基于线粒体COⅠ基因的沙鳅亚科鱼类DNA条形码及其分子系统发育研究
|
摘要
选择线粒体COⅠ基因作为分子标记,进行沙鳅亚科鱼类(Botiinae)DNA条形码及其分子系统发育研究。研究获得了沙鳅亚科7属19种共131个个体的COⅠ基因序列,利用MEGA5.0软件分析了沙鳅亚科鱼类COⅠ基因的序列特征,计算了种内及种间遗传距离。沙鳅亚科鱼类的分子系统发育关系的重建分别采用NJ法和Bayesian法。研究发现,沙鳅亚科COⅠ基因的碱基组成为:A 24.4%、T 29.5%、G 18.0%、C 28.1%。沙鳅亚科鱼类种内平均遗传距离为0.002±0.000,种间平均遗传距离为0.148±0.008。DNA条形码研究结果显示,所分析的19种沙鳅鱼类各自分别聚成单系分支,表明COⅠ基因在本研究中具有100%的物种鉴别率。同时,系统发育分析支持各属的单系性,并且结果显示沙鳅亚科鱼类聚为两个分支,其中一支由薄鳅属和副沙鳅属构成,另一分支则包括:(沙鳅属、色鳅属)和[中华沙鳅属、(缨须鳅属、安彦鳅属)]。因此,COⅠ基因可以作为有效的分子标记对沙鳅亚科进行DNA条形码研究以及分子系统发育研究。
To analyze the characteristics of the sequences and to calculate the genetic distance within and between species, the 648 bp mitochondrial COⅠ gene was used as DNA barcode to analyze phylogenetic relationships of Botiinae fishes in 131 sequences from 19 species representing 7 genera of Botiinae. MEGA5.0 software was used in the current study. Phylogenetic analyses were carried out using neighbor-joining and Bayesian methods. Our result revealed that the nucleotide compositions were 24.4% A, 29.5% T, 18.0% G, and 28.1% C. The mean inter- and intra-specific genetic distances were 0.148±0.008 and 0.002±0.000, respectively. Individuals of each species were clustered into monophyletic groups based on the molecular phylogenetic tree, indicating that the mitochondria COⅠ gene is suitable for species discrimination. Moreover, the phylogenetic analyses supported monophyly of genera within Botiinae. Two clades were recovered within the subfamily Botiinae: one clade includes the sister-group of Leptobotia and Parabotia and the other contains Botia + Chromobotia and Sinibotia +(Syncrossus, Yasuhikotakia). This study indicated that the mitochondria COⅠ gene is a potentially effective marker for DNA barcoding and phylogenetic studies of Botiinae fishes.
To analyze the characteristics of the sequences and to calculate the genetic distance within and between species, the 648 bp mitochondrial COⅠ gene was used as DNA barcode to analyze phylogenetic relationships of Botiinae fishes in 131 sequences from 19 species representing 7 genera of Botiinae. MEGA5.0 software was used in the current study. Phylogenetic analyses were carried out using neighbor-joining and Bayesian methods. Our result revealed that the nucleotide compositions were 24.4% A, 29.5% T, 18.0% G, and 28.1% C. The mean inter- and intra-specific genetic distances were 0.148±0.008 and 0.002±0.000, respectively. Individuals of each species were clustered into monophyletic groups based on the molecular phylogenetic tree, indicating that the mitochondria COⅠ gene is suitable for species discrimination. Moreover, the phylogenetic analyses supported monophyly of genera within Botiinae. Two clades were recovered within the subfamily Botiinae: one clade includes the sister-group of Leptobotia and Parabotia and the other contains Botia + Chromobotia and Sinibotia +(Syncrossus, Yasuhikotakia). This study indicated that the mitochondria COⅠ gene is a potentially effective marker for DNA barcoding and phylogenetic studies of Botiinae fishes.
