基于线粒体COⅠ和16S rRNA基因序列比较分析东海带鱼群体遗传多样性
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摘要
测定了东海带鱼(Trichiurus lepturus Linnaeus)三个群体(命名为A:122°32′E 29°55′N、B:123°30′E26°75N;C:124°24′E 27°26′N)72个个体的线粒体DNA16S rRNA和COⅠ基因序列,通过单基因序列和联合序列分析,研究了东海带鱼群体的遗传变异情况。分别得到1130 bp的COⅠ基因序列片段和554 bp的16S rRNA序列片段,其中COⅠ基因片段的T、C、A、G含量分别为29.0%、28.9%、24.4%和17.7%;16S rRNA基因片段的T、C、A、G含量分别为22.7%、27.6%、28.0%和21.7%。基于线粒体16S rRNA、COⅠ和16S+COⅠ基因序列分析,72个个体中分别确定43个,8个和49个单倍型,存在单倍型共享现象。群体的单倍型多样性指数为0.9766—0.9992,显示了群体内的单倍型较为丰富。3个群体间各序列平均核苷酸差异数(K)在5.111—9.024和0.0045—0.0076,核苷酸多样性指数(π)为0.0048—0.0084,显示不同带鱼群体遗传多态性丰富。使用邻接法构建的分子进化树揭示同一群体内大部分个体聚在一起。分析结果表明,群体A遗传背景比群体B、群体C较为丰富,群体内部个体差异大于群体间差异,群体间基因交流频率较高,遗传分化不明显,初步判定东海带鱼3个群体的遗传多样性偏低。
Asingle gene fragment and combined nucleotide sequences for two gene fragments of mitochondrial DNA(mtDNA),which were 16S ribosomal RNA(16S rRNA)and cytochrome oxidase c subunit 1(COⅠ),were analyzed for three populations of Trichiurus lepturus(T.lepturus,designated by A,B,and C).The length of 16S rRNA gene of mtDNA and COⅠwas 1130 and 554 bp,respectively.These two gene fragments were combined together to form a gene fragment with the length of 1684 bp for the purpose of subsequent genetic diversity analysis.The average contents of nucleotides T,C,A,and G were 29.0%,28.9%,24.4%and 17.7%,respectively in the mtDNA COⅠgene,while those mean contents were 22.7%,27.6%,28.0%and 21.7%respectively in 16S rRNA gene.In this study,43,8,and 49 haplotypes were defined in 72 individuals by using single and combined gene fragments,in which haplotypes were shared among the mentioned populations.The diversities of haplotypes varied between 0.9766 and 0.9992,indicating that the abundance of haplotypes was within different populations.The nucleotide differences and the nucleotide diversity in each population were in the ranges of 5.111—9.024 and 0.0045—0.0076,respectively.Genetic distances among the populations varied from 0.0048 to 0.00084.These results indicated that genetic diversity in three populations of T.lepturus was considerable.The construction of phylogenetic trees based on Neighbour-Joining(NJ)method showed that several individuals in the same population were aggregated.The achieved findings also indicated that high frequency of gene transfer among different populations resulted in low genetic differentiation.Population A contained richer genetic background than that of populations B and C.The difference within different populations was higher compared to among various populations.It could be concluded that the three mentioned populations of T.lepturus had low genetic diversity based on single and combined mtDNA genes.
