基于线粒体COI序列探讨安徽长江流域黄鳝群体遗传分化
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摘要
探讨安徽长江流域黄鳝群体遗传结构,采用线粒体COI的DNA条形码序列研究该区6个黄鳝野生群体(当涂、无为、繁昌、贵池、怀宁和望江)遗传分化。180个样本COI片段(665 bp)中共检出52个变异位点(变异率7.8%)、40种单倍型。序列中A、T、G、C碱基平均含量分别为24.7%、28.2%、17.1%、30.0%,A+T含量大于G+C含量。AMOVA分析中,高达68.45%遗传变异来自群体间,说明黄鳝群体间已产生显著遗传分化。群体间系统进化树显示:6个群体形成两大类群(当涂和繁昌群体为一类群,其余群体为另一类群),分析表明结果与各群体地理位置密切相关。同时由NCBI下载合鳃鱼科几个物种的COI同源序列,构建系统进化树,显示黄鳝与同属的山黄鳝聚为一支,并与不同属的合鳃鱼和穴栖蛇胸鳝聚为一支。研究表明,基于COI的DNA条形码序列适于黄鳝群体遗传结构研究。
In the study, partial sequences of the mitochondrial DNA cytochrome c oxidase subunit I gene(COI) of six Monopterus albus populations, which were collected from Yangtze River basin in Anhui Province, were amplified by PCR to explore genetic differentiation. The length of COI sequences of 180 M. albus individuals were all 665 bp, 40 haplotypes were identified and 52 mutation sites were detected. The nucleotide composition of A, T, G, C was 24.7%, 28.2%, 17.1%, 30.0%, respectively; A+T content was higher than G+C content. Analysis of Molecular Variance(AMOVA) indicated significant genetic differentiation among populations. The six populations could be divided into two groups based on the genetic distance and phylogenetic analysis of COI sequences, which were closely related to geographical location of each population. The molecular phylogenetic tree(NJ-tree) of Synbranchidae showed that M. albus were more closely related to Monopterus cuchia than Ophisternon aenigmaticuma and Synbranchus marmoratus. The results indicated that mitochondrial COI barcode sequence was suited for the study of population genetics study.
In the study, partial sequences of the mitochondrial DNA cytochrome c oxidase subunit I gene(COI) of six Monopterus albus populations, which were collected from Yangtze River basin in Anhui Province, were amplified by PCR to explore genetic differentiation. The length of COI sequences of 180 M. albus individuals were all 665 bp, 40 haplotypes were identified and 52 mutation sites were detected. The nucleotide composition of A, T, G, C was 24.7%, 28.2%, 17.1%, 30.0%, respectively; A+T content was higher than G+C content. Analysis of Molecular Variance(AMOVA) indicated significant genetic differentiation among populations. The six populations could be divided into two groups based on the genetic distance and phylogenetic analysis of COI sequences, which were closely related to geographical location of each population. The molecular phylogenetic tree(NJ-tree) of Synbranchidae showed that M. albus were more closely related to Monopterus cuchia than Ophisternon aenigmaticuma and Synbranchus marmoratus. The results indicated that mitochondrial COI barcode sequence was suited for the study of population genetics study.
引文
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[24]毛云涛,甘小妮,王绪祯.基于线粒体COI基因的沙鳅亚科鱼类DNA条形码及其分子系统发育研究[J].水生生物学报,2014,38(4):737-744.
[25]张迪,雷光春,龚成,等.基于COI基因序列的太湖新银鱼遗传多样性[J].湖泊科学,2012,24(2):299-306.
[26]Sun X X,Xu D D,Lou B,et al.Genetic diversity and population structure of Eleutheronema rhadinumin the East and South China Seas revealed in mitochondrial COI sequences[J].Chinese Journal of Oceanology and Limnology,2013,31(6):1276-1283.
[27]刘连为,许强华,陈新军.基于线粒体COI和Cytb基因序列的北太平洋柔鱼种群遗传结构研究[J].水产学报,2012,36(11):1675-1684.
[2]贺顺连,刘学文,郭照良,等.3种黄鳝遗传多样性分析[J].湖南农业大学学报:自然科学版,2004,30(2):145-147.
[3]蔡欣,张海容.川渝部分地区野生黄鳝RAPD引物筛选及其在绵阳群体的验证[J].西南科技大学学报,2010,25(4):96-99.
[4]杨太有,温树红,郝艳军,等.黄河流域黄鳝自然群体遗传多样性和遗传结构的研究[J].水生生物学报,2011,35(3):532-537.
