松江鲈线粒体DNA控制区结构和遗传多样性分析
ANALYSIS OF THE STRUCTURE OF MITOCHONDRIAL DNA CONTROL REGION AND THE GENETIC DIVERSITY OF TRACHIDERMUS FASCIATUS IN DIFFERENT POPULATIONS
-
摘要: 为探讨松江鲈(Trachidermus fasciatus Heckel)线粒体控制区特征及其群体遗传结构, 研究测定分析了中国和日本沿海共8个群体的线粒体控制区序列, 分析了其结构特征, 识别出终止序列区(ETAS)、中央保守区(CD)和保守序列区(CSB)的特征序列。遗传多样性分析结果显示: 69个松江鲈个体共检测到47个单倍型, 呈现出核苷酸多样性(0.0079)较低和单倍型多样性(0.978)较高的特点。单倍型邻接关系树和单倍型网络关系图均显示松江鲈分为中国和日本两大世系。遗传分化系数(Fst)和分子方差分析(AMOVA)结果表明, 松江鲈中国群体和日本群体之间存在的遗传差异较显著, 中国沿海各群体之间亦存在着一定程度的遗传差异, 该分化主要由历史环境变动、当代环境因素和自身生态习性等原因造成。Abstract: Roughskin sculpin, also known as Trachidermus fasciatus, is a catadromous fish that live in the seawater along the coast of the northwest Pacific Ocean. The fish population size has been largely reduced in recent years due to the deterioration of the habitats, water pollution and the construction of dams. To protect the fish resource and to improve the fishery management, we need to better understand the genetic structure of the fish population. In this study, we collected 69 individuals from 8 sampling sites near the coast of China and Japan, including Hangzhouwan (HZ), Wendeng (WD), Rongcheng (RC), Dongying (DY), Qinhuangdao (QH), Dalian (DL), Dandong (DD) and Ariake Sea (AS). The mitochondrial control region of T. fasciatus was amplified with polymerase chain reaction (PCR) technology and was sequenced with the forward and reverse primers by the automatic sequencer. We found that the 8 populations exhibited high haplotype diversity (0.978) and low nucleotide diversity (0.0079). Our analysis of the control region revealed the terminal associated sequence, the central conserved domains and the conserved sequence block domains. Moreover, the analysis of NJ phylogenetic trees and median-networks demonstrated that these populations could be divided into the Chinese lineage and the Japanese lineage. Finally, both the genetic differentiation index (Fst) and the analysis of molecular variance (AMOVA) indicated a significant genetic differentiation between the Japanese population and the Chinese populations, as well as a moderate differentiation within the Chinese populations.
-
-
[1] Xiao W H, Zhang Y P. Genetics and evolution of mitochondrial DNA in fish [J]. Acta Hydrobiologica Sinica, 2000, 24(4): 384-391 [肖武汉, 张亚平. 鱼类线粒体DNA的遗传与进化. 水生生物学报, 2000, 24(4): 384-391]
[2] Walberg M W, Clayton D A. Sequence and properties of the human KB cell and mouse L cell D-loop regions of mitochondrial DNA [J]. Nucleic Acids Research, 1981, 9(20): 5411-5430
[3] Rosel P E, Haygood M G, Perrin W F. Phylogenetic relationship among the true porpoise (Cetacean: Phocoenidae) [J]. Molecular Phylogenetics and Evolution, 1995, 4(4): 463-474
[4] Lee W J, Conroy J, Howell W H, et al. Structure and evolution of teleost mitochondrial control regions [J]. Journal of Molecular Evolution, 1995, 41(1): 54-66
[5] Yang B, Chen X Y, Yang J X. Structure of the mitochondrial DNA control region and population genetic diversity analysis of Anabarilius graham (Regan) [J]. Zoological Research, 2008, 29(4): 379-385 [杨博, 陈小勇, 杨君兴. 白鱼线粒体DNA控制区结构和种群遗传多样性分析. 动物学研究, 2008, 29(4): 379-385]
