SU Tianfeng, JIANG Shigui. Structure and phylogenetic analysis of mitochondrial DNA control region of genus Trachurus[J]. South China Fisheries Science, 2011, 7(1): 18-25. DOI: 10.3969/j.issn.2095-0780.2011.01.003
Citation: SU Tianfeng, JIANG Shigui. Structure and phylogenetic analysis of mitochondrial DNA control region of genus Trachurus[J]. South China Fisheries Science, 2011, 7(1): 18-25. DOI: 10.3969/j.issn.2095-0780.2011.01.003

Structure and phylogenetic analysis of mitochondrial DNA control region of genus Trachurus

More Information
  • Received Date: July 07, 2010
  • Revised Date: July 29, 2010
  • We used PCR to amplify the complete sequences of mitochondrial DNA (mtDNA) control region of 2 Trachurus japonicus from South China Sea, and then aligned them by Clustal X with 8 other species of the genus Trachurus from GenBank. According to the alignment and structure comparison, the mtDNA control region of the genus Trachurus can be divided into 3 domains: termination associated sequence domain (TAS), central conserved domain (CD) and conserved sequence block domain (CSB).We identified 2 termination-associated sequences (TAS) and 3 conserved blocks (CSB-F, CSB-E and CSB-D) in CD domain as well as 3 conserved sequence blocks (CSB-1, CSB-2 and CSB-3) in CSB domain. Taking Siniperca chuatsi as outgroup, the molecular phylogenetic relationship among 9 Carangidae was analyzed using neighbor-joining (NJ) method and maximum parsimony method in MEGA 4.0. Results show that the genus Trachurus fishes belong to a monophyletic group: T.picturatus, T.murphyi, T.symmetricus, T.capensis and T.Trachurus gather into one cluster; T.mediterraneus, T.declivis, T.japonicus and T.novaezelandiae gather another. T.japonicus does not form into an independent group but is merged into T.declivis and T.novaezelandiae. Thus, it is suggested that T.japonicus and T.novaezelandiae may be 2 synonyms.

  • [1]
    伍汉霖, 邵广昭, 赖春福. 拉汉世界鱼类名典[M]. 基隆: 水产出版社, 1999. https://xueshu.baidu.com/usercenter/paper/show?paperid=d1a399a58f751d887b00f7e32bc1d765&site=xueshu_se

    WU Hanlin, SHAO Guangzhao, LAI Chunfu. Latin-Chinese dictionary of fishes names[M]. Keelung : The Suei Chan Press, 1999. (in Chinese) https://xueshu.baidu.com/usercenter/paper/show?paperid=d1a399a58f751d887b00f7e32bc1d765&site=xueshu_se
    [2]
    中国科学院动物研究所, 中国科学学院海洋研究所, 上海水产学院. 南海鱼类志[M]. 北京: 科学出版社, 1962: 213-421.

    Institute of Zoology, Chinese Academy of Science, Institute of Oceanology, Chinese Academy of Sciences, Shanghai Fisheries University. Fish fauna of the South China Sea[M]. Beijing: Science Press, 1962: 213-421. (in Chinese)
    [3]
    郭新红, 刘少军, 刘巧, 等. 鱼类线粒体研究新进展[J]. 遗传学报, 2004, 31(9): 983-1000. https://xueshu.baidu.com/usercenter/paper/show?paperid=25713e1ff4e884760e4e4364b31966b8&site=xueshu_se&hitarticle=1

    GUO Xinhong, LIU Shaojun, LIU Qiao, et al. New progresses on mitochondrial DNA in fish[J]. Acta Genetica Sinica, 2004, 31(9): 983-1000. (in Chinese) https://xueshu.baidu.com/usercenter/paper/show?paperid=25713e1ff4e884760e4e4364b31966b8&site=xueshu_se&hitarticle=1
    [4]
    刘焕章. 鱼类线粒体DNA控制区的结构与进化: 以鳑鲏鱼类为例[J]. 自然科学进展, 2002, 12(3): 266-270. doi: 10.3321/j.issn:1002-008X.2002.03.008

