基于线粒体COⅠ的DNA条形码在对虾科种类鉴定中的研究
|
摘要
对虾科包含有26个属,约有200多种对虾,由于同属内的对虾在形态上非常相似,只呈现细微的差别,因此使得只基于形态学对对虾科物种的鉴别非常困难。为确定DNA条形码技术在对虾科物种鉴别的可行性,本研究中,采用线粒体细胞色素c氧化酶亚基Ⅰ(COⅠ)基因研究了32种对虾的核苷酸组成、对虾种间及种内遗传距离,用邻接法构建32种对虾COⅠ基因序列系统发生树。结果显示,对虾COⅠ基因组成偏倚明显,A+T含量(61.5%)显著高于G+C(38.5%)。基于Kimura双参数模型计算,32个物种的种内平均遗传距离为0.003,种间平均遗传距离(0.468)是种内遗传距离的156倍,符合Hebert提出的种间遗传距离大于或等于10倍种内遗传距离的标准。在系统进化树中,32种对虾中有30种对虾都以较高的置信度聚合成独立的分支。可见,线粒体COⅠ基因作为对虾科DNA条形码在物种的鉴别上具有很好的应用性,可以作为形态学分类系统的必要补充和佐证。
The Penaeidae comprises 26 genera and approximately 200 species as most of Penaeidae shrimps in the same genus are morphologically similar, and just exhibited subtle morphological differences, which makes identification of Penaeidae shrimps a difficult task based on taxonomic keys alone. In order to define the practicability of DNA barcoding in identification of Penaeidae shrimps, in this study, we used COⅠ gene to examine 32 kinds of Penaeidaes' nucleotide composition, interspecific genetic distance and intraspeccific genetic distance, and to build neighbor-joining tree of 32 kinds of Penaeidae based on mt DNA COⅠ gene. As a result, the COⅠ sequences of32 kinds of Penaeidae present base preference. On average, the content of A+T(61.50%)was significantly higher than that of G+C(38.50%). As calculated by Kimera-2-parameter model, the mean distance within-species was0.003, the mean distance pairwise-species(0.468)is 156 times greater than the mean distance within-species. The phylogeny showed that 30 kinds of Penaeidae from 32 kinds of Penaeidae could converge upon a monophyly with high support values. We can see the good applicability of mitochondrial COⅠ-based DNA barcoding in Penaeidaes' identification and use it as a necessary complement and a test of morphological taxonomic system.
The Penaeidae comprises 26 genera and approximately 200 species as most of Penaeidae shrimps in the same genus are morphologically similar, and just exhibited subtle morphological differences, which makes identification of Penaeidae shrimps a difficult task based on taxonomic keys alone. In order to define the practicability of DNA barcoding in identification of Penaeidae shrimps, in this study, we used COⅠ gene to examine 32 kinds of Penaeidaes' nucleotide composition, interspecific genetic distance and intraspeccific genetic distance, and to build neighbor-joining tree of 32 kinds of Penaeidae based on mt DNA COⅠ gene. As a result, the COⅠ sequences of32 kinds of Penaeidae present base preference. On average, the content of A+T(61.50%)was significantly higher than that of G+C(38.50%). As calculated by Kimera-2-parameter model, the mean distance within-species was0.003, the mean distance pairwise-species(0.468)is 156 times greater than the mean distance within-species. The phylogeny showed that 30 kinds of Penaeidae from 32 kinds of Penaeidae could converge upon a monophyly with high support values. We can see the good applicability of mitochondrial COⅠ-based DNA barcoding in Penaeidaes' identification and use it as a necessary complement and a test of morphological taxonomic system.
引文
[1]Hebert P D N,Ratnasingham S,de Waard 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(S):S96-S99.
[2]Waugh J.DNA barcoding in animal species:progress,potential and pitfalls[J].Bioessays,2007,29(2):188-197.
