基于DNA条码基因的鳢科鱼类系统进化与物种鉴定
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摘要
鳢科(Channidae)鱼类在亚洲分布广泛,其中中国的土著种类是重要养殖品种,国外很多种类主要作为观赏鱼引进我国。本研究利用线粒体COΙ基因序列,对分布于我国的鳢科鱼类不同种群样本序列,及在Gen Bank中获得其他鳢科鱼类的序列进行分析,探讨其作为DNA条形码基因对鳢科进行物种鉴定和系统进化分析的可行性。通过对本研究采集的149个鳢样本和122条Gen Bank中已有序列进行分析,结果显示,所研究的鳢科鱼类的COΙ基因576 bp片段中不存在碱基插入缺失现象,其平均碱基含量A+T(51.4%)高于G+C含量(48.6%),存在偏倚性;多态位点占47.2%。利用Mega 6.0软件基于Kimura’s 2-parameter模型计算25种鳢种内平均遗传距离为0.028,其中巴卡鳢(Channidae barca)种内遗传距离最大,为0.137,超过了某些种间遗传距离;种间遗传距离为0.030~0.302,平均为0.217。其中最大距离0.302为饰鳍鳢(Channidae ornatipinnis)和黑体鳢(Channidae melasoma)之间,甚至超过了与外群之间的距离。利用邻接法(Neighbour-Joining,NJ)和最大似然法(Maximum Likelihood Tree,ML)分别构建系统进化树,同种个体获得较高支持率,而不同种间的关系支持率较低,同时发现存在由多个种组成的巴卡鳢和南鳢复合支系。本研究表明,进行我国土著鳢科鱼类物种鉴定时COI基因是有效的工具,而进行外来观赏鱼鉴定,尤其是巴卡鳢、斯氏鳢等物种进行鉴定时,需结合多方面信息;COI基因不适合鳢科鱼类种间遗传进化关系的研究。
Snakeheads are of important cultural value as ornamental fishes in China. In this study, the mitochondrial COI(cytochrome oxidase subunit I) gene fragments 576 bp long were used to analyze the phylogenetic and diversity of snakeheads in and out of China, to probe the probability of the COI gene to be used as a barcoding sequence for species identification. Including 149 specimens of different geographic populations of C. argus, C. maculata, C. asiatica, and C. gachua native to China, and 122 sequences of other species downloaded from GenBank, a total of 271 snakehead individuals of 25 species, were analyzed. Of all the sequences, no insertion-deletion sites existed. The average content of A+T(51.4%) was higher than that of G+C(48.6%). The average intraspecies genetic distance was 0.028, but reached 0.137 in C. barca, which was higher than some interspecies distances. The interspecies distances ranged from 0.030 to 0.302, with an average of 0.217. The largest distance exists between C. ornatipinnis and C. melasoma, exceeding some distances to outgroup. Phylogenetic trees based on the neighbor-joining and maximum likelihood method were constructed. Most individuals from the same species formed a monophyly, and high bootstrap values were obtained for them, but this was not the case for several other species. However, the relationships of species have low bootstrap values, indicating improper phylogenetic analysis of the COI gene for snakeheads. Furtherly, a C. barca compound and a C. gachua compound were formed according to the phylogenetic trees. The results of this research indicate that the COI gene is proper for the species identification of native species of snakeheads in China, but more information regarding imported ornamental snakeheads is needed.