引文
[1]Tang Q Y,Yu D,Liu H Z.Leptobotia zebra should be revised as Sinibotia zebra(Cypriniformes:Botiidae)[J].Zoological Research,2008,29(1):1—9[唐琼英,俞丹,刘焕章.斑纹薄鳅(Leptobotia zebra)应该为斑纹沙鳅(Sinibotia zebra).动物学研究,2008,29(1):1—9]
[2]Chen J X.A study on the classification of the Botoid fishes of China[J].Zoological Research,1980,1(1):3—26[陈景星.中国沙鳅亚科鱼类系统分类的研究.动物学研究,1980,1(1):3—26]
[3]Zhu S Q.Synopsis of Freshwater Fishes of China[M].Nanjing:Jiangsu Science and Technology Publishing House.1995,1—549[朱松泉.中国淡水鱼类检索.南京:江苏科学技术出版社.1995,1—549]
[4]Nalbant T T,Nalbant T T.Sixty million years of evolution.Part one:family Botiidae(Pisces:Ostariophysi:Cobitidae)[J].Travaux Du Muséum D'histoire Naturelle“Grigore ntipa”,2002,44:343—379
[5]Kottelat M.Botia kubotai,a new species of loach(Teleostei:Cobitidae)from the Ataran River basin(Myanmar),with comments on botiine nomenclature and diagnosis of a new genus[J].Zootaxa,2004,40(1):1—18
[6]Zhang C G,Zhao Y H,Xing Y C,et al.Fish species diversity and conservation in Beijing and adjacent areas[J].Biodiversity Science,2011,19(5):597—604[张春光,赵亚辉,邢迎春,等.北京及其邻近地区野生鱼类物种多样性及其资源保育.生物多样性,2011,19(5):597—604]
[7]Frezal L,Leblois R.Four years of DNA barcoding:Current advances and prospects[J].Infection Genetics and Evolution,2008,8(5):727—736
[8]Bhattacharjee M J,Laskar B A,Dhar B,et al.Identification and re-evaluation of freshwater catfishes through DNA barcoding[J].PLoS One,2012,7(11):e49950.doi:10.1371/journal.pone.0049950
[9]Kochzius M,Seidel C,Antoniou A,et al.Identifying fishes through DNA barcodes and microarrays[J].PLoS One,2010,5(9):e12620.doi:10.1371/journal.pone.0012620
[10]Peng J L,Wang X Z,He S P.The progress and application of DNA barcoding[J].Acta Hydrobiologica Sinica,2008,32(6):916—919[彭居俐,王绪祯,何舜平.DNA条形码技术的研究进展及其应用.水生生物学报,2008,32(6):916—919]
[11]Wang X,Huang B.Advancement of DNA barcoding in animal taxonomy[J].Biotechnology Bulletin,2006,4(4):67—72[王鑫,黄兵.DNA条形编码技术在动物分类中的研究进展.生物技术通报,2006,4(4):67—72]
[12]Hebert PDN,Cywinska A,Ball S L,et al.Biological identifications through DNA barcodes[J].Proceedings of the Royal Society B-Biological Sciences,2003,270(1512):313—321
[13]Tavares E S,Baker A J.Single mitochondrial gene barcodes reliably identify sister-species in diverse clades of birds[J].BMC Evolutionary Biology,2008,8(81)doi:10.1186/1471-2148-8-81
[14]Hebert PDN,Ratnasingham S,deWaard J R.Barcoding animal life:cytochrome c oxidase subunit 1 divergences among closely related species[J].Proceedings of the Royal Society B-Biological Sciences,2003,270(Supplement 1):S96—S99
[15]Vences M,Thomas M,Bonett R M,et al.Deciphering amphibian diversity through DNA barcoding:chances and challenges[J].Philosophical Transactions of the Royal Society B-Biological Sciences,2005,360(1462):1859—1868
[16]Ward R D,Zemlak T S,Innes B H,et al.DNA barcoding Australia's fish species[J].Philosophical Transactions of the Royal Society B-Biological Sciences,2005,360(1462):1847—1857
[17]Witt JDS,Threloff D L,Hebert PDN.DNA barcoding reveals extraordinary cryptic diversity in an amphipod genus:implications for desert spring conservation[J].Molecular Ecology,2006,15(10):3073—3082
[18]Aquilino S V,Tango J M,Fontanilla I K,et al.DNA barcoding of the ichthyofauna of Taal Lake,Philippines[J].Molecular Ecology Resources,2011,11(4):612—619
[19]Lakra W S,Verma M S,Goswami M,et al.DNA barcoding Indian marine fishes[J].Molecular Ecology Resources,2011,11(1):60—71