[3]Zhang J B,Hanner R.DNA barcoding is a useful tool for the identification of marine fishes from Japan[J].Biochemical Systematics and Ecology,2011,39(1):31-42.
[4]Will K W,Mishler B D,Wheeler Q D.The perils of DNA barcoding and the need for integrative taxonomy[J].Systematic Biology,2005,54(5):844-851.
[5]Ekrem T,Willassen E,Stur E.A comprehensive DNAsequence library is essential for identification with DNAbarcodes[J].Molecular Phylogenetics and Evolution,2007,43(2):530-542.
[6]Zou S M,Li Q,Kong L F,et al.Comparing the usefulness of distance,monophyly and character-based DNAbarcoding methods in species identification:a case study of Neogastropoda[J].PLo S One,2011,6(10):e26619.
[7]宫亚运,章群,曹艳,吕金磊,杨喜书.基于线粒体COⅠ基因的中国近海棱鳀属鱼类DNA条形码[J].水产学报,2016,40(10):1513-1520.Gong Y Y,Zhang Q,Cao Y,et al.DNA barcoding of Thryssa in coastal waters of China based on the mitochondrial cytochrome oxidase subunit I sequence[J].Journal of Fisheries of China,2016,40(10):1513-1520(in Chinese).
[8]Ni L H,Li Q,Kong L F,et al.DNA barcoding and phylogeny in the family Mactridae(Bivalvia:Heterodonta):evidence for cryptic species[J].Biochemical Systematics and Ecology,2012,44:164-172.
[9]Holthuis L B.The recent genera of the Caridean and Stenopodidean shrimps(Crustacea,Decapoda):with an appendix on the order Amphionidacea[M].Leiden:Nationaal Natuurhistorisch Museum,1993:328.
[10]Farfante I P,Kensley B.Penaeoid and Sergestoid Shrimps and Prawns of the World:Keys and Diagnosesfor the Families and Genera[M].Paris:Museum National d’Histoire Naturelle,1997:233.
[11]Dall W,Hill B J,Rothlisberg N W,et al.The biology of the penaeidae[J].Advances in Marine Biology,1990,27:1-489.
[12]Cheng J,Sha Z L,Liu R Y.DNA barcoding of genus Metapenaeopsis(Decapoda:Penaeidae)and molecular phylogeny inferred from mitochondrial and nuclear DNA sequences[J].Biochemical Systematics and Ecology,2015,61:376-384.
[13]Costa F O,de Waard J R,Boutillier J,et al.Biological identifications through DNA barcodes:the case of the crustacea[J].Canadian Journal of Fisheries and Aquatic Sciences,2007,64(2):272-295.
[14]Green M,Sambrook J.Molecular Cloning:A Laboratory Manual[M].CSH,2012.
[15]Folmer O,Black M,Hoeh W,et al.DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates[J].Molecular Marine Biology and Biotechnology,1994,3(5):294-299.
[16]潘宝平,吴琪,张素萍,等.文蛤属(Meretrix)16Sr RNA基因及ITS1序列的系统学分析[J].海洋与湖沼,2006,37(4):342-347.Pan B P,Wu Q,Zhang S P,et al.Molecular phylogeny of meretrix(Mollusca,Bivalvia)based on 16S r RNAgenes and ITS1 sequences[J].Oceanologia et Limnologia Sinica,2006,37(4):342-347(in Chinese).
[17]Thompson J D,Gibson T J,Plewnia F,et al.The CLUSTAL_X windows interface:flexible strategies for multiple sequences alignment aided by quality analysis tools[J].Nucleic Acids Research,1997,25(24):4876-4882.
[18]Tamura K,Stecher G,Peterson D,et al.MEGA6:molecular evolutionary genetics analysis version 6.0[J].molecular Biology and Evolution,2013,30(12):2725-2729.
[19]Meyran J C,Monnerot M,Taberlet P.Taxonomic status and phylogenetic relationships of some species of the genus Gammarus(Crustacea,Amphipoda)deduced from mitochondrial DNA sequences[J].Molecular phylogenetics and Evolution,1997,8(1):1-10.