Snakeheads are of important cultural value as ornamental fishes in China. In this study, the mitochondrial COI(cytochrome oxidase subunit I) gene fragments 576 bp long were used to analyze the phylogenetic and diversity of snakeheads in and out of China, to probe the probability of the COI gene to be used as a barcoding sequence for species identification. Including 149 specimens of different geographic populations of C. argus, C. maculata, C. asiatica, and C. gachua native to China, and 122 sequences of other species downloaded from GenBank, a total of 271 snakehead individuals of 25 species, were analyzed. Of all the sequences, no insertion-deletion sites existed. The average content of A+T(51.4%) was higher than that of G+C(48.6%). The average intraspecies genetic distance was 0.028, but reached 0.137 in C. barca, which was higher than some interspecies distances. The interspecies distances ranged from 0.030 to 0.302, with an average of 0.217. The largest distance exists between C. ornatipinnis and C. melasoma, exceeding some distances to outgroup. Phylogenetic trees based on the neighbor-joining and maximum likelihood method were constructed. Most individuals from the same species formed a monophyly, and high bootstrap values were obtained for them, but this was not the case for several other species. However, the relationships of species have low bootstrap values, indicating improper phylogenetic analysis of the COI gene for snakeheads. Furtherly, a C. barca compound and a C. gachua compound were formed according to the phylogenetic trees. The results of this research indicate that the COI gene is proper for the species identification of native species of snakeheads in China, but more information regarding imported ornamental snakeheads is needed.
引文
[1]Li X,Musikasinthorn P,Kumazawa Y.Molecular phylogenetic analyses of snakeheads(Perciformes:Channidae)using mitochondrial DNA sequences[J].Ichthyological Research,2006,53(2):148-159.
[2]Pearl River Fisheries Research Institute,Chinese Academy of Fishery Sciences.Freshwater Fishes of Guangdong Province[M].Guangzhou:Guangdong Sience&Technology Press,1991.[中国水产科学研究院珠江水产研究所.广东淡水鱼类志[M].广州:广东科技出版社,1991.]
[3]Administration Bureau of Fisheries and Fishery management of Ministry of Agriculture.Annual Book of China Fishery Statistics 2016[M].Beijing:China Agriculture Press,2016.[农业部渔业渔政管理局,2016中国渔业统计年鉴[M].北京:中国农业出版社,2016.]
[4]Zhang C G,Musikasinthon P,Watanabe K.Channa nox,a new channid fish lacking a pelvic fin from Guangxi,China[J].Ichthyological Research,2002,49(2):140-146.
[5]Britz R.Channa andrao,a new species of dwarf snakehead from West Bengal,India(Teleostei:Channidae)[J].Zootaxa,2013,3731:287-294
[6]Britz R,Adamson E,Raghavan R,et al.Channa pseudomarulius,a valid species of snakehead from the Western Ghats region of Peninsular India(Teleostei:Channidae),with comments on Ophicephalus grandinosus,O.theophrasti andO.leucopunctatus[J].Zootaxa,2017,4299:529-545.
[7]Zhu S R,Fu J J,Wang Q,et al.Identification of Channa species using the partial cytochrome c oxidase subunit I(COI)gene as a DNA barcoding marker[J].Biochemical Systematics and Ecology,2013,51:117-122.
[8]Zhu S R,Meng Q L,Sun Y X,et al.Phylogenetic analysis of Channa based on the mitochondrial 16S r RNA gene sequence[J].Journal of Yangtze University(Natural Science Edition),2015,12(27):25-29.[朱树人,孟庆磊,孙玉旋,等.基于线粒体16S r RNA基因序列的鳢属鱼类系统进化探讨[J].长江大学学报(自然科学版),2015,12(27):25-29.]
[9]Chen C,He J J,Shao Q C,et al.Sequencing and phylogenetic relationship analysis of mitochondrial COI gene[J].Journal of Jiangsu Agriculture Science,2016,44(8):297-299.[陈晨,贺晶晶,邵青臣,等.乌鳢(Channa argus)线粒体COI基因序列测定及其系统发育关系分析[J].江苏农业科学,2016,44(8):297-299.]
[10]Xue D,Zhang Q,Gao X C,et al.The analysis of genetic variation based on m tdna control region sequences of Channa gachus in the Lancang River in Yunnan Province and and the main rivers in Hainan Province of China[J].Acta Hydrobiologyica Sinica,2015,39(6):1107-1116.[薛丹,章群,郜星晨,等.基于线粒体控制区的云南澜沧江和海南岛主要水系宽额鳢遗传变异分析[J].水生生物学报,2015,39(6):1107-1116.]
