Volume 33 Issue 3
May  2012
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Article Contents
ZHENG Wen-Juan, LAI Yu-Hong, YOU Xin-Yu, QIN Xi-Han, ZHU Shi-Hua. Genetic diversity of Pseudosciaena polyactis in Zhoushan based on mitochondrial DNA D-loop region sequences. Zoological Research, 2012, 33(3): 329-336. doi: 10.3724/SP.J.1141.2012.03329
Citation: ZHENG Wen-Juan, LAI Yu-Hong, YOU Xin-Yu, QIN Xi-Han, ZHU Shi-Hua. Genetic diversity of Pseudosciaena polyactis in Zhoushan based on mitochondrial DNA D-loop region sequences. Zoological Research, 2012, 33(3): 329-336. doi: 10.3724/SP.J.1141.2012.03329

Genetic diversity of Pseudosciaena polyactis in Zhoushan based on mitochondrial DNA D-loop region sequences

doi: 10.3724/SP.J.1141.2012.03329
  • Received Date: 2011-11-15
  • Rev Recd Date: 2012-02-21
  • Publish Date: 2012-06-22
  • Pseudosciaena polyactis is an economically important species of marine fish in China that is currently declining due to overexploitation, environmental pollution and related factors. Research in to the genetic structure of Pseudosciaena polyactis populations plays a key role in protecting and promoting sustainable utilization. We collected 53 individuals of Pseudosciaena polyactis from Zhoushan, Zhejiang and sequenced and amplified the mitochondrial DNA (mtDNA) D-loop region using Polymerase Chain Reactions (PCR). The sequence length of the 53 individuals ranged from 795 to 801 bp. The sequences were analyzed by Clustal X1.83, MEGA3.1 and DnaSP4.0. The results showed that the average base content of T, C, A, G was 30.3%, 23.1%, 32.3% and 14.3%, respectively and there were 93 transition or transversion sites, including 53 single nucleotide mutation sites and 40 parsimony informative sites, which accounted for 11.6% of the length of the analyzed sequences. In total, we identified 52 haplotypes and found haplotype diversity (hd) of 0.9993, average number of nucleotide differences were 9.73875 (k), and nucleotide diversity (π) of 0.01233. The average genetic distance of haplotypes was 0.012, and the average transition/transversion was 4.305. Based on mitochondrial DNA D-loop region sequences, these results indicate that the genetic diversity of the Pseudosciaena polyactis population in Zhoushan is currently at a medium level.
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  • [1]
    Agnèse JF, Zentz F, Legros O, Sellos D. 2006. Phylogenetic relationships and phylogeography of the Killifish species of the subgenus Chromaphyosemion (Radda, 1971) in West Africa, inferred from mitochondrial DNA sequences [J]. Mol Phylogenet Evol, 40(2): 332-346.
    [2]
    Bielawski JP, Pumo DE. 1997. Randomly amplified polymorphic DNA (RAPD) analysis of Atlantic coast striped bass [J]. Heredity, 78(1): 32-40.
    [3]
    Chen JH, Lin LS, Ling JZ, Li JS, Ding FY. 2004. Effects of summer close season and rational utilization on redlip croaker (Larimichthys polyactis Bleeker) resource in the East China Sea region [J]. Chn J Fish Sci, 11(6): 554-560. [程家骅, 林龙山, 凌建忠, 李建生, 丁峰元. 2004. 东海区小黄鱼伏季休渔效果及其资源合理利用探讨[J]. 中国 水产科学, 11(6): 554-560.]
    [4]
    Chen JJ, Xu ZL, Chen XZ. 2010. The spatial distribution pattern of fishing ground for small yellow croaker in China Seas [J]. J Fish Chn, 34(2): 236-244. [陈佳杰, 徐兆礼, 陈雪忠. 2010. 我国沿海小黄鱼渔场的 空间格局 [J]. 水产学报, 34(2): 236-244.]
    [5]
    Clement M, Posada D, Crandall KA. 2000. TCS: A computer program to estimate gene genealogies [J]. Mol Ecol, 9(10): 1657-1659.
    [6]
    Excoffier L, Laval G, Schneider S. 2005. Arlequin ver. 3.0: An integrated software package for population genetics data analysis [J]. Evol Bioinform Online, 1(1): 47-50.
