China,Redai Dili(Tropical Geography),33(6):647-658(张崧,孙现领,王为,黄日辉,赖宜迅,刘韫,朱雷,宋婷,金杏杏,张欢欢,田雪莲,2013,广东深圳大鹏半岛海岸地貌特征,热带地理,33(6):647-658)
Zhou R.L.,ed.,2001,Coelenterata anthozoa scleractinia-Her matypic coral,Science Press,Beijing,China,pp.8-18(邹仁林,主编,2001,中国动物志-石珊瑚,科学出版杜,中国北京,pp.8-18)