辽宁沿海鲬mtDNA控制区结构和遗传多样性分析
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摘要
用PCR扩增直接测序的方法,获得辽宁沿海25尾鲬线粒体DNA控制区基因的876~878bp全序列。通过GenBank中已有的鲬属鱼类控制区同源序列比对及形态特征分析发现,辽宁沿海鲬实为褐斑鲬而非印度鲬。同时,利用高度变异的控制区序列,对辽宁沿海褐斑鲬进行序列多态性分析和遗传多样性分析。结果显示,25尾褐斑鲬间共有22个变异位点,辽宁沿海褐斑鲬群体的遗传多样性处于中等偏低水平,单倍型多样性指数和核苷酸多样性指数分别为0.92±0.04和0.0026±0.0017。核苷酸不配对分析表明,辽宁沿海褐斑鲬群体在19 000~63 000年前经历了群体扩张。对比其他已报道鱼类控制区的结构识别序列,对鲬属鱼类控制区的结构进行分析,识别了终止序列区、中央保守区和保守序列区,并找到DNA复制终止相关的序列ETAS,中央保守区的保守序列CSB-F、CSB-E、CSB-D以及保守序列区的保守序列CSB1、CSB2、CSB3。这一结果可为将来全面了解鲬的种群分化研究及其物种资源保护提供基础资料。
A total of 876—878 bp mtDNA D-loop sequences were amplified in 25 samples of sand gurnard Platycephalus sp.collected from coastal waters in Liaoning province by PCR amplification and directly sequenced.The samples were identified as Platycephalus sp.1 instead of Platycephalusindicusbased on morphological characters and DNA barcoding with the aid of the homologous sequences retrieved from GenBank,and the genetic diversity was analyzed by variable mtDNA D-loop sequences.Twenty-two loci of variation were found,with H of 0.92±0.04 andπof 0.0026±0.0017,indicating that the variation level was varied from moderate to low.The mismatch distribution of the control region sequences implied that Platycephalus sp.1 in the Liaoning coast had undergone population expansion,possibly before last19 000—63 000 years.The mtDNA D-loop sequence of the gurnard was found to be separated into three domains,namely,terminal associated sequence domain,central conserved sequence domain and conserved sequence block domain.The extended terminal associated sequence(ETAS),three conserved sequence blocks(CSB-F,CSB-E,and CSB-D)in the central conserved sequence domain and three conserved sequence blocks(CSB1,CSB2,and CSB3)in the conserved sequence block domain were also identified.The findings provide a foundation for further research on population differentiation and resource conservation of this species.
A total of 876—878 bp mtDNA D-loop sequences were amplified in 25 samples of sand gurnard Platycephalus sp.collected from coastal waters in Liaoning province by PCR amplification and directly sequenced.The samples were identified as Platycephalus sp.1 instead of Platycephalusindicusbased on morphological characters and DNA barcoding with the aid of the homologous sequences retrieved from GenBank,and the genetic diversity was analyzed by variable mtDNA D-loop sequences.Twenty-two loci of variation were found,with H of 0.92±0.04 andπof 0.0026±0.0017,indicating that the variation level was varied from moderate to low.The mismatch distribution of the control region sequences implied that Platycephalus sp.1 in the Liaoning coast had undergone population expansion,possibly before last19 000—63 000 years.The mtDNA D-loop sequence of the gurnard was found to be separated into three domains,namely,terminal associated sequence domain,central conserved sequence domain and conserved sequence block domain.The extended terminal associated sequence(ETAS),three conserved sequence blocks(CSB-F,CSB-E,and CSB-D)in the central conserved sequence domain and three conserved sequence blocks(CSB1,CSB2,and CSB3)in the conserved sequence block domain were also identified.The findings provide a foundation for further research on population differentiation and resource conservation of this species.
引文
[1]刘瑞玉.海洋生物名录[M].北京:科学出版社,2008:887-1066.
[2]刘静,陈咏霞,马琳.黄渤海鱼类图志[M].北京:科学出版社,2015:219-224.
[3]刘蝉馨,秦克静,丁耕芜,等.辽宁省动物志·鱼类[M].沈阳:辽宁科学技术出版社,1987:1-229.
[4]秦岩.褐斑鲬分类地位及其形态学、遗传学研究[D].青岛:中国海洋大学,2014.
[5] Qin Y,Song N,Zou J W,et al.A new record of a flathead fish(Teleostei:Platycephalidae)from China based on morphological characters and DNA barcoding[J].Chinese Journal of Oceanology and Limnology,2013,31(3):617-624.
[6] Puckridge M,Andreakis N,Appleyard S A,et al.Cryptic diversity in flathead fishes(Scorpaeniformes:Platycephalidae)across the Indo-West Pacific uncovered by DNA barcoding[J].Molecular Ecology Resources,2013,13(1):32-42.