    LIU Huanzhang. Structure and evolution of mitochondrial DNA control region in fish: Take Rhodeus ocellatus as an example[J]. Progr Nat Sci, 2002, 12(3): 266-270. (in Chinese) doi: 10.3321/j.issn:1002-008X.2002.03.008
    [5]
    曾青兰, 刘焕章. 大口胭脂鱼线粒体DNA控制区序列的研究[J]. 湖北大学学报: 自然科学版, 2001, 23(3): 261-264. doi: 10.3969/j.issn.1000-2375.2001.03.021

    ZENG Qinglan, LIU Huanzhang. Study on mitochondrial DNA control region of the Ictiobus cyprinellus[J]. J Hubei Univ: Natural Science, 2001, 23(3): 261-264. (in Chinese) doi: 10.3969/j.issn.1000-2375.2001.03.021
    [6]
    郑冰蓉, 张亚平, 肖蘅, 等. 鲤属鱼类mtDNA控制区序列的变异性分析[J]. 水产学报, 2002, 26(4): 289-294.

    ZHENG Bingrong, ZHANG Yaping, XIAO Heng, et al. The sequence variation feature of mtDNA D-loop region of Cyprinus[J]. J Fish China, 2002, 26(4): 289-294. (in Chinese)
    [7]
    张燕, 张鹗, 何舜平. 中国鲿科鱼类线粒体DNA控制区结构及其系统发育分析[J]. 水生生物学报, 2003, 27(5): 463-467. doi: 10.3321/j.issn:1000-3207.2003.05.004

    ZHANG Yan, ZHANG E, HE Shunping. Studies on the structure of the control region of the Bagridae in China and its phylogenetic significance[J]. Acta Hydrobiological Sinica, 2003, 27(5): 463-467. (in Chinese) doi: 10.3321/j.issn:1000-3207.2003.05.004
    [8]
    赫崇波, 高祥刚, 王效敏, 等. 圆斑星鲽线粒体基因组全序列结构及其进化[J]. 中国水产科学, 2007, 14(4): 584-592. doi: 10.3321/j.issn:1005-8737.2007.04.009

    HE Chongbo, GAO Xianggang, WANG Xiaomin, et al. Structure and evolution of complete mitochondrial genome of spotted halibut Verasper variegatus[J]. J Fish Sci China, 2007, 14(4): 584-592. (in Chinese) doi: 10.3321/j.issn:1005-8737.2007.04.009
    [9]
    诸廷俊, 杨金权, 唐文乔. 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, 2008, 17(2): 152-157. https://xueshu.baidu.com/usercenter/paper/show?paperid=b55fe9a1202052c0c326f8d6a472e79b&site=xueshu_se&hitarticle=1

    ZHU Tingjun, YANG Jinquan, TANG Wenqiao. MtDNA control region sequence structure of the genus Coilia in Yangtze River estuary[J]. J Shanghai Fish Univ, 2008, 17(2): 152-157. (in Chinese) https://xueshu.baidu.com/usercenter/paper/show?paperid=b55fe9a1202052c0c326f8d6a472e79b&site=xueshu_se&hitarticle=1
    [10]
    邵爱华, 朱江, 史全良. 暗纹东方鲀线粒体DNA控制区结构和系统发育分析[J]. 中国水产科学, 2007, 14(3): 352-360. doi: 10.3321/j.issn:1005-8737.2007.03.002

    SHAO Aihua, ZHU Jiang, SHI Quanliang, et al. Characterization and phylogenetic analysis of control region of mitochondrial genome from Takifugu fasciatus[J]. J Fish Sci China, 2007, 14(3): 352-360. (in Chinese) doi: 10.3321/j.issn:1005-8737.2007.03.002
    [11]
    赵金良, 王伟伟, 李思发, 等. 鳜类鱼类的线粒体DNA控制区结构及其系统发育分析[J]. 遗传学报, 2006, 33(9): 793-799. https://xueshu.baidu.com/usercenter/paper/show?paperid=73ea5ac23d7b1bfa03e86298d133066b&site=xueshu_se&hitarticle=1

    ZHAO Jinliang, WANG Weiwei, LI Sifa, et al. Structure of the mitochondrial DNA control region of the Sinipercine fishes and their phylogenetic relationship[J]. Acta Genetica Sinica, 2006, 33(9): 793-799. (in Chinese) https://xueshu.baidu.com/usercenter/paper/show?paperid=73ea5ac23d7b1bfa03e86298d133066b&site=xueshu_se&hitarticle=1
    [12]
    朱世华, 郑文娟, 邹记兴, 等. 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, 2007, 28(6): 606-614. doi: 10.3321/j.issn:0254-5853.2007.06.005

