泥东风螺线粒体基因组及其遗传多样性分析
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摘要
为研究泥东风螺线粒体基因组遗传进化和遗传多样性,采用PCR扩增和直接测序技术,对泥东风螺线粒体基因组全序列及3个野生群体线粒体基因测序,并用生物软件进行分析。研究结果表明,泥东风螺线粒体基因组上的tRNA-Met、tRNA-Tyr、tRNA-Cys、tRNA-Trp、tRNA-GLn、tRNA-Gly、tRNA-Glu和tRNA-Thr位于环形线粒体L链上;18种腹足纲动物线粒体全长基因相似性为70.1%～92.9%,种间的12SRNA和16SRNA相似性与线粒体基因组全长相似性相当;12SRNA的391～491bp区域和16SRNA的1～106bp和361～481bp区域为高度变异区,而16SRNA的1191～1317bp区域为高度保守区;以F5引物扩增测序3个野生群体,共检测到由40个多态位点组成的26个单倍型,野生群体单倍型多样性为(0.406±0.112)～(0.532±0.113),野生群体核苷酸多样性为(0.00094±0.00124)～(0.00111±0.00123);北海野生群体与连江和长乐野生群体之间的遗距离分别为0.00094和0.00099。其结果可以为泥东风螺遗传进化、人工增殖和种质资源保护评估提供参考。
The complete mitochondrial genome sequences and 16 SRNA and COXⅠ genes sequences were analyzed in snail Babylonia lutosa and three wild population of the snail by PCR amplification and direct sequencing and by the biological software to evaluate the snail genetic evolution and population genetic diversity.The results showed that the tRNA-Met,tRNA-Tyr,tRNA-Cys,tRNA-Trp,tRNA-GLn,tRNAGLy,tRNA-GLu and tRNA-Thr were located in the L chain of circular mitochondria.There was mitochondrial genome similarities of 70.1%—92.9%in 18 species in Gastropoda,with more similarities of 12 S RNA′s and 16SRNA′s in the complete mitochondrial genome than in other mitochondrial genes.The highly variable areas were found in 391—491bp area of 12 SRNA,in 1—91bp and 361—481bp area of 16 S RNA,with highly conservative area in 1191—1317bp area of 16 SRNA.A total of 40 polymorphic nuclecotide sites were detected in three wild populations,which were defined as 26 haplotypes.Amplification and sequencing of F5 primers revealed that the snail had haplotype diversity of(0.406±0.112)—(0.532±0.113)and nucleotide diversity of(0.00094±0.00124)—(0.00111±0.00123).The genetic distance was found to be 0.00099 between Bei Hai population and Chang Le population and 0.00094 between Bei Hai and Lian Jiang population.The findings can provide reference for evaluation of evolution,artificial breeding and germplasm resources protection of snail B.lutosa.
The complete mitochondrial genome sequences and 16 SRNA and COXⅠ genes sequences were analyzed in snail Babylonia lutosa and three wild population of the snail by PCR amplification and direct sequencing and by the biological software to evaluate the snail genetic evolution and population genetic diversity.The results showed that the tRNA-Met,tRNA-Tyr,tRNA-Cys,tRNA-Trp,tRNA-GLn,tRNAGLy,tRNA-GLu and tRNA-Thr were located in the L chain of circular mitochondria.There was mitochondrial genome similarities of 70.1%—92.9%in 18 species in Gastropoda,with more similarities of 12 S RNA′s and 16SRNA′s in the complete mitochondrial genome than in other mitochondrial genes.The highly variable areas were found in 391—491bp area of 12 SRNA,in 1—91bp and 361—481bp area of 16 S RNA,with highly conservative area in 1191—1317bp area of 16 SRNA.A total of 40 polymorphic nuclecotide sites were detected in three wild populations,which were defined as 26 haplotypes.Amplification and sequencing of F5 primers revealed that the snail had haplotype diversity of(0.406±0.112)—(0.532±0.113)and nucleotide diversity of(0.00094±0.00124)—(0.00111±0.00123).The genetic distance was found to be 0.00099 between Bei Hai population and Chang Le population and 0.00094 between Bei Hai and Lian Jiang population.The findings can provide reference for evaluation of evolution,artificial breeding and germplasm resources protection of snail B.lutosa.
引文
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[28]秦溱,王晓清,曾志南,等.泥东风螺4个群体遗传多样性的AFLP分析[J].湖南农业大学学报:自然科学版,2014,40(3):299-304.
[2]张汉华,吴进锋,陈利雄,等.东风螺人工育苗、养殖及产业化发展前景[J].南方水产,2004(11):2-5.