[7] Kelly M E.Forensic DNA Biology[M].San Diego:Academic Press,2013:129-132.
[8] Tamumra K,Peterson D,Peterson N,et al.MEGA5:molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance,and maximum parsimony methods[J].Molecular Biology and Evolution,2011,28(10):2731-2739.
[9] 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(3):564-567.
[10]Liu J X,Gao T X,Wu S F,et al.Pleistocene isolation in the marginal ocean basins and limited dispersal in a marine fish,Liza haematocheila(Temminck&Schlegel,1845)[J].Molecular Ecology,2007,16(2):275-288.
[11]Bandelt H,Forster P,Rohl A.Median joining networks for inferring intraspecific phylogenics[J].Molecular Biology Evolution,1999,16(1):37-48.
[12]Tajima F.Statistical method for testing the neutral mutation hypothesis by DNA polymorphism[J].Genetics,1989,123(3):585-595.
[13]Fu Y X.Statistical tests of neutrality of mutations against population growth,hitchhiking and background selection[J].Genetics,1997,147(2):915-925.
[14]邵爱华,朱江,史全良,等.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.
[15]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[J].海洋通报,2010,29(3):283-288.
[16]赵林林,毕潇潇,宋林,等.松江鲈线粒体DNA控制区结构和遗传多样性分析[J].水生生物学报,2016,40(1):34-41.
[17]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.
[18]刘焕章.鱼类线粒体DNA控制区的结构和进化:以鳑鲏鱼类为例[J].自然科学进展,2002,12(3):266-270.
[19]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.
[20]唐琼英,刘焕章,杨秀平,等.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,2005,29(6):645-653.
[21]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.
[22]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[J].水生生物学报,2014,38(5):980-986.
[23]苏天凤,江世贵.竹鱼属鱼类线粒体DNA控制区结构及其系统发育分析[J].南方水产科学,2011,7(1):18-25.
[24]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[J].动物学研究,2008,29(4):379-385.
[25]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.
[26]魏刚,周丽,曾令江,等.大鳍鳠线粒体控制区结构及其比较分析[J].西南大学学报:自然科学版,2015,37(1):46-52.
[27]赫崇波,曹洁,刘卫东,等.圆斑星鲽及相关种类线粒体DNA控制区结构分析[J].遗传,2007,29(7):829-836.
[28]谭围,郭昱嵩,王中铎,等.笛鲷鱼类的线粒体DNA控制区结构及其系统发育分析[J].海洋学报,2010,32(1):139-145.
[29]Grant W S,Bowen B W.Shallow population histories in deep evolutionary lineages of marine fishes:insights from sardines and anchovies and lessons for conservation[J].J Hered,1998,89(5):415-426.
[30]李玉龙,刘修泽,于旭光,等.基于线粒体COⅠ基因和CR序列的辽宁沿海弯棘斜棘群体遗传多样性和遗传结构分析[J].水生生物学报,2017,41(3):581-588.
[31]李玉龙,刘修泽,李轶平,等.基于mtDNA COⅠ基因序列的辽宁沿海细纹狮子鱼群体遗传多样性分析[J].海洋渔业,2016,38(2):120-129.
[32]Kong X Y,Li Y L,Shi W,et al.Genetic variation and evolutionary demography of Fenneropenaeus chinensis populations,as revealed by the analysis of mitochondrial control region sequences[J].Genetics and Molecular Biology,2010,33(2):379-389.
[33]李玉龙,董婧,王彬,等.基于线粒体COⅠ基因的海蜇不同地理群体遗传特征分析[J].应用生态学报,2016,27(7):2340-2347.
[34]李玉龙,王彬,王文波,等.基于COⅠ基因分析辽东湾海蜇群体遗传多样性[J].水产科学,2016,35(4):404-409.
[35]Han Z Q,Gao T X,Yanagimoto T,et al.Genetic population structure of Nibea albiflora in the Yellow and East China seas[J].Fisheries Science,2008(74):544-552.
[36]赵明,宋伟,马春艳,等.基于线粒体COⅠ基因序列的棘头梅童鱼7个野生群体遗传结构分析[J].中国水产科学,2015,22(2):233-242.
[2]刘静,陈咏霞,马琳.黄渤海鱼类图志[M].北京:科学出版社,2015:219-224.
[3]刘蝉馨,秦克静,丁耕芜,等.辽宁省动物志·鱼类[M].沈阳:辽宁科学技术出版社,1987:1-229.
[4]秦岩.褐斑鲬分类地位及其形态学、遗传学研究[D].青岛:中国海洋大学,2014.