[11]Lakra W S,Goswami M.,Gopalakrishnan A,et al.Genetic relatedness among fish species of genus Channa using mitochondrial DNA genes[J].Biochemical Systematics and Ecology,2010,38(6):1212-1219.
[12]Conte-Grand C,Britz R,Dahanukar N,et al.Barcoding snakeheads(Teleostei,Channidae)revisited:Discovering greater species diversity and resolving perpetuated taxonomic confusions[J].PLo S ONE,2017,12(9):e0184017.
[13]Hebert P D,Ratnasingham S,de Waard J R.Barcoding animal life:Cytochrome c oxidase subunit 1 divergences among closely related species[J].Proceedings:Biological Sciences,2003,270:S96-S99.
[14]Joly S,Davies T J,Archambault A,et al.Ecology in the age of DNA barcoding:The resource,the promise and the challenges ahead[J].Molecular Ecology Resources,2014,14(2):221-232.
[15]Zhu S Q.Synopsis of Freshwater Fishes of China[M].Nanjing:Phoenix Science Press,1995:1-549.[朱松泉.中国淡水鱼类检索[M].南京:江苏科学技术出版社,1995:1-549.]
[16]Pearl River Fisheries Research Institute of Chinese Academy of Fishery Sciences,Shanghai Fisheries University,East China Sea Fisheries Research Institute of Chinese Academy of Fishery Sciences,et al.Fishes in Freshwater and Estuarine Delta of Hainan Island[M].Guangzhou:Guangdong Sience&Technology Press,1986.[中国水产科学研究院珠江水产研究所,上海水产大学,中国水产科学研究院东海水产研究所,等.海南岛淡水及河口鱼类志[M].广州:广东科技出版社,1986.]
[17]Gong Y Y,Li W,Zhao J,et al.Identification and classification application of mitochondrial COI gene in ornamental fish[J].Genomics and Applied Biology,2017,36(9):3728-3734.[公月月,李伟,赵建,等.线粒体COΙ基因在观赏鱼中物种鉴定与分类应用[J].基因组学与应用生物学,2017,36(9):3728-3734.]
[18]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.
[19]Zhang X C,Zhu X P,Chen K C,et al.Comparison of the northern snakehead(Channa argus)and blotched snakehead(Channa maculata)and their reciprocal hybrids(C.maculata♀×C.argus♂and C.argus♀×C.maculata♂)based on complete mitochondrial DNA sequences[J].Mitochondrial DNA,2015,26(5):805-806.
[20]Chen L,Huang B D,Xue D,et al.DNA barcoding of Terapontidae and taxonomic status of a new record ofTerapon puta in costal waters of China[J].Marine Fisheries,2017,39(2):121-130.[陈璐,黄伯炎,薛丹,等.中国沿海鯻科鱼类DNA条形码研究及新记录种三线鯻分类地位探讨[J].海洋渔业,2017,39(2):121-130.]
[21]Chen Y X,Wu R X,Liang N,et al.Phylogenetic relationship in family sparidae of China in mitochondrial COI gene sequence[J].Oceanologia et Limnologia Sinica,2015,46(3):611-619.[陈咏霞,吴仁协,梁娜,等.基于线粒体COI基因序列的中国鲷科鱼类系统进化关系[J].海洋与湖沼,2015,46(3):611-619.]
[22]Yi X,Wang P P,Wang J,et al.The research of COI-based DNA barcoding in Penaeidaes’identification[J].Journal of Fisheries of China,2018,42(1):1-9.[易啸,王攀攀,王军,等.基于线粒体COI的DNA条形码在对虾科种类鉴定中的研究[J].水产学报,2018,42(1):1-9.]
[23]Adamson E A S,Hurwood D A,Mather P B A.Reappraisal of the evolution of Asian snakehead fishes(Pisces,Channidae)using molecular data from multiple genes and fossil calibration[J].Molecular Phylogenetics and Evolution,2010,56(2):707-717.
[24]Benziger A,Philip S,Raghavan R,et al.Unraveling a 146years old taxonomic puzzle:Validation of Malabar snakehead,species-status and its relevance for channid systematics and evolution[J].PLo S ONE,2011,6(6):e21272.