[20]Mecklenburg C W,Mller P R,Dirk S.Biodiversity of arctic marine fishes:taxonomy and zoogeography[J].Marine Biodiversity,2011,41(1):109—140
[21]Ardura A,Linde A R,Moreira J C,et al.DNA barcoding for conservation and management of Amazonian commercial fish[J].Biological Conservation,2010,143(6):1438—1443
[22]Cawthorn D M,Steinman H A,Witthuhn R C.Establishment of a mitochondrial DNA sequence database for the identification of fish species commercially available in South Africa[J].Molecular Ecology Resources,2011,11(6):979—991
[23]Wong L L,Peatman E,Lu J,et al.DNA barcoding of catfish:species authentication and phylogenetic assessment[J].PLoS One,2011,6(3),e17812.doi:10.1371/journal.pone.0017812
[24]Fu T Y,Ye M R.On a new species of the family Cobitidae Leptobotia microphthalma,SP.NOV[J].Zoological Research,1983,4(2):121—124[傅天佑,叶妙荣.薄鳅属一新种——小眼薄鳅.动物学研究,1983,4(2):121—124]
[25]Fink S V,Fink W L.Interrelationship of ostariophysan fishes[J].Zoological Journal of Linnean Society,1981,72(4):297—353
[26]Kocher T D,Thomas W K,Meyer A,et al.Dynamics of mitochondrial-DNA evolution in animals-amplification and sequencing with conserved primers[J].Proceedings of the National Academy Sciences of the U S A,1989,86(16):6196—6200
[27]Kimura M.A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide-sequences[J].Journal of Molecular Evolution,1980,16(2):111—120
[28]Saccone C,De Giorgi C,Gissi C,et al.Evolutionary genomics in Metazoa:the mitochondrial DNA as a model system[J].Gene,1999,238(1):195—209
[29]Kumar S.Molecular clocks:four decades of evolution[J].Nature Reviews Genetics,2005,6(8):654—662
[30]Kottelat M.Conspectus Cobitidum:An inventory of the loaches of the world(Teleostei:Cypriniformes:Cobitoidei)[J].Raffles Bulletin of Zoology,2012,Supplement(26):1—175
[2]Chen J X.A study on the classification of the Botoid fishes of China[J].Zoological Research,1980,1(1):3—26[陈景星.中国沙鳅亚科鱼类系统分类的研究.动物学研究,1980,1(1):3—26]
[3]Zhu S Q.Synopsis of Freshwater Fishes of China[M].Nanjing:Jiangsu Science and Technology Publishing House.1995,1—549[朱松泉.中国淡水鱼类检索.南京:江苏科学技术出版社.1995,1—549]
[4]Nalbant T T,Nalbant T T.Sixty million years of evolution.Part one:family Botiidae(Pisces:Ostariophysi:Cobitidae)[J].Travaux Du Muséum D'histoire Naturelle“Grigore ntipa”,2002,44:343—379
[5]Kottelat M.Botia kubotai,a new species of loach(Teleostei:Cobitidae)from the Ataran River basin(Myanmar),with comments on botiine nomenclature and diagnosis of a new genus[J].Zootaxa,2004,40(1):1—18
[6]Zhang C G,Zhao Y H,Xing Y C,et al.Fish species diversity and conservation in Beijing and adjacent areas[J].Biodiversity Science,2011,19(5):597—604[张春光,赵亚辉,邢迎春,等.北京及其邻近地区野生鱼类物种多样性及其资源保育.生物多样性,2011,19(5):597—604]
[7]Frezal L,Leblois R.Four years of DNA barcoding:Current advances and prospects[J].Infection Genetics and Evolution,2008,8(5):727—736
[8]Bhattacharjee M J,Laskar B A,Dhar B,et al.Identification and re-evaluation of freshwater catfishes through DNA barcoding[J].PLoS One,2012,7(11):e49950.doi:10.1371/journal.pone.0049950
[9]Kochzius M,Seidel C,Antoniou A,et al.Identifying fishes through DNA barcodes and microarrays[J].PLoS One,2010,5(9):e12620.doi:10.1371/journal.pone.0012620
[10]Peng J L,Wang X Z,He S P.The progress and application of DNA barcoding[J].Acta Hydrobiologica Sinica,2008,32(6):916—919[彭居俐,王绪祯,何舜平.DNA条形码技术的研究进展及其应用.水生生物学报,2008,32(6):916—919]
