3个地理群体仿刺参D-loop序列的变异及系统发生分析
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摘要
为研究中国大连(CD)、朝鲜罗津(KN)和俄罗斯海参崴(RV)3个仿刺参群体的遗传结构,实验采用PCR扩增和测序技术,对3个群体共计71头仿刺参的线粒体D-loop序列进行了分析。结果显示,D-loop序列长度为447~465 bp,平均A+T含量(59.2%)显著高于G+C含量;共检测到119个变异位点,多态位点比例为24.24%,其中简约信息位点为53个,共有40种基因型,群体共享基因型7个。遗传多样性参数分析显示,3个群体均显示出较丰富的遗传多样性;分子方差(AMOVA)分析表明,3个群体间遗传分化较弱或只有中度分化,且93.04%的变异来自群体内。CD群体与RV群体之间遗传距离最远,为0.042,KN群体与RV群体之间遗传距离最近,为0.037 4。将本研究所得序列结合GenBank中青岛(QD)和威海(WH)仿刺参的D-loop序列构建系统发育树,QD与WH仿刺参首先聚为一小支,然后与CD群体聚为一大支,KN群体与RV群体聚为独立一支,这一聚类方式符合地理隔离模式。
Mitochondrial D-loop sequences were analyzed to study the genetic structure of the sea cucumber Apostichopus japonicus. In this study,71 individuals from three natural populations w ere collected from Dalian,China( CD),Rajin,North Korea( KN) and Vladivostok,Russia( RV). 447- 465 bp D-loop sequences w ere obtained using PCR amplification. The mean content of A + T( 59. 2%) w as higher than G + C. The proportion of polymorphic sites w as 24. 24%,in w hich parsimony informative sites w ere 53. Forty haplotypes w ere identified from 71 samples,among w hich 7 haplotypes w ere shared by three populations. Genetic diversity parameters show ed high genetic diversity among populations. The fixation indices( FST) of analysis of molecular variance( AMOVA) w ithin populations w as 93. 04%,w hich indicated that the genetic differentiation of the three populations w as w eak or only moderately differentiated. The genetic distances among populations w ere 0. 037 4( KN and RV) and 0. 042( CD and RV). The molecular phylogenetic tree w as constructed w ith the D-loop sequences of Qingdao( QD) and Weihai( WH) from GenBank w ith NJ method using softw are MEGA 4. 0. Populations of QD and WH clustered into a small branch,then w ith CD, w hile KN and RV clustered into the other branch. The results w ere consistent w ith their geographical isolation mode.
Mitochondrial D-loop sequences were analyzed to study the genetic structure of the sea cucumber Apostichopus japonicus. In this study,71 individuals from three natural populations w ere collected from Dalian,China( CD),Rajin,North Korea( KN) and Vladivostok,Russia( RV). 447- 465 bp D-loop sequences w ere obtained using PCR amplification. The mean content of A + T( 59. 2%) w as higher than G + C. The proportion of polymorphic sites w as 24. 24%,in w hich parsimony informative sites w ere 53. Forty haplotypes w ere identified from 71 samples,among w hich 7 haplotypes w ere shared by three populations. Genetic diversity parameters show ed high genetic diversity among populations. The fixation indices( FST) of analysis of molecular variance( AMOVA) w ithin populations w as 93. 04%,w hich indicated that the genetic differentiation of the three populations w as w eak or only moderately differentiated. The genetic distances among populations w ere 0. 037 4( KN and RV) and 0. 042( CD and RV). The molecular phylogenetic tree w as constructed w ith the D-loop sequences of Qingdao( QD) and Weihai( WH) from GenBank w ith NJ method using softw are MEGA 4. 0. Populations of QD and WH clustered into a small branch,then w ith CD, w hile KN and RV clustered into the other branch. The results w ere consistent w ith their geographical isolation mode.
引文
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[20]袁媛,高玮玮,吴琪,等.黄、渤海地区青蛤(Cyclina sinensis)种群的ITS序列遗传变异与遗传结构分析[J].海洋与湖沼,2008,39(6):665-670.
[21]Shaklee J B,Tamaru C S,Waples R S.Speciation and evolution of marine fishes studied by the electrophoretic analysis of proteins[J].Spacific Science,1982,36(2):141-157.
[22]Kim M J,Choi T J,An H S.Population genetic structure of sea cucumber,Stichopus japonicus in Korea using microsatellite markers[J].Aquaculture Research,2008,39(10):1038-1045.
[23]谭杰,孙慧玲,刘萍,等.3个仿刺参地理种群遗传变异的微卫星DNA分析[J].水产学报,2007,31(4):437-442.
[24]Chang Y Q,Feng Z G,Yu J P,et al.Genetic variability analysis in five populations of the sea cucumber Stichopus(Apostichopus)japonicus from China,Russia,South Korea and Japan as revealed by microsatellite markers[J].Marine Ecology,2009,30(4):455-461.