[5]周宇芳,胡杭娇,张龙韬,等.长江中下游黄鳝遗传多样性的微卫星分析[J].生物技术通报,2011,11:187-192.
[6]Cai X,Yu S M,Mipam T,et al.Phylogenetic lineages of Monopterus albus(Synbranchiformes:Synbranchidae)in China inferred from mitochondrial control region[J].Journal of Zoological Systematics and Evolutionary Research,2013,51(1):38-44.
[7]胡玉婷,江河,胡王,等.安徽长江流域黄鳝六个地理种群的遗传变异研究[J].四川动物,2015,34(1):21-28.
[8]Hebert P D N,Cywinska A,Ball S L,et al.Biological identification through DNA barcodes[J].Proc R Soc Lond B Biol Sci,2003,270:313-321.
[9]Vences M,Thomas M,Bonett R M,et al.Deciphering amphibian diversity through DNA barcoding:chances and challenges[J].Phil Trans R Soc B,2005,360:1859-1868.
[10]Ward R D,Zemlak T S,Innes B H,et al.DNA barcoding Australia's fish species[J].Phil Trans R Soc B,2005,360:1847-1857.
[11]Cui Z X,Liu Y,Liu J,et al.Molecular identification of Pampusfishes(Perciformes,Stromateidae)[J].Ichthyological Research,2010,57(1):32-39.
[12]Smith P J,Steinke D,Dettai A,et al.DNA barcodes and species identifications in Ross Sea and Southern Ocean fishes[J].Polar Biology,2012,35(9):1297-1310.
[13]Sun P,Shi Z H,Yin F,et al.Genetic variation analysis of Mugil cephalus in China sea based on mitochondrial COI gene sequences[J].Biochemical Genetics,2012,50(3-4):180-191.
[14]裴男才,陈步峰.生物DNA条形码:十年发展历程、研究尺度和功能[J].生物多样性,2013,21(5):616-627.
[15]Thompson J D,Gibson T J,Plewniak F.The Clustal X windows interface:flexible strategies for multiple sequences alignment aided by quality analysis tools[J].Nucleic Acids Res,1997,25(4):4876-4882.
[16]Galtier N,Gouy M,Gautier C.Sea View and Phylo_win:two graphic tools for sequence alignment and molecular phylogeny[J].Computer Applications in the Biosciences,1996,12:543-548.
[17]Librado P,Rozas J.Dna SP v5:A software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,2009,25:1451-1452.
[18]Tamura K,Dudley J,Nei M,et al.MEGA 4:Molecular Evolutionary Genetics Analysis(MEGA)software version 4.0[J].Molecular Biology and Evolution,2007,24:1596-1599.
[19]Excoffier L,Lischer H E L.Arlequin suite ver 3.5:A new series of programs to perform population genetics analyses under Linux and Windows[J].Molecular Ecology Resources,2010,10:564-567.
[20]Wright S.Evolution and the genetics of populations[C].Chicago:University of Chicago Press,1978:580.
[21]彭居俐,王绪祯,王丁,等.基于线粒体CO1序列的DNA条形码在鲤科鲌属鱼类物种鉴定中的应用[J].水生生物学报,2009,33(2):271-276.
[22]杨天燕,孟玮,马燕武,等.基于线粒体COI和Cytb基因序列对新疆两水系斑重唇鱼遗传结构的分析[J].淡水渔业,2014,44(4):41-47.
[23]于亚男,宋超,侯俊利,等.基于线粒体COI基因部分序列的长江口虾虎鱼科鱼类系统分类[J].淡水渔业,2014,44(5):3-8.
[24]毛云涛,甘小妮,王绪祯.基于线粒体COI基因的沙鳅亚科鱼类DNA条形码及其分子系统发育研究[J].水生生物学报,2014,38(4):737-744.
[25]张迪,雷光春,龚成,等.基于COI基因序列的太湖新银鱼遗传多样性[J].湖泊科学,2012,24(2):299-306.
[26]Sun X X,Xu D D,Lou B,et al.Genetic diversity and population structure of Eleutheronema rhadinumin the East and South China Seas revealed in mitochondrial COI sequences[J].Chinese Journal of Oceanology and Limnology,2013,31(6):1276-1283.
[27]刘连为,许强华,陈新军.基于线粒体COI和Cytb基因序列的北太平洋柔鱼种群遗传结构研究[J].水产学报,2012,36(11):1675-1684.