    [7]
    Fu YX. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection [J]. Genetics, 147(2): 915-925.
    [8]
    Grant WS, Bowen BW. 1998. Shallow population histories in deep evolutionary lineages of marine fishes: Insights from sardines and anchovies and lessons for conservation [J]. J Hered, 89(5): 415-426.
    [9]
    Huang H, Cheng QQ, Huang H. 2010. Recent progress and prospect of small yellow croaker (Pseudosciaena polyactis Bleeker) [J]. Mod Fish Inf, 25(9): 9-12. [黄昊, 程起群, 黄昊. 2010. 小黄鱼生物学研究进 展[J]. 现代渔业信息, 25(9): 9-12.]
    [10]
    Jiang SG, Yang HR, Su TF, Gong SY. 2004. Genetic diversity of three geographical populations of Pagrosomus major revealed by RAPD analysis [J]. J Fish Chn, 28(3): 334-338. [江世贵, 杨慧荣, 苏天凤, 龚世园. 2004. 3 个不同地理群体真鲷遗传变异的RAPD 分析 [J]. 水产学报, 28(3): 334-338.]
    [11]
    Jiang YY, Kong XY, Yu ZN, Zhuang ZM, Jin XS. 2003. Genetic diversity of Scomberomorus niphonius in the Yellow Sea revealed by mtDNA D-loop sequence [J]. J Fish Sci Chn, 10(3): 177-183. [姜艳艳, 孔晓瑜, 喻子牛, 庄志猛, 金显仕. 2003. 黄海蓝点马鲛mtDNA D-loop 序列 变异分析 [J]. 中国水产科学, 10(3): 177-183.]
    [12]
    Jin XS. 1996. Ecology and population dynamics of small yellow croaker (Pseudosciaena polyactis bleeker) in the Yellow Sea [J]. J Fish Sci Chn, 3(1): 32-46. [ 金显仕. 1996. 黄海小黄鱼 (Pseudosciaena polyactis) 生态和种群动态的研究 [J]. 中国水产科学, 3(1): 32-46.]
    [13]
    Kumar S, Tamura K, Nei M. 1994. MEGA: molecular evolutionary genetics analysis software for microcomputers [J]. Cabios, 10(2): 189-191.
    [14]
    Lee WJ, Conroy J, Howell WH, Kocher TD. 1995. Structure and evolution of teleost mitochondrial control regions [J]. J Mol Evol, 41(1): 54-66.
    [15]
    Lin LS. 2004. Analysis on extant abundance of small yellow croaker Pseudosciaena polyactis in the East China Sea [J]. Mar Fish, 26(1): 18-23. [林龙山. 2004. 东海区小黄鱼现存资源量分析[J]. 海洋渔业, 26(1): 18-23.]
    [16]
    Lin LS, Chen JH, Ren YP, Ling JZ. 2004. Analysis of population biology of small yellow croaker Pseudosciaena polyactis in the East China Sea region [J]. J Fish Sci Chn, 11(4): 333-338. [林龙山, 程家骅, 任一平, 凌建忠. 2004. 东海区小黄鱼种群生物学特性的分析 [J]. 中国水产 科学, 11(4): 333-338.]
    [17]
    Liu JX, Gao TX, Zhuang ZM, Jin XS, Yokogawa K, Zhang YP. 2006. Late Pleistocene divergence and subsequent population expansion of two closely related fish species, Japanese anchovy (Engraulis japonicus) and Australian anchovy (Engraulis australis) [J]. Mol Phylogent Evol, 40(3): 712-723.
    [18]
    Liu SF, Wu RX, Zhu L, Zhuang ZM. 2010. Complete sequence and gene organization of mitochondrial DNA of the small yellow croaker Larimichthys polyactis [J]. Oceanol Limnol Sin, 41(6): 885-894. [柳淑 芳, 吴仁协, 朱玲, 庄志猛. 2010. 小黄鱼 (Larimichthys polyactis) 线粒体基因组结构与特征 [J]. 海洋与湖沼, 41(6): 885-894.]