Asingle gene fragment and combined nucleotide sequences for two gene fragments of mitochondrial DNA(mtDNA),which were 16S ribosomal RNA(16S rRNA)and cytochrome oxidase c subunit 1(COⅠ),were analyzed for three populations of Trichiurus lepturus(T.lepturus,designated by A,B,and C).The length of 16S rRNA gene of mtDNA and COⅠwas 1130 and 554 bp,respectively.These two gene fragments were combined together to form a gene fragment with the length of 1684 bp for the purpose of subsequent genetic diversity analysis.The average contents of nucleotides T,C,A,and G were 29.0%,28.9%,24.4%and 17.7%,respectively in the mtDNA COⅠgene,while those mean contents were 22.7%,27.6%,28.0%and 21.7%respectively in 16S rRNA gene.In this study,43,8,and 49 haplotypes were defined in 72 individuals by using single and combined gene fragments,in which haplotypes were shared among the mentioned populations.The diversities of haplotypes varied between 0.9766 and 0.9992,indicating that the abundance of haplotypes was within different populations.The nucleotide differences and the nucleotide diversity in each population were in the ranges of 5.111—9.024 and 0.0045—0.0076,respectively.Genetic distances among the populations varied from 0.0048 to 0.00084.These results indicated that genetic diversity in three populations of T.lepturus was considerable.The construction of phylogenetic trees based on Neighbour-Joining(NJ)method showed that several individuals in the same population were aggregated.The achieved findings also indicated that high frequency of gene transfer among different populations resulted in low genetic differentiation.Population A contained richer genetic background than that of populations B and C.The difference within different populations was higher compared to among various populations.It could be concluded that the three mentioned populations of T.lepturus had low genetic diversity based on single and combined mtDNA genes.
引文
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[7]Weng Z H,Xie Y J,Xiao Z Q,et al.Molecular identification of the taxonomic status of Sinonovacula rivularis and genus Sinonovacula using mitochondrial COⅠand 16SrRNA fragments[J].Acta Hydrobiologica Sinica,2013,37(4):684-690[翁朝红,谢仰杰,肖志群,等.线粒体COⅠ和16S rRNA片段确定近江蛏和缢蛏属的分类地位.水生生物学报,2013,37(4):684-690]
[8]Zhao H Q.Studies on the feeding habits of Trichiurus lepturus in East China Sea[D].Zhoushan:Zhejiang Ocean University.2014[赵洪强.东海带鱼食性研究.舟山:浙江海洋大学.2014]
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[10]Chai X J,Zhu Y H,Wang Y B,et al.Study on the Embryonic development of Trichiurus lepturus in the East China Sea[J].Journal of Zhejiang Ocean University(Natural Science),2015,34(5):429-432[柴学军,朱云海,王跃斌,等.东海带鱼的胚胎发育研究.浙江海洋学院学报(自然科学版),2015,34(5):429-432]
[11]Wang Y,Xu H X.Dymamic analysis on Trichiurus japonicus resources in summer closed fishing system in East China Sea[J].Journal of Zhejiang Ocean University(Natural Science),2009,28(4):384-388[王垚,徐汉祥.伏季休渔制度下东海区带鱼资源动态分析.浙江海洋学院学报(自然科学版),2009,28(4):384-388]
[12]Zheng W J,Du Y C,Lin J,et al.Genetic diversity analysis of Trichiurus lepturus in Zhoushan based on mitochondrial and D-loop region partial sequences[J].Acta Hydrobiologica Sninca,2015,39(2):408-423[郑文娟,杜一超,林洁,等.基于线粒体DNA D-loop区部分序列分析舟山海域带鱼种群遗传结构.水生生物学报,2015,39(2):408-423]
[13]Liu Y,Cui Z.The complete mitochondrial genome sequence of the cutlassfish Trichiurus japonicas(Perciformes:Trichiuridae):genome characterization and phylogenetic considerations[J].Marine Genomics,2009,2(2):133-142
[14]Rychlik W.OLIGO 7 primer analysis software[J].Methods in Molecular Biology,2007,402:35-60