[20]刘帅,李墨非,叶嘉,等.基于线粒体16S r RNA和COI基因序列探讨对虾属(Penaeus)物种系统发生关系[J].生物学杂志,2012,29(5):37-42.Liu S,Li M F,Ye J,et al.The molecular phylogenetic analysis of Penaeus based on 16S r RNA and COI sequences[J].Journal of Biology,2012,29(5):37-42(in Chinese).
[21]陈爱辉,李朝霞,封功能.基于线粒体COI基因序列的文蛤属(软体动物门:帘蛤科)系统发育关系[J].动物学研究,2009,30(3):233-239.Chen A H,Li Z X,Feng G N.Relationships of the Genus Meretrix(Mollusca:Veneridae)based on mitochondrial COI gene sequences[J].Zoological Research,2009,30(3):233-239(in Chinese).
[22]Harrison J S.Evolution,biogeography,and the utility of mitochondrial 16S and COI genes in phylogenetic analysis of the crab genus Austinixa(Decapoda:Pinnotheridae)[J].Molecular Phylogenetics and Evolution,2004,30(3):743-754.
[23]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.
[24]柳淑芳,陈亮亮,戴芳群,等.基于线粒体CO1基因的DNA条形码在石首鱼科(Sciaenidae)鱼类系统分类中的应用[J].海洋与湖沼,2010,41(2):223-232.Liu S F,Chen L L,Dai F Q,et al.Applicaction of DNAbarcoding gene CO1 for classifying family sciaenidae[J].Oceanologia et Limnologia Sinica,2010,41(2):223-232(in Chinese).
[25]Bucklin A,Wiebe P H,Smolenack S B,et al.DNA barcodes for species identification of euphausiids(Euphausiacea,Crustacea)[J].Journal of Plankton Research,2007,29(6):483-493.
[26]Johnson S B,Warén A,Vrijenhoek R C.DNA barcod-ing of Lepetodrilus limpets reveals cryptic species[J].Journal of Shellfish Research,2008,27(1):43-51.
[27]Schwentner M,Clavier S,Fritsch M,et al.Cyclestheria hislopi(Crustacea:Branchiopoda):a group of morphologically cryptic species with origins in the Cretaceous[J].Molecular Phylogenetics and Evolution,2013,66(3):800-810.
[28]Wiens J J,Penkrot T A.Delimiting species using DNAand morphological variation and discordant species limits in spiny lizards(Sceloporus)[J].Systematic Biology,2002,51(1):69-91.
[29]Hebert P D N,Stoeckle M Y,Zemlak T S,et al.Identification of birds through DNA barcodes[J].PLo S Biology,2004,2(10):e312.
[30]Burns J M,Janzen D H,Hajibabaei M,et al.DNA barcodes and cryptic species of skipper butterflies in the genus Perichares in area de conservación Guanacaste,Costa Rica[J].Proceedings of the National Academy of Sciences of the United States of America,2008,105(17):6350-6355.
[31]Wiemers M,Fiedler K.Does the DNA barcoding gap exist?-a case study in blue butterflies(Lepidoptera:Lycaenidae)[J].Frontiers in Zoology,2007,4:8.
[32]Perez K E,Defreitas N,Slapcinsky J,et al.Molecular phylogeny,evolution of shell shape,and DNA barcoding in polygyridae(Gastropoda:Pulmonata),an endemic North American clade of land snails[J].American Malacological Bulletin,2014,32(1):1-31.
[33]Lavery S,Chan T Y,Tam Y K,et al.Phylogenetic relationships and evolutionary history of the shrimp genus Penaeus s.l.derived from mitochondrial DNA[J].Molecular Phylogenetics and Evolution,2004,31(1):39-49.
[2]Waugh J.DNA barcoding in animal species:progress,potential and pitfalls[J].Bioessays,2007,29(2):188-197.