[5] Qin Y,Song N,Zou J W,et al.A new record of a flathead fish(Teleostei:Platycephalidae)from China based on morphological characters and DNA barcoding[J].Chinese Journal of Oceanology and Limnology,2013,31(3):617-624.
[6] Puckridge M,Andreakis N,Appleyard S A,et al.Cryptic diversity in flathead fishes(Scorpaeniformes:Platycephalidae)across the Indo-West Pacific uncovered by DNA barcoding[J].Molecular Ecology Resources,2013,13(1):32-42.
[7] Kelly M E.Forensic DNA Biology[M].San Diego:Academic Press,2013:129-132.
[8] Tamumra K,Peterson D,Peterson N,et al.MEGA5:molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance,and maximum parsimony methods[J].Molecular Biology and Evolution,2011,28(10):2731-2739.
[9] 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(3):564-567.
[10]Liu J X,Gao T X,Wu S F,et al.Pleistocene isolation in the marginal ocean basins and limited dispersal in a marine fish,Liza haematocheila(Temminck&Schlegel,1845)[J].Molecular Ecology,2007,16(2):275-288.
[11]Bandelt H,Forster P,Rohl A.Median joining networks for inferring intraspecific phylogenics[J].Molecular Biology Evolution,1999,16(1):37-48.
[12]Tajima F.Statistical method for testing the neutral mutation hypothesis by DNA polymorphism[J].Genetics,1989,123(3):585-595.
[13]Fu Y X.Statistical tests of neutrality of mutations against population growth,hitchhiking and background selection[J].Genetics,1997,147(2):915-925.
[14]邵爱华,朱江,史全良,等.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.
[15]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[J].海洋通报,2010,29(3):283-288.
[16]赵林林,毕潇潇,宋林,等.松江鲈线粒体DNA控制区结构和遗传多样性分析[J].水生生物学报,2016,40(1):34-41.
[17]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.
[18]刘焕章.鱼类线粒体DNA控制区的结构和进化:以鳑鲏鱼类为例[J].自然科学进展,2002,12(3):266-270.
[19]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.
[20]唐琼英,刘焕章,杨秀平,等.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,2005,29(6):645-653.
[21]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.
[22]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[J].水生生物学报,2014,38(5):980-986.
[23]苏天凤,江世贵.竹鱼属鱼类线粒体DNA控制区结构及其系统发育分析[J].南方水产科学,2011,7(1):18-25.
[24]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[J].动物学研究,2008,29(4):379-385.
[25]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.
[26]魏刚,周丽,曾令江,等.大鳍鳠线粒体控制区结构及其比较分析[J].西南大学学报:自然科学版,2015,37(1):46-52.
[27]赫崇波,曹洁,刘卫东,等.圆斑星鲽及相关种类线粒体DNA控制区结构分析[J].遗传,2007,29(7):829-836.
[28]谭围,郭昱嵩,王中铎,等.笛鲷鱼类的线粒体DNA控制区结构及其系统发育分析[J].海洋学报,2010,32(1):139-145.
[29]Grant W S,Bowen B W.Shallow population histories in deep evolutionary lineages of marine fishes:insights from sardines and anchovies and lessons for conservation[J].J Hered,1998,89(5):415-426.
[30]李玉龙,刘修泽,于旭光,等.基于线粒体COⅠ基因和CR序列的辽宁沿海弯棘斜棘群体遗传多样性和遗传结构分析[J].水生生物学报,2017,41(3):581-588.
[31]李玉龙,刘修泽,李轶平,等.基于mtDNA COⅠ基因序列的辽宁沿海细纹狮子鱼群体遗传多样性分析[J].海洋渔业,2016,38(2):120-129.
[32]Kong X Y,Li Y L,Shi W,et al.Genetic variation and evolutionary demography of Fenneropenaeus chinensis populations,as revealed by the analysis of mitochondrial control region sequences[J].Genetics and Molecular Biology,2010,33(2):379-389.
[33]李玉龙,董婧,王彬,等.基于线粒体COⅠ基因的海蜇不同地理群体遗传特征分析[J].应用生态学报,2016,27(7):2340-2347.
[34]李玉龙,王彬,王文波,等.基于COⅠ基因分析辽东湾海蜇群体遗传多样性[J].水产科学,2016,35(4):404-409.
[35]Han Z Q,Gao T X,Yanagimoto T,et al.Genetic population structure of Nibea albiflora in the Yellow and East China seas[J].Fisheries Science,2008(74):544-552.
[36]赵明,宋伟,马春艳,等.基于线粒体COⅠ基因序列的棘头梅童鱼7个野生群体遗传结构分析[J].中国水产科学,2015,22(2):233-242.