[11]Wang X,Huang B.Advancement of DNA barcoding in animal taxonomy[J].Biotechnology Bulletin,2006,4(4):67—72[王鑫,黄兵.DNA条形编码技术在动物分类中的研究进展.生物技术通报,2006,4(4):67—72]
[12]Hebert PDN,Cywinska A,Ball S L,et al.Biological identifications through DNA barcodes[J].Proceedings of the Royal Society B-Biological Sciences,2003,270(1512):313—321
[13]Tavares E S,Baker A J.Single mitochondrial gene barcodes reliably identify sister-species in diverse clades of birds[J].BMC Evolutionary Biology,2008,8(81)doi:10.1186/1471-2148-8-81
[14]Hebert PDN,Ratnasingham S,deWaard J R.Barcoding animal life:cytochrome c oxidase subunit 1 divergences among closely related species[J].Proceedings of the Royal Society B-Biological Sciences,2003,270(Supplement 1):S96—S99
[15]Vences M,Thomas M,Bonett R M,et al.Deciphering amphibian diversity through DNA barcoding:chances and challenges[J].Philosophical Transactions of the Royal Society B-Biological Sciences,2005,360(1462):1859—1868
[16]Ward R D,Zemlak T S,Innes B H,et al.DNA barcoding Australia's fish species[J].Philosophical Transactions of the Royal Society B-Biological Sciences,2005,360(1462):1847—1857
[17]Witt JDS,Threloff D L,Hebert PDN.DNA barcoding reveals extraordinary cryptic diversity in an amphipod genus:implications for desert spring conservation[J].Molecular Ecology,2006,15(10):3073—3082
[18]Aquilino S V,Tango J M,Fontanilla I K,et al.DNA barcoding of the ichthyofauna of Taal Lake,Philippines[J].Molecular Ecology Resources,2011,11(4):612—619
[19]Lakra W S,Verma M S,Goswami M,et al.DNA barcoding Indian marine fishes[J].Molecular Ecology Resources,2011,11(1):60—71
[20]Mecklenburg C W,Mller P R,Dirk S.Biodiversity of arctic marine fishes:taxonomy and zoogeography[J].Marine Biodiversity,2011,41(1):109—140
[21]Ardura A,Linde A R,Moreira J C,et al.DNA barcoding for conservation and management of Amazonian commercial fish[J].Biological Conservation,2010,143(6):1438—1443
[22]Cawthorn D M,Steinman H A,Witthuhn R C.Establishment of a mitochondrial DNA sequence database for the identification of fish species commercially available in South Africa[J].Molecular Ecology Resources,2011,11(6):979—991
[23]Wong L L,Peatman E,Lu J,et al.DNA barcoding of catfish:species authentication and phylogenetic assessment[J].PLoS One,2011,6(3),e17812.doi:10.1371/journal.pone.0017812
[24]Fu T Y,Ye M R.On a new species of the family Cobitidae Leptobotia microphthalma,SP.NOV[J].Zoological Research,1983,4(2):121—124[傅天佑,叶妙荣.薄鳅属一新种——小眼薄鳅.动物学研究,1983,4(2):121—124]
[25]Fink S V,Fink W L.Interrelationship of ostariophysan fishes[J].Zoological Journal of Linnean Society,1981,72(4):297—353
[26]Kocher T D,Thomas W K,Meyer A,et al.Dynamics of mitochondrial-DNA evolution in animals-amplification and sequencing with conserved primers[J].Proceedings of the National Academy Sciences of the U S A,1989,86(16):6196—6200
[27]Kimura M.A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide-sequences[J].Journal of Molecular Evolution,1980,16(2):111—120
[28]Saccone C,De Giorgi C,Gissi C,et al.Evolutionary genomics in Metazoa:the mitochondrial DNA as a model system[J].Gene,1999,238(1):195—209
[29]Kumar S.Molecular clocks:four decades of evolution[J].Nature Reviews Genetics,2005,6(8):654—662
[30]Kottelat M.Conspectus Cobitidum:An inventory of the loaches of the world(Teleostei:Cypriniformes:Cobitoidei)[J].Raffles Bulletin of Zoology,2012,Supplement(26):1—175