[3]陈利雄,吴进锋.东风螺的增养殖技术及产业化前景[J].齐鲁渔业,2004,21(10):9-11.
[4]冯永勤,王建勋,廖威.泥东风螺人工繁育技术研究[J].科学养鱼,2006(4):35-36.
[5]钟春雨.泥东风螺围栏养殖技术[J].中国水产,2008(3):57.
[6]郑雅友,苏新红,曾志南,等.两种培育方法对泥东风螺稚螺生长与存活的影响[J].福建水产,2014,36(6):459-464.
[7]林国清,林丹,陈曦飞,等.泥东风螺(Babylonia lutosa)规模化人工育苗技术和早期发育观察[J].福建水产,2015,40(1):20-28.
[8]叶泉土,巫旗生,曾志南,等.不同底播密度对泥东风螺(Babylonia lutosa)幼螺生长和存活的影响[J].福建水产,2015,40(1):36-42.
[9]叶泉土,刘勇,曾志南,等.泥东风螺增殖放流跟踪调查及效果分析[J].福建水产,2015,40(2):140-147.
[10]Wolstenholme D R.Animal mitochondrial DNA:structure and evolution[J].Int Rev Cytol,1992(141):173-216.
[11]Miya M,Takeshima H,Endo H,et al.Major patterns of higher teleostean phylogenies:a new perspective based on 100complete mitochondrial DNA sequences[J].Mol Phylogenet Evol,2003,26(1):121-138.
[12]Lavoue S,Miya M,Saitoh K,et al.Phylogenetic relationships among anchovies,sardines,herrings and their relatives(Clupeiformes),inferred from whole mitogenome sequences[J]. Mol Phylogenet Evol,2007,43(3):1096-1105.
[13]苏天凤,黄建华,吴进锋,等.2种东风螺线粒体基因序列多态性研究[J].中国水产科学,2007,14(3):369-376.
[14]汪桂玲,李家乐,白志毅.三角帆蚌五个野生群体线粒体DNA 16SrRNA遗传特性[J].生态学杂志,2010,29(2):377-381.
[15]王成辉,李思发,刘至治,等.3种中华绒螯蟹群体线粒体COⅡ基因序列测定与进化分析[J].水产学报,2008,32(1):8-12.
[16]田鑫江,吴宁,黎中宝,等.6种鳗鲡(Anguilla)线粒体DNA COⅡ基因序列分析及其系统发育[J].海洋与湖沼,2011,42(2):279-283.
[17]杨丽萍,卢迈新,叶星,等.尼罗罗非鱼线粒体基因组全序列测定与系统进化分析[J].中国生物化学与分子生物学报,2010,26(5):484-490.
[18]Xiong G,Ma X,Wang X Q,et al.The complete mitochondrial genome of the Babylonia lutosa[J].Mitochondrial DNA,2015,26(2):187-188.
[19]Lohse M,Drechsel O,Kahlau S,et al.Organellar genome DRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets[J].Nucleic Acids Res,2013,41(Web Server issue):575-581.
[20]Librado P,Rozas J.DnaSP v5:a software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,2009,25(11):1451-1452.
[21]Tamura K,Peterson D,Peterson N,et al.MEGA5:molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance,and maximum parsimony methods[J].Mol Biol Evol,2011,28(10):2731-2739.
[22]Jacobs H T,Elliott D J,Math V B,et al.Nucleotide sequence and gene organization of sea urchin mitochondrial DNA[J].J Mol Biol,1988,202(2):185-217.
[23]Lunt D H,Whipple L E,Hyman B C.Mitochondrial DNA variable number tandem repeats(VNTRs):utility and problems in molecular ecology[J].Mol Ecol,1998,7(11):1441-1455.
[24]Arnason E,Rand D M.Heteroplasmy of short tandem repeats in mitochondrial DNA of Atlantic cod,Gadus morhua[J].Genetics,1992,132(1):211-220.
[25]Anderson F E.Phylogeny and historical biogeography of the loliginid squids(Mollusca:cephalopoda)based on mitochondrial DNA sequence data[J].Mol Phylogenet Evol,2000,15(2):191-214.
[26]Folmer O,Black M,Hoeh W,et al.DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates[J].Mol Mar Biol Biotechnol,1994,3(5):294-299.
[27]Xiong G,Ma X,Wang X.Development and characterization of 18microsatellite markers for the Babylonia lutosa[J].Conservation Genet Resour,2015,2(7):471-472.
[28]秦溱,王晓清,曾志南,等.泥东风螺4个群体遗传多样性的AFLP分析[J].湖南农业大学学报:自然科学版,2014,40(3):299-304.