[15]Kessing B,Croom H,Martin A,et al.The simple fool’s guide to PCR[M].Department of Zoology,University of Hawaii,Honolulu.1989,1-23
[16]Clark M J,Chen R,Lam H Y,et al.Performance comparison of exome DNA sequencing technologies[J].Nature Biotechnology,2011,29(10):908-914
[17]Hall T A.BioEdit:a user-friendly biological sequence alignment editor and analysis program for windows95/98/NT[J].Nucleic Acids Symposium Series,1999,41:95-98
[18]Librado P,Rozas J.DnaSP v5:a software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,2009,25(11):1451-1452
[19]Tajima F.The effect of change in population size on DNA polymorphism[J].Genetics,1989,123(3):597-601
[20]Tamura K,Peterson D,Peterson N,et al.MEGA5:Molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance,and maximum parsimony methods[J].Molecular Biology Evolution,2011,28(10):2731-2739
[21]Liu X,Guo Y,Wang Z,et al.The complete mitochondrial genome sequence of Trichiurus nanhaiensis(Perciformes:Trichiuridae)[J].Mitochondrial DNA,2013,24(5):516-517
[22]Meng Z N.The genetic diversity in Pseudosciaena polyactis,Trichiurus lepturus,Eupleurogrammus muticus and the molecular phylogeny of eight Sciaenoid species in the neritic waters of China[D].Xiamen:Xiamen University.2003[蒙子宁.中国近海小黄鱼、带鱼和小带鱼的遗传多样性以及八种石首鱼类的分子系统进化.厦门大学,厦门.2003]
[23]Li P F,Zhu W B,He Z T,et al.DNA barcoding construction and genetic diversity revealed by mtDNA COⅠof Trichiurus lepturus in the East China sea[J].Journal of Zhejiang Ocean University(Natural Science),2013,32(1):6-9[李鹏飞,朱文斌,贺舟挺,等.东海带鱼DNA条形码的建立及COⅠ序列变异分析.浙江海洋学院学报(自然科学版),2013,32(1):6-9]
[24]Xiao Y S.Molecular Phylogeography of Six Marine Fishes in the Northwestern Pacific[D].Ocean University of China,Qingdao.2011[肖永双.西北太平洋五种海洋鱼类的分子系统地理学研究.中国海洋大学,青岛.2011]
[25]Teletchea F.Molecular indentification methods of fish species:reassessment and possible applications[J].Reviews in Fish Biology and Fisheries,2009,19(3):265-293
[26]Chen S Y,Xu S X,Zhang Z Y,et al.Study of genetic diversity of wild and culture populations of Pseudosciaena crocea using two molecular markers[J].Marine Sciences,2011,35(12):82-87[陈淑吟,徐士霞,张志勇,等.大黄鱼野生群体与养殖群体遗传多样性研究.海洋科学,2011,35(12):82-87]
[27]Wang Z L.Study on the morphology and germplasm resource divergence of different geographical groups of small yellow croaker[D].Zhejiang Ocean University.Zhoushan.2016[王肇霖.不同地理群体小黄鱼形态和种质资源差异研究.浙江海洋大学,舟山.2016]
[28]Chai X J,Hu Z H,Wang Y B,et al.Genetic diversity and the relationship of Nibea japonica and Nibea miichthiodies using mitochondrial DNA gene[J].Biochemical Systematics and Ecology,2013,48(2):274-280
[29]Peng S M,Shi Z H,Hou J L.Comparative analysis on the genetic diversity of cultured and wild silver pomfret populations based on mtD-loop and COⅠgene[J].Journal of Fisheries of China,2010,34(1):19-25[彭士明,施兆鸿,侯俊利.基于线粒体D-loop区与COⅠ基因序列比较分析养殖与野生银鲳群体遗传多样性.水产学报,2010,34(1):19-25]
[30]Deng C X.Genetic diversity of Eleutheronema on the East and South China Seas based on mitochondrial COⅠgene sequences analysis[D].Jinan University.Guangzhou.2014[邓春兴.基于COⅠ基因序列的中国东南沿海四指马鲅属鱼类的遗传多样性分析.暨南大学,广州.2014]
[31]Cao Y,Zhang Q,Gong Y Y,et al.Genetic variation of Scomberomorus niphonius in the coastal waters of China based on mtDNA COⅠsequences[J].Marine Fisheries,2015,37(6):485-493[曹艳,章群,宫亚运,等.基于线粒体COⅠ序列的中国沿海蓝点马鲛遗传多样性.海洋渔业,2015,37(6):485-493]
[32]Grant W S,Bowen B W.Shallow population histories in deep evolutionary lineages of marine fishes:insights from sardines and anchovies and lessons for conservation[J].Journal of Heredity,1998,89(5):415-426
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