基于CO Ⅰ基因的DNA条形码技术在石首鱼科鱼类系统分类中的应用
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摘要
为探讨DNA条形码技术在石首鱼科鱼类物种鉴定中的有效性,本研究扩增测序7个物种的石首鱼科CO Ⅰ基因序列,并从GenBank下载同源序列,最终获得石首鱼科14属23种65个个体的CO Ⅰ基因进行序列分析和系统进化研究。结果表明,石首鱼科CO Ⅰ基因序列中A+T含量高于G+C含量,且第1个密码子位点G+C含量显著高于第2和第3密码子位点。石首鱼科种内遗传距离为0～0.014,平均种内遗传距离为0.004,种间遗传距离为0.050～0.368,平均种间遗传距离为0.202,是种内遗传距离的50.5倍。在系统进化树上,除仅有单一序列的物种外,其他种类的不同个体分别聚为独立的一支;黄鱼属、梅童鱼属有明显的单系性,而白姑鱼属、黄姑鱼属、叫姑鱼属没有呈现明显的单系性。以上结果表明,线粒体CO Ⅰ基因可以实现石首鱼科鱼类的有效鉴定,并且可以用来进行属、种水平的系统进化分析。
To study the applicability of DNA barcode technology to identify fish of Sciaenidae,CO Ⅰ sequences of 7 species of Sciaenidae were amplified and homologous sequences were obtained from GenBank.Ultimately,CO Ⅰsequences of 65 Sciaenidae individuals which belonged to 14 genera,23 species were analyzed in this study.Results showed that the A+T content of Sciaenidae CO Ⅰsequences were higher than G+C content,and the G+C content of the first codon site was significantly higher than 2 nd and 3 nd codon site.Intraspecial genetic distance was 0～0.014(average 0.004),interspecial genetic distance was 0.050～0.368(average 0.202),and average interspecial genetic distance was 50.5 times of the intraspecial genetic distance.In the phylogenetic tree,individuals of the same species were grouped into separate branches.Larimichthys and Collichthys formed monophyletic groups separately,while Argyrosomus,Nibea and Johnius didn't.The results indicated that the mitochondrial CO Ⅰgene could be used for the effective identification and phylogenetic analysis of Sciaenidae.
To study the applicability of DNA barcode technology to identify fish of Sciaenidae,CO Ⅰ sequences of 7 species of Sciaenidae were amplified and homologous sequences were obtained from GenBank.Ultimately,CO Ⅰsequences of 65 Sciaenidae individuals which belonged to 14 genera,23 species were analyzed in this study.Results showed that the A+T content of Sciaenidae CO Ⅰsequences were higher than G+C content,and the G+C content of the first codon site was significantly higher than 2 nd and 3 nd codon site.Intraspecial genetic distance was 0～0.014(average 0.004),interspecial genetic distance was 0.050～0.368(average 0.202),and average interspecial genetic distance was 50.5 times of the intraspecial genetic distance.In the phylogenetic tree,individuals of the same species were grouped into separate branches.Larimichthys and Collichthys formed monophyletic groups separately,while Argyrosomus,Nibea and Johnius didn't.The results indicated that the mitochondrial CO Ⅰgene could be used for the effective identification and phylogenetic analysis of Sciaenidae.
引文
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[10]陈泉梅．中国石首鱼科鱼类分子系统学研究[D]．广州:暨南大学，2007．
[11]吕金磊．中国近海石首鱼科鱼类DNA条形码及分子系统学研究[D]．广州:暨南大学，2017.
[2]孟庆闻．鱼类分类学[M]．北京:中国农业出版社，1996．
[3]孙典荣，陈铮．南海鱼类检索[M]．青岛:海洋出版社，2013．
[4]Ward R D,Zemlak T S,Innes B H,et al.DNAbarcoding Australia’s fish species[J].Philosophical Transactions of the Royal Society B,2005,360:1847-1857．
[5]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．
[6]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．
[7]Knight A,Mindell D P.Substitution bias,weighting of DNA sequence evolution,and the phylogenetic position of fea’s viper[J].Systematic Biology,1993,42(1):18-31．
[8]Hebert P D N,Cywinska A,Ball S L,et al.Biological identifications through DNA barcodes[J].Proceedings of the Royal Society B,2003,270(1512):313-321．
[9]Hebert P D N,Ratnasingham S,de Waard J R.Barcoding animal life:cytochrome c oxidase subunit Idivergences among closely related species[J].Proceedings of the Royal Society B,2003,270(Suppl1):96-99．
[10]陈泉梅．中国石首鱼科鱼类分子系统学研究[D]．广州:暨南大学，2007．
[11]吕金磊．中国近海石首鱼科鱼类DNA条形码及分子系统学研究[D]．广州:暨南大学，2017.