[3]Zhang J B,Hanner R.DNA barcoding is a useful tool for the identification of marine fishes from Japan[J].Biochemical Systematics and Ecology,2011,39(1):31-42.
[4]Will K W,Mishler B D,Wheeler Q D.The perils of DNA barcoding and the need for integrative taxonomy[J].Systematic Biology,2005,54(5):844-851.
[5]Ekrem T,Willassen E,Stur E.A comprehensive DNAsequence library is essential for identification with DNAbarcodes[J].Molecular Phylogenetics and Evolution,2007,43(2):530-542.
[6]Zou S M,Li Q,Kong L F,et al.Comparing the usefulness of distance,monophyly and character-based DNAbarcoding methods in species identification:a case study of Neogastropoda[J].PLo S One,2011,6(10):e26619.
[7]宫亚运,章群,曹艳,吕金磊,杨喜书.基于线粒体COⅠ基因的中国近海棱鳀属鱼类DNA条形码[J].水产学报,2016,40(10):1513-1520.Gong Y Y,Zhang Q,Cao Y,et al.DNA barcoding of Thryssa in coastal waters of China based on the mitochondrial cytochrome oxidase subunit I sequence[J].Journal of Fisheries of China,2016,40(10):1513-1520(in Chinese).
[8]Ni L H,Li Q,Kong L F,et al.DNA barcoding and phylogeny in the family Mactridae(Bivalvia:Heterodonta):evidence for cryptic species[J].Biochemical Systematics and Ecology,2012,44:164-172.
[9]Holthuis L B.The recent genera of the Caridean and Stenopodidean shrimps(Crustacea,Decapoda):with an appendix on the order Amphionidacea[M].Leiden:Nationaal Natuurhistorisch Museum,1993:328.
[10]Farfante I P,Kensley B.Penaeoid and Sergestoid Shrimps and Prawns of the World:Keys and Diagnosesfor the Families and Genera[M].Paris:Museum National d’Histoire Naturelle,1997:233.
[11]Dall W,Hill B J,Rothlisberg N W,et al.The biology of the penaeidae[J].Advances in Marine Biology,1990,27:1-489.
[12]Cheng J,Sha Z L,Liu R Y.DNA barcoding of genus Metapenaeopsis(Decapoda:Penaeidae)and molecular phylogeny inferred from mitochondrial and nuclear DNA sequences[J].Biochemical Systematics and Ecology,2015,61:376-384.
[13]Costa F O,de Waard J R,Boutillier J,et al.Biological identifications through DNA barcodes:the case of the crustacea[J].Canadian Journal of Fisheries and Aquatic Sciences,2007,64(2):272-295.
[14]Green M,Sambrook J.Molecular Cloning:A Laboratory Manual[M].CSH,2012.
[15]Folmer O,Black M,Hoeh W,et al.DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates[J].Molecular Marine Biology and Biotechnology,1994,3(5):294-299.
[16]潘宝平,吴琪,张素萍,等.文蛤属(Meretrix)16Sr RNA基因及ITS1序列的系统学分析[J].海洋与湖沼,2006,37(4):342-347.Pan B P,Wu Q,Zhang S P,et al.Molecular phylogeny of meretrix(Mollusca,Bivalvia)based on 16S r RNAgenes and ITS1 sequences[J].Oceanologia et Limnologia Sinica,2006,37(4):342-347(in Chinese).
[17]Thompson J D,Gibson T J,Plewnia F,et al.The CLUSTAL_X windows interface:flexible strategies for multiple sequences alignment aided by quality analysis tools[J].Nucleic Acids Research,1997,25(24):4876-4882.
[18]Tamura K,Stecher G,Peterson D,et al.MEGA6:molecular evolutionary genetics analysis version 6.0[J].molecular Biology and Evolution,2013,30(12):2725-2729.