[25]Serrao N R,Steinke D,Hanner R H.Calibrating snakehead diversity with DNA barcodes:expanding taxonomic coverage to enable identification of potential and established invasive species[J].PLo S ONE,2014,9(6):e99546.
[26]Tan M P,Jamsari A F J,Muchlisin Z A,et al.Mitochondrial genetic variation and population structure of the striped snakehead,Channa striata,in Malaysia and Sumatra,Indonesia[J].Biochemical Systematics&Ecology,2015,60:99-105.
[2]Pearl River Fisheries Research Institute,Chinese Academy of Fishery Sciences.Freshwater Fishes of Guangdong Province[M].Guangzhou:Guangdong Sience&Technology Press,1991.[中国水产科学研究院珠江水产研究所.广东淡水鱼类志[M].广州:广东科技出版社,1991.]
[3]Administration Bureau of Fisheries and Fishery management of Ministry of Agriculture.Annual Book of China Fishery Statistics 2016[M].Beijing:China Agriculture Press,2016.[农业部渔业渔政管理局,2016中国渔业统计年鉴[M].北京:中国农业出版社,2016.]
[4]Zhang C G,Musikasinthon P,Watanabe K.Channa nox,a new channid fish lacking a pelvic fin from Guangxi,China[J].Ichthyological Research,2002,49(2):140-146.
[5]Britz R.Channa andrao,a new species of dwarf snakehead from West Bengal,India(Teleostei:Channidae)[J].Zootaxa,2013,3731:287-294
[6]Britz R,Adamson E,Raghavan R,et al.Channa pseudomarulius,a valid species of snakehead from the Western Ghats region of Peninsular India(Teleostei:Channidae),with comments on Ophicephalus grandinosus,O.theophrasti andO.leucopunctatus[J].Zootaxa,2017,4299:529-545.
[7]Zhu S R,Fu J J,Wang Q,et al.Identification of Channa species using the partial cytochrome c oxidase subunit I(COI)gene as a DNA barcoding marker[J].Biochemical Systematics and Ecology,2013,51:117-122.
[8]Zhu S R,Meng Q L,Sun Y X,et al.Phylogenetic analysis of Channa based on the mitochondrial 16S r RNA gene sequence[J].Journal of Yangtze University(Natural Science Edition),2015,12(27):25-29.[朱树人,孟庆磊,孙玉旋,等.基于线粒体16S r RNA基因序列的鳢属鱼类系统进化探讨[J].长江大学学报(自然科学版),2015,12(27):25-29.]
[9]Chen C,He J J,Shao Q C,et al.Sequencing and phylogenetic relationship analysis of mitochondrial COI gene[J].Journal of Jiangsu Agriculture Science,2016,44(8):297-299.[陈晨,贺晶晶,邵青臣,等.乌鳢(Channa argus)线粒体COI基因序列测定及其系统发育关系分析[J].江苏农业科学,2016,44(8):297-299.]
[10]Xue D,Zhang Q,Gao X C,et al.The analysis of genetic variation based on m tdna control region sequences of Channa gachus in the Lancang River in Yunnan Province and and the main rivers in Hainan Province of China[J].Acta Hydrobiologyica Sinica,2015,39(6):1107-1116.[薛丹,章群,郜星晨,等.基于线粒体控制区的云南澜沧江和海南岛主要水系宽额鳢遗传变异分析[J].水生生物学报,2015,39(6):1107-1116.]
[11]Lakra W S,Goswami M.,Gopalakrishnan A,et al.Genetic relatedness among fish species of genus Channa using mitochondrial DNA genes[J].Biochemical Systematics and Ecology,2010,38(6):1212-1219.
[12]Conte-Grand C,Britz R,Dahanukar N,et al.Barcoding snakeheads(Teleostei,Channidae)revisited:Discovering greater species diversity and resolving perpetuated taxonomic confusions[J].PLo S ONE,2017,12(9):e0184017.
[13]Hebert P D,Ratnasingham S,de Waard J R.Barcoding animal life:Cytochrome c oxidase subunit 1 divergences among closely related species[J].Proceedings:Biological Sciences,2003,270:S96-S99.