    ZHU Shihua, ZHENG Wenjuan, ZOU Jixing, et al. Mitochondrial DNA control region structure and molecular phylogenetic relationship of Carangidae[J]. Zool Res, 2007, 28(6): 606-614. (in Chinese) doi: 10.3321/j.issn:0254-5853.2007.06.005
    [13]
    CÁRDENAS L, HERNÁNDEZ C E, POULIN E, et al. Origin, diversification, and historical biogeography of the genus Trachurus (Perciformes: Carangidae)[J]. Mol Phylogenet Evol, 2005, 35(2): 496-507. doi: 10.1016/j.ympev.2005.01.011
    [14]
    THOMPSON J D, GIBSON T J, PLEWNIAK F, et al. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools[J]. Nucleic Acids Res, 1997, 25(24): 4876-82. doi: 10.1093/nar/25.24.4876
    [15]
    TAMURA K, DUDLEY J, NEI M, et al. MEGA 4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0[J]. Mol Biol Evol, 2007, 24(8): 1596-1599. doi: 10.1093/molbev/msm092
    [16]
    ROZAS J, SANCHEZ-DELBARRIO J C, MESSEGUER X, et al. DnaSP, DNA polymorphism analyses by the coalescent and other methods[J]. Bioinformatics, 2003, 19(18): 2496-2497. doi: 10.1093/bioinformatics/btg359
    [17]
    杨路存, 陈桂琛, 刘荣堂, 等. 3种鼢鼠线粒体DNA控制区结构及其系统发育分析[J]. 草业科学, 2009, 26(2): 100-106. https://xueshu.baidu.com/usercenter/paper/show?paperid=dbc3653adead7c5b73f9317d39025d66&site=xueshu_se

    YANG Lucun, CHEN Guichen, LIU Rongtang, et al. Studies on the structure of the mitochondrial DNA control region and phylogenetic relationships of 3 zokor species[J]. Pratac Sci, 2009, 26(2): 100-106. (in Chinese) https://xueshu.baidu.com/usercenter/paper/show?paperid=dbc3653adead7c5b73f9317d39025d66&site=xueshu_se
    [18]
    WOLSTENHOLME D R. Animal mitochondrial DNA: structure and evolution[M]//WOLSTENHOLME D R, JEON K W. Mitochondrial Genomes. San Diego: Academic Press, 2006: 173-372.
    [19]
    LEE W J, CONROY J, HOWELL W H. Structure and evolution of teleost mitochondrial control regions[J]. J Mol Evol, 1995, 41(1): 54-66. doi: 10.1007/BF00174041
    [20]
    SBISA E, TANZARIELLO F, REYES A, et al. Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications[J]. Gene, 1997, 205(1/2): 125-140. doi: 10.1016/S0378-1119(97)00404-6
  • Related Articles

    [1]LI Min, LI Yufang, ZHANG Peng, CHEN Zuozhi. Analysis of population genetic structure of bullet tuna(Auxis rochei) in the South China Sea based on mitochondrial control region sequences[J]. South China Fisheries Science, 2016, 12(4): 88-95. DOI: 10.3969/j.issn.2095-0780.2016.04.011
    [2]HU Yuting, HU Wang, LING Jun, JIANG He, DUAN Guoqing, PAN Tingshuang. Comparative and phylogenetic analysis of mitochondrial Cytochrome b gene and control region from natural triploid (Carassius auratus gibelio) in Chuzhou[J]. South China Fisheries Science, 2015, 11(2): 101-108. DOI: 10.3969/j.issn.2095-0780.2015.02.015
    [3]MAN Qimeng, FENG Juan, OU Youjun, SU Peiting, XU Liwen. Cluster analysis on 15 strains of pathogenic Nocardia seriolae from fish[J]. South China Fisheries Science, 2013, 9(5): 86-92. DOI: 10.3969/j.issn.2095-0780.2013.05.014
    [4]SU Tianfeng, JIANG Shigui, MA Zhiming, LI Xia. Structure and evolution of mitochondrial control regions in Evynnis cardinalis[J]. South China Fisheries Science, 2012, 8(6): 1-8. DOI: 10.3969/j.issn.2095-0780.2012.06.001
    [5]RONG Chaozhen, ZU Guozhang, HU Jianhua, SUN Shouqi, SUN Tangli. Structure of mitochondrial DNA control region and genetic diversity of Misgurnus anguillicaudatus[J]. South China Fisheries Science, 2011, 7(5): 55-62. DOI: 10.3969/j.issn.2095-0780.2011.05.009
    [6]MAO Yangli, CAI Houcai, LI Chengjiu, GAO Tianxiang. Molecular phylogenetics of genus Mytilus based on COI and 16S rRNA sequences[J]. South China Fisheries Science, 2010, 6(5): 27-36. DOI: 10.3969/j.issn.1673-2227.2010.05.005
    [7]WANG Jiangyong, SUN Xiuxiu, WANG Ruixuan, SU Youlu. Isolation, identification and phylogenetic analysis of pathogen from Haliotis diversicolor Reeve with withering syndrome[J]. South China Fisheries Science, 2010, 6(5): 21-26. DOI: 10.3969/j.issn.1673-2227.2010.05.004
    [8]LUO Jiacong, XIAO Yongshuang, SONG Lin, GAO Tianxiang, Zhang Yan. Phylogenetic separation of lancelets in China revealed by mitochondrial COI and Cyt b gene analysis[J]. South China Fisheries Science, 2007, 3(2): 8-14.
    [9]MU Xidong, BAI Junjie, YE Xing, WANG Xuejie, HU Yinchang, LUO Jianren. Sequence analysis of mitochondrial cytochrome b gene of Carassius auratus var.and phylogenetic relationships of C. auratus var.and C. auratus[J]. South China Fisheries Science, 2007, 3(1): 26-30.
    [10]JIANG Shigui, ZHANG Dianchang, LU: Junlin, LI Jianzhu. Phylogenetic relationships of three species of Labeoninae based on sequences of mitochondrial 16S rRNA genes[J]. South China Fisheries Science, 2005, 1(1): 1-5.
  • Cited by

    Periodical cited type(9)

    1. 吴俊颉,李光华,金方彭,赵静霞,雷春云,高海涛,符世伟,周睿,罗永新,薛绍伟,张文魁,冷云,梁用本,马春明,王艳. 基于线粒体D-loop区的抚仙湖鱇浪白鱼遗传多样性分析. 水生生物学报. 2022(03): 385-394 .
    2. 王运良,潘忠琪,陈可可,陶瑞松,苏成勇,郝家胜,杨群. 基于线粒体基因组控制区序列的中国冰清绢蝶遗传分化和谱系生物地理研究. 昆虫学报. 2019(04): 475-488 .
    3. 李玉龙,刘修泽,吉光,于旭光,李轶平,付杰,王小林,郭栋,董婧. 辽宁沿海鲬mtDNA控制区结构和遗传多样性分析. 水产科学. 2018(06): 818-824 .
    4. 管嘉俊,韩卓君,郑惠芳,李文红,郭忠宝. 广西主要养殖区内逃逸尼罗罗非鱼线粒体D-loop控制区序列分析. 激光生物学报. 2018(05): 451-459 .
    5. 阮行建,邹晓荣,张敏,李玉伟. 东南太平洋智利竹筴鱼生物学特征与个体繁殖力研究. 海洋通报. 2017(03): 333-339 .
    6. 赵林林,毕潇潇,宋林,高天翔. 松江鲈线粒体DNA控制区结构和遗传多样性分析. 水生生物学报. 2016(01): 35-41 .
    7. 肖炜,王腾,李大宇,邹芝英,祝璟琳,韩珏,杨弘. 埃及品系尼罗罗非鱼不同选育世代mtDNA D-loop区遗传多样性分析. 南方水产科学. 2015(03): 29-34 . 本站查看
    8. 苏天凤,江世贵,马之明,李夏. 二长棘犁齿鲷线粒体DNA控制区结构和进化. 南方水产科学. 2012(06): 1-8 . 本站查看
    9. 董丽娜,黄梓荣,李永振,陈国宝. 南海金线鱼属Nemipterus鱼类COⅠ和Cytb基因片段的比较分析. 中国水产科学. 2012(02): 355-363 .

    Other cited types(10)

Catalog

    Article views (4854) PDF downloads (2608) Cited by(19)
    Related

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return