[19]Meyran J C,Monnerot M,Taberlet P.Taxonomic status and phylogenetic relationships of some species of the genus Gammarus(Crustacea,Amphipoda)deduced from mitochondrial DNA sequences[J].Molecular phylogenetics and Evolution,1997,8(1):1-10.
[20]刘帅,李墨非,叶嘉,等.基于线粒体16S r RNA和COI基因序列探讨对虾属(Penaeus)物种系统发生关系[J].生物学杂志,2012,29(5):37-42.Liu S,Li M F,Ye J,et al.The molecular phylogenetic analysis of Penaeus based on 16S r RNA and COI sequences[J].Journal of Biology,2012,29(5):37-42(in Chinese).
[21]陈爱辉,李朝霞,封功能.基于线粒体COI基因序列的文蛤属(软体动物门:帘蛤科)系统发育关系[J].动物学研究,2009,30(3):233-239.Chen A H,Li Z X,Feng G N.Relationships of the Genus Meretrix(Mollusca:Veneridae)based on mitochondrial COI gene sequences[J].Zoological Research,2009,30(3):233-239(in Chinese).
[22]Harrison J S.Evolution,biogeography,and the utility of mitochondrial 16S and COI genes in phylogenetic analysis of the crab genus Austinixa(Decapoda:Pinnotheridae)[J].Molecular Phylogenetics and Evolution,2004,30(3):743-754.
[23]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.
[24]柳淑芳,陈亮亮,戴芳群,等.基于线粒体CO1基因的DNA条形码在石首鱼科(Sciaenidae)鱼类系统分类中的应用[J].海洋与湖沼,2010,41(2):223-232.Liu S F,Chen L L,Dai F Q,et al.Applicaction of DNAbarcoding gene CO1 for classifying family sciaenidae[J].Oceanologia et Limnologia Sinica,2010,41(2):223-232(in Chinese).
[25]Bucklin A,Wiebe P H,Smolenack S B,et al.DNA barcodes for species identification of euphausiids(Euphausiacea,Crustacea)[J].Journal of Plankton Research,2007,29(6):483-493.
[26]Johnson S B,Warén A,Vrijenhoek R C.DNA barcod-ing of Lepetodrilus limpets reveals cryptic species[J].Journal of Shellfish Research,2008,27(1):43-51.
[27]Schwentner M,Clavier S,Fritsch M,et al.Cyclestheria hislopi(Crustacea:Branchiopoda):a group of morphologically cryptic species with origins in the Cretaceous[J].Molecular Phylogenetics and Evolution,2013,66(3):800-810.
[28]Wiens J J,Penkrot T A.Delimiting species using DNAand morphological variation and discordant species limits in spiny lizards(Sceloporus)[J].Systematic Biology,2002,51(1):69-91.
[29]Hebert P D N,Stoeckle M Y,Zemlak T S,et al.Identification of birds through DNA barcodes[J].PLo S Biology,2004,2(10):e312.
[30]Burns J M,Janzen D H,Hajibabaei M,et al.DNA barcodes and cryptic species of skipper butterflies in the genus Perichares in area de conservación Guanacaste,Costa Rica[J].Proceedings of the National Academy of Sciences of the United States of America,2008,105(17):6350-6355.
[31]Wiemers M,Fiedler K.Does the DNA barcoding gap exist?-a case study in blue butterflies(Lepidoptera:Lycaenidae)[J].Frontiers in Zoology,2007,4:8.
[32]Perez K E,Defreitas N,Slapcinsky J,et al.Molecular phylogeny,evolution of shell shape,and DNA barcoding in polygyridae(Gastropoda:Pulmonata),an endemic North American clade of land snails[J].American Malacological Bulletin,2014,32(1):1-31.
[33]Lavery S,Chan T Y,Tam Y K,et al.Phylogenetic relationships and evolutionary history of the shrimp genus Penaeus s.l.derived from mitochondrial DNA[J].Molecular Phylogenetics and Evolution,2004,31(1):39-49.