    [19]
    Liu ZZ, Yang JQ, Wang ZQ, Tang WQ. 2009. Genetic structure and population history of Beleophthalmus petinirostris in Yangtze river estuary and its southern adjacent regions [J]. Zool Res, 30(1): 1-10. [刘 至治, 杨金权, 王正琦, 唐文乔. 2009. 长江口及其南部邻近地区大 弹涂鱼种群遗传结构及种群历史分析[J]. 动物学研究, 30(1): 1-10.]
    [20]
    Meng ZN, Zhuang ZM, Jin XS, Tang QS, Su YQ. 2003. Genetic diversity in small yellow croaker (Pseudosciaena polyactis) by RAPD analysis [J]. Biodivers Sci, 11(3): 197-203. [蒙子宁, 庄志猛, 金显仕, 唐启升, 苏 永全. 2003. 黄海和东海小黄鱼遗传多样性的RAPD 分析 [J]. 生物 多样性, 11(3): 197-203.]
    [21]
    Mao Y, Jiang QF, Zeng HS, Wang J. 2010. Genetic diversity of Pseudosciaena crocea (Richardson) based on mitochondrial DNA control region sequences [J]. J Xiamen Univ:Nat Sci, 49(3): 440-444. [毛勇, 蒋秋芬, 曾华嵩, 王军. 2010. 大黄鱼线粒体DNA 控制区遗 传多样性分析[J]. 厦门大学学报:自然科学版, 49(3): 440-444.]
    [22]
    Niu SF, Su YQ, Wang J, Zhang LY, Zeng HS, Zhang M. 2011. Genetic polymorphism of mitochondrial control region and cyt b in Trachurus japonicus from Fujian coastal waters [J]. J Fish Sci Chn, 18(1): 66-74. [牛素芳, 苏永全, 王军, 张丽艳, 曾华嵩, 张曼. 2011. 福建近海竹 荚鱼线粒体DNA 控制区和细胞色素b 遗传多态性[J]. 中国水产科 学, 18(1): 66-74.]
    [23]
    Peng B, Zhang Q, Zhao S, Yue XL. 2010. Genetic diversity analysis of Larimichthys polyactis in coastal waters of China based on Cytochrome b gene [J]. Guangdong Agric Sci, 37(2): 131-135. [彭博, 章群, 赵爽, 乐小亮. 2010. 中国近海小黄鱼遗传变异的细胞色素b 序列分析 [J]. 广东农业科学, 37(2): 131-135.]
    [24]
    Quan JX, Dai JX, Shen SD, Deng JY, Zhuang ZM. 2000. Genetic variation analysis of two mullet populations through randomly amplified polymorphic DNA(RAPD) method [J]. Acta Oceanol Sin, 22(5): 82-87. [权洁霞, 戴继勋, 沈颂东, 邓景耀, 庄志猛. 2000. 梭鱼人工养殖群 体与自然群体的随机扩增多态DNA(RAPD)分析 [J]. 海洋学报, 22(5): 82-85.]
    [25]
    Rogers AR, Harpending H. 1992. Population growth makes waves in the distribution of pairwise genetic differences [J]. Mol Biol Evol, 9(3): 552-569.
    [26]
    Shaklee JB, Tamaru CS, Waples RS. 1982. Speciation and evolution of marine fishes studied by the electrophoretic analysis of proteins [J]. Pac Sci, 36(2): 141-157.
    [27]
    Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism [J]. Genet, 123(3): 585-595.
    [28]
    Tang QY, Liu HZ, Yang XP, Xiong BX. 2005. Studies on the structure of the mitochondrial DNA control region and Phylogenetic Relationships of the subfamily Botiinae [J]. Acta Hydrobiol Sin, 29(6): 645-653. [唐 琼英, 刘焕章, 杨秀平, 熊邦喜. 2005. 沙鳅亚科鱼类线粒体DNA 控制区结构分析及系统发育关系的研究 [J]. 水生生物学报, 29(6): 645-653.]
    [29]
    Xia YZ, Sheng Y, Chen YY. 2006. DNA sequence variation in the mitochondrial control region of lenok (Brachymystax lenok) populations in China [J]. Biodivers Sci, 14(1): 48-54. [夏颖哲, 盛岩, 陈宜瑜. 2006. 利用线粒体DNA控制区序列分析细鳞鲑种群的遗传 结构 [J]. 生物多样性, 14(1): 48-54.]
    [30]
    Xu GP, Zhong XM, Ding YP, Liu PT, Tang JH, Xu P. 2005. The research on genetic diversity of Pseudosciaena polyactis population from the southern part of the Yellow Sea [J]. Mar Sci, 29(11): 34-38. [许广平, 仲霞铭, 丁亚平, 刘培庭, 汤建华, 许璞. 2005. 黄海南部小黄鱼群 体遗传多样性研究[J]. 海洋科学, 29(11): 34-38.]
    [31]
    Yan LP, Hu F, Ling JZ, Li SF. 2006. Study on age and growth of Larimichthys polyactis in the East China Sea [J]. J Ocean Univ Chn, 36(1): 95-100. [严利平, 胡芬, 凌建忠, 李圣法. 2006. 东海北部和 黄海南部小黄鱼年龄与生长的研究 [J]. 中国海洋大学学报: 自然 科学版, 36(1): 95-100.]
    [32]
    Yan XL, Tang WQ, Yang JQ. 2009. Population genetic structure of tapertail anchovy (Coilia mystus) in coastal waters of southeast China based on mtDNA control region sequences [J]. Biodivers Sci, 17(2): 143-150. [阎雪岚, 唐文乔, 杨金权. 2009. 基于线粒体控制区的序列变异分析 中国东南部沿海凤鲚种群遗传结构 [J]. 生物多样性, 17(2): 143-150.]
    [33]
    Yang JQ, Hu XL, Tang WQ, Lin HD. 2008. mtDNA control region sequence variation and genetic diversity of Coilia nasus in Yangtze River estuary and its adjacent waters [J]. Chn J Zool, 43(1): 8-15. [杨金权, 胡雪莲, 唐文乔, 林弘都. 2008. 长江口邻近水域刀鲚的线粒体控制区序列 变异与遗传多样性[J]. 动物学杂志, 43(1): 8-15.]
    [34]
    Zhou H, Li DQ, Zhang YG, Yi XR, Liu Y. 2006. Study on mitochondrial DNA genetic diversity of Tibetan Antelope [J]. Hereditas, 28(3): 299-305. [周慧, 李迪强, 张于光, 易湘蓉, 刘毅. 2006. 藏羚羊 mtDNA D-loop 区遗传多样性研究[J]. 遗传, 28(3): 299-305.]
    [35]
    Zhou Q, Wang W. 2004. Detecting natural selection at the DNA level [J]. Zool Res, 25(1): 73-80. [周琦, 王文. 2004. DNA 水平自然选择作用 的检测 [J]. 动物学研究, 25(1): 73-80.]
    [36]
    Zhu SH, Yang YC, Shen XQ, Zou JX, Zheng WJ, Yu HW, Huang B. 2006.Phylogenetic relationships of Lutjanus inferred from mitochondrial cytochrome b sequences [J]. Acta Zool Sin, 52(3): 514-521. [朱世华, 杨迎春, 沈锡权, 邹记兴, 郑文娟, 余红卫, 黄勃. 2006. 从细胞色 素b 基因序列探讨笛鲷属的分子系统发生关系 [J]. 动物学报, 52(3): 514-521.]
    [37]
    Zhu SH, Zheng WJ, Zou JX, Yang YC, Shen XQ. 2007. Mitochondrial DNA control region structure and molecular phylogenetic relationship of carangidae[J]. Zool Res, 28(6): 606-614. [朱世华, 郑文娟, 邹记兴, 杨迎春, 沈锡权. 2007. 鲹科鱼类线粒体DNA 控制区结构及系统发 育关系[J]. 动物学研究, 28(6): 606-614.]
    [38]
    Zhu TJ, Yang JQ, Tang WQ. 2008. MtDNA control region sequence structure of the genus Coilia in Yangtze River estuary [J]. J Shanghai Fish Univ, 17(2): 152-157. [诸廷俊, 杨金权, 唐文乔. 2008. 长江口 鲚属鱼类线粒体DNA 控制区结构分析[J]. 上海水产大学学报, 17((2): 152-157.]
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