[6] Su T F, Jiang S G. Structure and phylogenetic analysis of mitochondrial DNA control region of genus Trachurus [J]. South China Fisheries Science, 2011, 7(1): 18-25 [苏天凤, 江世贵. 竹筴鱼属鱼类线粒体DNA控制区结构及其系统发育分析. 南方水产科学, 2011, 7(1): 18-25]
[7] Wang Y H. Notes on the scientific name, type-locality and geographical distribution of roughskin sculpin (Trachidermis fasciatus Heckel 1840) [J]. Marine Fisheries, 2006, 28(4): 209-303 [王幼槐. 关于松江鲈学名和模式产地以及地理分布之探讨. 海洋渔业, 2006, 28(4): 209-303]
[8] Wang J Q, Pan L D, Liang T H, et al. Preliminary study on embryonic development of the roughskin sculpin, Trachidermus fasciatus (Scorpaeniformes: Cottidae) [J]. Journal of Fudan University (Natural Science), 2004, 43(2): 250-254 [王金秋, 潘连德, 梁天红, 等. 松江鲈鱼(Trachidermus fasciatus)胚胎发育的初步观察. 复旦学报(自然科学版), 2004, 43(2): 250-254]
[9] Takeshita N, Onikura N, Matsui S, et al. Embryonic, larval and juvenile development of the roughskin sculpin, Trachidermus fasciatus (Scorpaeniformes, Cottidae) [J]. Ichthyological Research, 1997, 44(3): 257-265
[10] Norio O, Naohiko T, Seiichi M, et al. Estimation of the frequency of maturity and sexual differences in the maturation period of the roughskin sculpin Trachidermus fasciatus [J]. Fisheries Science, 2007, 73(3): 735-737
[11] Wang J Q, Shi C, Cheng G. Isozyme Analysis for a wild population of roughskin sculpin, Trachidermus fasciatus, from the Yalu River Basin in China [J]. Journal of Fudan University (Natural Science), 2002, 41(6): 688-693 [王金秋, 石椿, 成功. 鸭绿江流域中国境内松江鲈鱼(Trachidermus fasciatus)天然群体的同工酶分析. 复旦学报(自然科学版), 2002, 41(6): 688-693]
[12] Xu J R, Han X L, Li N, et al. Analysis of genetic diversity in roughskin sculpin Trachidermus fasciatus by AFLP markers [J]. Journal of Dalian Fisheries University, 2008, 23(6): 437-441 [徐建荣, 韩晓磊, 李宁, 等. 松江鲈群体遗传多样性的AFLP分析. 大连水产学院学报, 2008, 23(6): 437-441]
[13] Xu J R, Han X L, Yu J F, et al. Analysis of genetic diversity of Trachidermus fasciatus by ISSR [J]. Freshwater Fisheries, 2009, 139(11): 21-24 [徐建荣, 韩晓磊, 郁建锋, 等. 松江鲈群体遗传多样性的ISSR分析. 淡水渔业, 2009, 139(11): 21-24]
[14] Excoffier L, Laval G, Schneider S. Arlequin version 3.01: An integrated software package for population genetics data analysis [J]. Evolutionary Bioinformatics, 2005, 1: 47-50
[15] Zhu S H, Zheng W J, Zou J X, et al. Mitochondrial DNA control region structure and molecular phylogenetic relationship of Carangidae [J]. Zoological Research, 2007, 28(6): 606-614 [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. 动物学研究, 2007, 28(6): 606-614]
[16] Cai S S, Xu S Y, Song N, et al. Mitochondrial dna control region structure and length polymorphism analysis of Setipinna tenuifilis [J]. Acta Hydrobiologica Sinica, 2014, 38(5): 980-986 [蔡珊珊, 徐胜勇, 宋娜, 等. 黄鲫线粒体DNA控制区结构及长度多态性分析. 水生生物学报, 2014, 38(5): 980-986]
[17] Tamura K, Dudley J, Nei M, et al. MEGA4: Molecular Evo-lutionary Genetics Analysis (MEGA) Software Version 4.0 [J]. Molecular Biology and Evolution, 2007, 24(8): 1596-1599
[18] Bandelt H J, Macaulay V A, Richards M, et al. Median networks: speedy construction and gredy reduction, one simulation, and two case studies from human mtDNA [J]. Molecular Phylogenetics and Evolution, 2000, 16: 8-28