[2]谭杰,孙慧玲,刘萍,等.仿刺参自然群体和养殖群体间遗传变异的微卫星标记研究[J].海洋水产研究,2007,28(3):38-43.
[3]高悦勉,孙静波.刺参种群同工酶的生化遗传分析[J].大连水产学院学报,2004,19(1):30-34.
[4]Yao B,Hu X L,Bao Z M,et al.Genetic variation in tw o sea cucumber(Apostichopus japonicus)stocks revealed by ISSR markers[J].Chinese Journal of Oceanology and Limnology,2007,25(1):91-96.
[5]Soliman T,Kanno M,Kijima A,et al.Population genetic structure and gene flow in the Japanese sea cucumber Apostichopus japonicus across Toyama Bay,Japan[J].Fisheries Science,2012,78(4):775-783.
[6]李娜,陈少波,谢起浪,等.闽浙地区香鱼线粒体Cytb基因和D-loop区序列多态性分析[J].遗传,2008,30(7):919-925.
[7]姚茜,杨频,陈立侨,等.罗氏沼虾三群体线粒体Dloop基因序列差异的初步研究[J].水产学报,2007,31(1):18-22.
[8]赵良杰,何光喜,周小玉,等.千岛湖大眼华鳊形态度量学和D-loop序列分析[J].水产学报,2013,37(3):351-358.
[9]Excoffier L,Laval G,Schneider S.Arlequin(ver3.0):An integrated softw are package for population genetics data analysis[J].Evolutionary Bioinformatics Online,2005,1:47-50.
[10]Tamura K,Dudley J,Nei M,et al.MEGA4:Molecular evolutionary genetics analysis(MEGA)softw are version 4.0[J].Molecular Biology and Evolution,2007,24(8):1596-1599.
[11]姜艳艳,孔晓瑜,喻子牛,等.黄海蓝点马鲛mtDNA D-loop序列变异分析[J].中国水产科学,2003,10(3):177-183.
[12]Rosel P E,Dizon A E,Haygood M G.Variability of the mitochondrial control region in populations of the harbour porpoise Phocoena phocoena on interoceanic and regional scales[J].Canadian Journal of Fisheries and Aquatic Sciences,1995,52(6):1210-1219.
[13]陶翠花.威海仿刺参野生种群遗传多样性分析[D].济南:山东大学,2009.
[14]Shen X,Tian M,Liu Z H,et al.Complete mitochondrial genome of the sea cucumber Apostichopus japonicus(Echinodermata:Holothuroidea):The first representative from the subclass Aspidochirotacea with the echinoderm ground pattern[J].Gene,2009,439(1/2):79-86.
[15]李颖,刘萍,孙慧玲,等.仿刺参(Apostichopus japonicus)mtDNA三个基因片段的序列分析[J].海洋与湖沼,2006,37(2):143-153.
[16]Cantatore P,Roberti M,Rainaldi G,et al.The complete nucleotide sequence,gene organization,and genetic code of the mitochondrial genome of Paracentrotus lividus[J].The Journal of Biological Chemistry,1989,264(19):10965-10975.
[17]周慧,李迪强,张于光,等.藏羚羊mtDNA D-loop区遗传多样性研究[J].遗传,2006,28(3):299-305.
[18]郑文娟,来育洪,尤昕煜,等.舟山小黄鱼线粒体DNA D-loop区序列变异的遗传多样性分析[J].动物学研究,2012,33(3):329-336.
[19]胡静,齐兴柱,尹绍武,等.波纹唇鱼mtDNA D-loop序列变异分析[J].海洋科学,2012,36(4):50-56.
[20]袁媛,高玮玮,吴琪,等.黄、渤海地区青蛤(Cyclina sinensis)种群的ITS序列遗传变异与遗传结构分析[J].海洋与湖沼,2008,39(6):665-670.
[21]Shaklee J B,Tamaru C S,Waples R S.Speciation and evolution of marine fishes studied by the electrophoretic analysis of proteins[J].Spacific Science,1982,36(2):141-157.
[22]Kim M J,Choi T J,An H S.Population genetic structure of sea cucumber,Stichopus japonicus in Korea using microsatellite markers[J].Aquaculture Research,2008,39(10):1038-1045.
[23]谭杰,孙慧玲,刘萍,等.3个仿刺参地理种群遗传变异的微卫星DNA分析[J].水产学报,2007,31(4):437-442.
[24]Chang Y Q,Feng Z G,Yu J P,et al.Genetic variability analysis in five populations of the sea cucumber Stichopus(Apostichopus)japonicus from China,Russia,South Korea and Japan as revealed by microsatellite markers[J].Marine Ecology,2009,30(4):455-461.
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