[14]Joly S,Davies T J,Archambault A,et al.Ecology in the age of DNA barcoding:The resource,the promise and the challenges ahead[J].Molecular Ecology Resources,2014,14(2):221-232.
[15]Zhu S Q.Synopsis of Freshwater Fishes of China[M].Nanjing:Phoenix Science Press,1995:1-549.[朱松泉.中国淡水鱼类检索[M].南京:江苏科学技术出版社,1995:1-549.]
[16]Pearl River Fisheries Research Institute of Chinese Academy of Fishery Sciences,Shanghai Fisheries University,East China Sea Fisheries Research Institute of Chinese Academy of Fishery Sciences,et al.Fishes in Freshwater and Estuarine Delta of Hainan Island[M].Guangzhou:Guangdong Sience&Technology Press,1986.[中国水产科学研究院珠江水产研究所,上海水产大学,中国水产科学研究院东海水产研究所,等.海南岛淡水及河口鱼类志[M].广州:广东科技出版社,1986.]
[17]Gong Y Y,Li W,Zhao J,et al.Identification and classification application of mitochondrial COI gene in ornamental fish[J].Genomics and Applied Biology,2017,36(9):3728-3734.[公月月,李伟,赵建,等.线粒体COΙ基因在观赏鱼中物种鉴定与分类应用[J].基因组学与应用生物学,2017,36(9):3728-3734.]
[18]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.
[19]Zhang X C,Zhu X P,Chen K C,et al.Comparison of the northern snakehead(Channa argus)and blotched snakehead(Channa maculata)and their reciprocal hybrids(C.maculata♀×C.argus♂and C.argus♀×C.maculata♂)based on complete mitochondrial DNA sequences[J].Mitochondrial DNA,2015,26(5):805-806.
[20]Chen L,Huang B D,Xue D,et al.DNA barcoding of Terapontidae and taxonomic status of a new record ofTerapon puta in costal waters of China[J].Marine Fisheries,2017,39(2):121-130.[陈璐,黄伯炎,薛丹,等.中国沿海鯻科鱼类DNA条形码研究及新记录种三线鯻分类地位探讨[J].海洋渔业,2017,39(2):121-130.]
[21]Chen Y X,Wu R X,Liang N,et al.Phylogenetic relationship in family sparidae of China in mitochondrial COI gene sequence[J].Oceanologia et Limnologia Sinica,2015,46(3):611-619.[陈咏霞,吴仁协,梁娜,等.基于线粒体COI基因序列的中国鲷科鱼类系统进化关系[J].海洋与湖沼,2015,46(3):611-619.]
[22]Yi X,Wang P P,Wang J,et al.The research of COI-based DNA barcoding in Penaeidaes’identification[J].Journal of Fisheries of China,2018,42(1):1-9.[易啸,王攀攀,王军,等.基于线粒体COI的DNA条形码在对虾科种类鉴定中的研究[J].水产学报,2018,42(1):1-9.]
[23]Adamson E A S,Hurwood D A,Mather P B A.Reappraisal of the evolution of Asian snakehead fishes(Pisces,Channidae)using molecular data from multiple genes and fossil calibration[J].Molecular Phylogenetics and Evolution,2010,56(2):707-717.
[24]Benziger A,Philip S,Raghavan R,et al.Unraveling a 146years old taxonomic puzzle:Validation of Malabar snakehead,species-status and its relevance for channid systematics and evolution[J].PLo S ONE,2011,6(6):e21272.
[25]Serrao N R,Steinke D,Hanner R H.Calibrating snakehead diversity with DNA barcodes:expanding taxonomic coverage to enable identification of potential and established invasive species[J].PLo S ONE,2014,9(6):e99546.
[26]Tan M P,Jamsari A F J,Muchlisin Z A,et al.Mitochondrial genetic variation and population structure of the striped snakehead,Channa striata,in Malaysia and Sumatra,Indonesia[J].Biochemical Systematics&Ecology,2015,60:99-105.