[19] Liu H L, Zhang Q, Tang Y L, et al. Structure and genetic diversity of mtDNA D-Loop sequences among Trachidermus fasciatus stocks in Yellow Sea and Bohai Sea of China [J]. Marine Science Bulletin, 2010, 29(3): 283-288 [刘海林, 章群, 唐优良等. 黄渤海松江鲈鱼线粒体控制区结构与序列多态性分析. 海洋通报, 2010, 29(3): 283-288]
[20] Loeschcke V, Tomiuk J, Jian S K, et al. Conservation Gene-tics [M]. Basel: Birkhauser Veriag. 1994, 37-53
[21] Slatkin M. Gene flow and the geographic structure of natural populations. Science [J]. Science, 1987, 236(4803): 787-792
[22] Han Z Q, Gao T X, Yanagimoto T, et al. Genetic population structure of Nibea albiflorain the Yellow and East China seas [J]. Fisheries Science, 2008, 74(3): 544-552
[23] Gao T X, Bi X X, Zhao L L, et al. Population genetic structure of roughskin sculpin trachidermus fasciatus based on the mitochondrial Cytb sequence [J]. Acta Hydrobiologica Sinica, 2013, 37(2): 199-207 [高天翔, 毕潇潇, 赵林林, 等. 基于线粒体Cytb基因全序列的松江鲈群体遗传结构分析. 水生生物学报, 2013, 37(2): 199-207]
[24] Liu J X, Gao T X, Wu S F, et al. Pleistocene isolation in the Northwestern Pacific marginal seas and limited dispersal in a marine fish, Chelon haemotocheilus (Temminck and Schlegel, 1845) [J]. Molecular Ecology, 2007, 16(2): 275-288
[25] Han Z Q, Yanagimoto T, Zhang Y P, et al. Phylogeography study of Mmodytes personatus in Northwestern Pacific: Pleistocene isolation, temperature and current conducted se-condary contact [J]. PloS One, 2012, 7(5): e37425
[26] Mao Y L, Gao T X, Yanagimoto T, et al. Molecular phylogeography of Ruditapes philippinarum in the Northwestern Pacific Ocean based on CO1 gene [J]. Journal Experimental Marine Biology and Ecology, 2011, 407(2): 171-181
[27] Lambeck K, Esat T M, Potter E K. Links between climate and sea levels for the past three million years [J]. Nature, 2002, 419(6903): 199-206
[28] Hewitt GM. Some genetic consequences of ice ages, and their role in divergence and speciation [J]. Biological Journal of the Linnean Society, 1996, 58(3): 247-276
[29] Tamaki K, Honza E. Global tectonics and formation of marginal basins: role of the western Pacific [J]. Episodes, 1991, 14(30): 224-230
-
期刊类型引用(7)
1. 张帝，强俊，傅建军，徐钢春，周国勤，董在杰，陶易凡，路思琪，陆健，徐跑. 基于微卫星标记和线粒体D-loop序列的5个大口黑鲈群体遗传变异分析. 中国水产科学. 2022(09): 1277-1289 . 
百度学术
2. 潘贤辉，周康奇，陈忠，杜雪松，黄姻，覃俊奇，文露婷，潘志忠，邓潜，罗辉，叶华，林勇. 基于线粒体D-loop区和COI基因序列研究2个禾花鲤群体和野生鲤群体的遗传多样性与系统进化关系. 淡水渔业. 2019(06): 33-40 . 百度学术
3. Li Yulong，Liu Xiuze，Yu Xuguang，Li Yiping，Fu Jie，Dong Jing. The Genetic Structure and Diversity of Repomucenus curvicornis Inhabiting Liaoning Coast Based on Mitochondrial COⅠ Gene and Control Region. Animal Husbandry and Feed Science. 2018(01): 12-17 . 必应学术
4. 白晓慧，杨华，孟一耕，王娜，姜巨峰，吴会民，冯守明. 大鳞副泥鳅群体线粒体DNA D-loop序列遗传变异分析. 水产科学. 2018(05): 658-664 . 百度学术
5. 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 . 百度学术
6. 李玉龙，刘修泽，于旭光，李轶平，付杰，董婧. 基于线粒体COⅠ基因和控制区序列的辽宁沿海弯棘斜棘鳂群体遗传多样性和遗传结构分析. 水生生物学报. 2017(03): 581-588 . 本站查看
7. 胡玉婷，江河，段国庆，凌俊. 基于线粒体Cyt b基因的皖南山区温州光唇鱼种群遗传结构. 中国农学通报. 2017(32): 121-126 . 百度学术
其他类型引用(7)
计量
- 文章访问数: 1570
- HTML全文浏览量: 3
- PDF下载量: 271
- 被引次数: 14
下载: