DNA条形码技术在鱼类浮游生物鉴定中的应用及研究展望
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摘要
鱼类浮游生物的准确鉴定是鱼类浮游生物研究的基础。传统的基于形态特征的鉴定不仅费时费力,而且由于缺乏足够信息,鉴定存在困难,导致物种多样性被低估。为了对物种进行准确、快速地鉴定,急需在传统形态分类学基础上,建立并结合便捷准确的分子鉴定手段。DNA条形码技术是利用一段较短的DNA序列实现快速准确物种鉴定的工具,就像在商店里扫描仪读取条形码那样,对每一种生物也能通过快速分析其DNA中的一小段(线粒体细胞色素c氧化酶I亚基,mt COI)加以识别。DNA条形码提供了可信息化的分类标准和有效的分类学手段,已成为近年来生物类群的研究热点。文章介绍了DNA条形码的概念、原理、工作流程及其优点,分析了其在鱼类浮游生物鉴定中的应用可行性,并展望未来鱼类浮游生物学发展的前景:分子技术鉴定鱼类浮游生物相关规范标准的建立,传统形态鉴定与分子方法相结合的分类学研究,以及鱼类浮游生物的生态学研究。
As the main components of marine biota,ichthyoplankton plays vital roles in the marine biodiversity.However,morphological identification of ichthyoplankton was time-consuming and even impossible for some taxa.Diversity of marine ichthyoplankton was believed to be underestimated.To enable accurate and fast identification of species,it is imperative to establish molecular techniques,to complement the traditional morphological methodology.DNA barcoding(a technology to provide rapid,accurate and automated species identifications by using short orthologousDNA sequences)had been fundamentally important in the past few years in classification.Just like the barcodes on products are recognized,each living species can be identified by using a short fragment of the mitochondrial gene coding for cytochrome c oxidase subunit I(mt COI).DNA barcoding provides digitalized criteria and effective means for species identification.This paper reviewed some fundamental knowledge of DNA Barcoding,like the conception,principle,workflow and advantages of DNA barcoding.Meanwhile,the possibility and feasibility of DNA barcoding in identification of ichthyoplankton were discussed.And the outlook of ichthyoplankton was prospected,like the establishment of molecular standards for identification of ichthyoplankton,a taxonomic study combining morphological identification with molecular methods,ecological studies of ichthyoplankton.
As the main components of marine biota,ichthyoplankton plays vital roles in the marine biodiversity.However,morphological identification of ichthyoplankton was time-consuming and even impossible for some taxa.Diversity of marine ichthyoplankton was believed to be underestimated.To enable accurate and fast identification of species,it is imperative to establish molecular techniques,to complement the traditional morphological methodology.DNA barcoding(a technology to provide rapid,accurate and automated species identifications by using short orthologousDNA sequences)had been fundamentally important in the past few years in classification.Just like the barcodes on products are recognized,each living species can be identified by using a short fragment of the mitochondrial gene coding for cytochrome c oxidase subunit I(mt COI).DNA barcoding provides digitalized criteria and effective means for species identification.This paper reviewed some fundamental knowledge of DNA Barcoding,like the conception,principle,workflow and advantages of DNA barcoding.Meanwhile,the possibility and feasibility of DNA barcoding in identification of ichthyoplankton were discussed.And the outlook of ichthyoplankton was prospected,like the establishment of molecular standards for identification of ichthyoplankton,a taxonomic study combining morphological identification with molecular methods,ecological studies of ichthyoplankton.
引文
[1]沈国英,施并章.海洋生态学[M].北京:科学出版社.2002.
[2]NELSON J S.Fishes of the world[M].Tokyo:John Wiley&Sons,Inc.2006.
[3]SHAO KT,YANG JS,CHEN KC,et al.An identification guide of marine fish eggs from Taiwan[M].Taiwan:Institute of Zoology,Academia Sinica.2001.
[4]卞晓东,张秀梅,高天翔,等.沙氏下鱵鱼卵的形态学及遗传学鉴别[J].水产学报,2008,32(3):342-352.
[5]张仁斋,陆穗芬,赵传,等.中国近海鱼卵与仔鱼[M].上海,上海科学技术出版社,1985.
[6]黄海水产研究所.海洋水产资源调查手册[M].上海:上海科学技术出版社,1981.
[7]张孝威,何桂芬,沙学坤.牙鲆和条鳎卵子及仔、稚鱼的形态观察[J].海洋与湖沼,1965,7(2):158-174.
[8]陈真然,张孝威.斑鰶卵子和仔、稚、幼鱼的形态特征[J].海洋与湖沼,1965,7(3):205-214.
[9]许波涛,李加儿,周宏团.赤点石斑鱼的胚胎和仔鱼形态发育[J].水产学报,1985,9(4):369-374.
[10]陈昌生,黄佳鸣,何华武,等.高体鰤胚胎及仔稚幼鱼的形态观察[J].中国水产科学,1998,5(1):25-29.
[11]谢仰杰,张雅芝,胡家财,等.斜带髭鲷早期发育的形态观察[J].中国水产科学,2004,11(2):89-94.
[12]夏连军,施兆鸿,王建钢,等.黄鲷胚胎及卵黄囊仔鱼的形态发育[J].中国水产科学,2005,12(5):533-538.
[13]马学坤,柳学周,温海深,等.漠斑牙鲆胚胎及仔稚鱼发育的形态学观察[J].南方水产,2008,4(1):41-47.
[14]方家仲,褚茂兵,肖勤,等.大黄鱼早期发育的形态学研究[J].海洋科学,2003,27(6):1-6.
[15]钟俊生,楼宝,袁锦丰.鱼仔稚鱼早期发育的研究[J].上海水产大学学报,2005,14(3):231-237.
[16]王波,刘振华,孙丕喜,等.星斑川鲽胚胎发育的形态观察[J].海洋学报,2008,30(2):130-136.
[17]柳凌,张洁明,郭峰,等.人工条件下日本鳗鲡胚胎及早期仔鱼发育的生物学特征[J].水产学报,2010,34(12):1800-1811.
[18]OKIYAMA M.An atlas of the early stage fisher in Japan[M].Tokyo:Tokai University Press,1988.
[19]BUCKLIN A,STEINKE D,BLANCO-BERCIAL L.DNA barcoding of marine metazoan[J].Marine Science,2011(3):471-508.
[20]ARNOT DE,ROPER C,BAYOUMI RAL.Digital codes from hypervariable tandemly repeated DNA-sequences in the Plasmodium-Falciparum Circumsporozoite gene can genetically barcode isolates[J].Molecular and Biochemical Parasitology,1993,61(1):15-24.
[21]HEBERT PDN,CYWINSKA A,BALL SL,et al.Biological identifications through DNA barcodes[J].Proceedings of the Royal Society B:Biological Sciences,2003,270:313-322.
[22]HEBERT PDN,RATNASINGHAM S,DEWAARD JR.Barcoding animal life:cytochrome c oxidase subunit 1divergences among closely related species[J].Proceedings of the Royal Society of London B:Biological Sciences,2003b,270(Suppl.):S96-S99.
[23]尹晓宏,王江峰.DNA条形码技术在法医昆虫学中的研究进展[J].政法学刊,2010(2):4-15.
[24]WARD R D,ZEMLAK T S,INNES B H,et al.DNA barcoding Australia fish species[J].Philosophical Transactions of the Royal Society B Biological Sciences,2005,360(1462):1847-1857.
[25]WARD R D,COSTA F O,HOLMES B H,et al.DNA barcoding of shared fish species from the North Atlantic and Australasia:minimal divergence for most taxa,but Zeus faber and Lepidopus caudatuseach probably constitute two species[J].Aquatic Biology,2008,3(1):71-78.
[26]SMITH P J,MCVEAGH S M,STEINKE D.DNA barcoding for the identification of smoked fish products[J].Journal of Fish Biology,2008,72(2):464-471.
[27]SWARTZ E R,MWALE M,HANNER R.A role for barcoding in the study of African fish diversity and conservation[J].South African Journal of Science,2008,104:293-298.
[28]WAUGH J.DNA barcoding in animal species:progress,potential and pitfalls[J].BioEssays,2007,29(2):188-197.
[29]ROCK J,COSTA F O,WALKER D I,et al.DNA barcodes of fish of the Scotia Sea,Antarctica indicate priority groups for taxonomic and systematics focus[J].Antarctic Science,2008,20(3):253-262.
[30]高连明.DNA条形码在生物多样性编目与评价中的应用[J].生物多样性,2015,23(3):286-287.
[31]王太,张艳萍,管丽红,等.甘肃省鱼类资源现状及DNA条形码在鱼类物种鉴定中的应用[J].生物多样性,2015,23(3):306-313.
[32]杨倩倩,刘苏汶,茹炜岽,等.基于DNA条形码技术对浙江省外来入侵福寿螺进行分子鉴定[J].生物多样性,2016,24(3):341-350.
[33]林森杰,王路,郑连明,等.海洋生物DNA条形码研究现状与展望[J].海洋学报,2014,36(12):1-17.
[34]LAKRA WS,GOSWAMI M,GOPALAKRISHNAN A.Molecular identification and phylogenetic relationships of seven Indian Sciaenids(Pisces:Perciformes,Sciaenidae)based on16SrRNA and cytochrome c oxidase subunit I mitochondrial genes[J].Molecular Biology Reports,2009,36(5):831-839.
[35]王中铎,郭昱嵩,陈荣玲,等.南海常见硬骨鱼类COI条码序列[J].海洋与湖沼,2009,40(5):608-614.
[36]柳淑芳,陈亮亮,戴芳群,等.基于线粒体COI基因的DNA条形码在石首鱼科鱼类系统分类中的应用[J].海洋与湖沼,2010,41(2):223-232.
[37]程宝国,李三磊,徐冬冬,等.梭鱼和鲻鱼线粒体16SrRNA和COI基因片段的比较分析[J].浙江海洋学院学报(自然科学版),2012,31(2):103-106.
[38]宋超,于亚男,张涛,等.基于线粒体COI基因部分序列的长江口舌鳎科鱼类系统分类研究[J].动物学杂志,2014,49(5):716-726.
[39]于亚男,宋超,侯俊利,等.基于线粒体COI基因部分序列的长江口虾虎鱼科鱼类系统分类[J].淡水渔业,2014,44(5):3-8.
[40]PEGG G G,SINCLAIR B,BRISKEY L,et al.mtDNA barcode identification of fish larvae in the southern Great Barrier Reef Australia[J].Sei Mar,2006,70(S2):7-12.
[41]VALDEZ-MORENO M,VSQUEZ-YEOMANS L,ELASGUTIRREZ M,et al.Using DNA barcodes to connect adults and early life stages of marine fishes from the Yucatan Peninsula,Mexico:potential in fisheries management[J].Marine and Freshwater Research,2010,61(6):655-671.
[42]KO H L,WANG Y Z,CHIU T S,et al.Evaluating the Accuracy of Morphological Identification of Larval Fishes by Applying DNA Barcoding[J].PLOS ONE,2013,8(1):1-7.
[43]周美玉,陈晓,杨圣云.采用DNA条形码技术对厦门海域鱼卵、仔稚鱼种类的鉴定[J].海洋环境科学,2015,34(1):120-135.
[44]高东奎.鱼类浮游生物形态及分子鉴定方法的应用基础研究[D].青岛:中国海洋大学,2015.
[45]陈定标.浙江沿海鱼类DNA条形码及其在鱼卵仔鱼鉴定中的应用[D].舟山:浙江海洋大学,2017.
[46]刘守海,秦玉涛,刘材材,等.DNA条形码技术在仔稚鱼鉴定中的实践[J].海洋开发与管理,2017,34(2):92-95.
[2]NELSON J S.Fishes of the world[M].Tokyo:John Wiley&Sons,Inc.2006.
[3]SHAO KT,YANG JS,CHEN KC,et al.An identification guide of marine fish eggs from Taiwan[M].Taiwan:Institute of Zoology,Academia Sinica.2001.
[4]卞晓东,张秀梅,高天翔,等.沙氏下鱵鱼卵的形态学及遗传学鉴别[J].水产学报,2008,32(3):342-352.
[5]张仁斋,陆穗芬,赵传,等.中国近海鱼卵与仔鱼[M].上海,上海科学技术出版社,1985.
[6]黄海水产研究所.海洋水产资源调查手册[M].上海:上海科学技术出版社,1981.
[7]张孝威,何桂芬,沙学坤.牙鲆和条鳎卵子及仔、稚鱼的形态观察[J].海洋与湖沼,1965,7(2):158-174.
[8]陈真然,张孝威.斑鰶卵子和仔、稚、幼鱼的形态特征[J].海洋与湖沼,1965,7(3):205-214.
[9]许波涛,李加儿,周宏团.赤点石斑鱼的胚胎和仔鱼形态发育[J].水产学报,1985,9(4):369-374.
[10]陈昌生,黄佳鸣,何华武,等.高体鰤胚胎及仔稚幼鱼的形态观察[J].中国水产科学,1998,5(1):25-29.
[11]谢仰杰,张雅芝,胡家财,等.斜带髭鲷早期发育的形态观察[J].中国水产科学,2004,11(2):89-94.
[12]夏连军,施兆鸿,王建钢,等.黄鲷胚胎及卵黄囊仔鱼的形态发育[J].中国水产科学,2005,12(5):533-538.
[13]马学坤,柳学周,温海深,等.漠斑牙鲆胚胎及仔稚鱼发育的形态学观察[J].南方水产,2008,4(1):41-47.
[14]方家仲,褚茂兵,肖勤,等.大黄鱼早期发育的形态学研究[J].海洋科学,2003,27(6):1-6.
[15]钟俊生,楼宝,袁锦丰.鱼仔稚鱼早期发育的研究[J].上海水产大学学报,2005,14(3):231-237.
[16]王波,刘振华,孙丕喜,等.星斑川鲽胚胎发育的形态观察[J].海洋学报,2008,30(2):130-136.
[17]柳凌,张洁明,郭峰,等.人工条件下日本鳗鲡胚胎及早期仔鱼发育的生物学特征[J].水产学报,2010,34(12):1800-1811.
[18]OKIYAMA M.An atlas of the early stage fisher in Japan[M].Tokyo:Tokai University Press,1988.
[19]BUCKLIN A,STEINKE D,BLANCO-BERCIAL L.DNA barcoding of marine metazoan[J].Marine Science,2011(3):471-508.
[20]ARNOT DE,ROPER C,BAYOUMI RAL.Digital codes from hypervariable tandemly repeated DNA-sequences in the Plasmodium-Falciparum Circumsporozoite gene can genetically barcode isolates[J].Molecular and Biochemical Parasitology,1993,61(1):15-24.
[21]HEBERT PDN,CYWINSKA A,BALL SL,et al.Biological identifications through DNA barcodes[J].Proceedings of the Royal Society B:Biological Sciences,2003,270:313-322.
[22]HEBERT PDN,RATNASINGHAM S,DEWAARD JR.Barcoding animal life:cytochrome c oxidase subunit 1divergences among closely related species[J].Proceedings of the Royal Society of London B:Biological Sciences,2003b,270(Suppl.):S96-S99.
[23]尹晓宏,王江峰.DNA条形码技术在法医昆虫学中的研究进展[J].政法学刊,2010(2):4-15.
[24]WARD R D,ZEMLAK T S,INNES B H,et al.DNA barcoding Australia fish species[J].Philosophical Transactions of the Royal Society B Biological Sciences,2005,360(1462):1847-1857.
[25]WARD R D,COSTA F O,HOLMES B H,et al.DNA barcoding of shared fish species from the North Atlantic and Australasia:minimal divergence for most taxa,but Zeus faber and Lepidopus caudatuseach probably constitute two species[J].Aquatic Biology,2008,3(1):71-78.
[26]SMITH P J,MCVEAGH S M,STEINKE D.DNA barcoding for the identification of smoked fish products[J].Journal of Fish Biology,2008,72(2):464-471.
[27]SWARTZ E R,MWALE M,HANNER R.A role for barcoding in the study of African fish diversity and conservation[J].South African Journal of Science,2008,104:293-298.
[28]WAUGH J.DNA barcoding in animal species:progress,potential and pitfalls[J].BioEssays,2007,29(2):188-197.
[29]ROCK J,COSTA F O,WALKER D I,et al.DNA barcodes of fish of the Scotia Sea,Antarctica indicate priority groups for taxonomic and systematics focus[J].Antarctic Science,2008,20(3):253-262.
[30]高连明.DNA条形码在生物多样性编目与评价中的应用[J].生物多样性,2015,23(3):286-287.
[31]王太,张艳萍,管丽红,等.甘肃省鱼类资源现状及DNA条形码在鱼类物种鉴定中的应用[J].生物多样性,2015,23(3):306-313.
[32]杨倩倩,刘苏汶,茹炜岽,等.基于DNA条形码技术对浙江省外来入侵福寿螺进行分子鉴定[J].生物多样性,2016,24(3):341-350.
[33]林森杰,王路,郑连明,等.海洋生物DNA条形码研究现状与展望[J].海洋学报,2014,36(12):1-17.
[34]LAKRA WS,GOSWAMI M,GOPALAKRISHNAN A.Molecular identification and phylogenetic relationships of seven Indian Sciaenids(Pisces:Perciformes,Sciaenidae)based on16SrRNA and cytochrome c oxidase subunit I mitochondrial genes[J].Molecular Biology Reports,2009,36(5):831-839.
[35]王中铎,郭昱嵩,陈荣玲,等.南海常见硬骨鱼类COI条码序列[J].海洋与湖沼,2009,40(5):608-614.
[36]柳淑芳,陈亮亮,戴芳群,等.基于线粒体COI基因的DNA条形码在石首鱼科鱼类系统分类中的应用[J].海洋与湖沼,2010,41(2):223-232.
[37]程宝国,李三磊,徐冬冬,等.梭鱼和鲻鱼线粒体16SrRNA和COI基因片段的比较分析[J].浙江海洋学院学报(自然科学版),2012,31(2):103-106.
[38]宋超,于亚男,张涛,等.基于线粒体COI基因部分序列的长江口舌鳎科鱼类系统分类研究[J].动物学杂志,2014,49(5):716-726.
[39]于亚男,宋超,侯俊利,等.基于线粒体COI基因部分序列的长江口虾虎鱼科鱼类系统分类[J].淡水渔业,2014,44(5):3-8.
[40]PEGG G G,SINCLAIR B,BRISKEY L,et al.mtDNA barcode identification of fish larvae in the southern Great Barrier Reef Australia[J].Sei Mar,2006,70(S2):7-12.
[41]VALDEZ-MORENO M,VSQUEZ-YEOMANS L,ELASGUTIRREZ M,et al.Using DNA barcodes to connect adults and early life stages of marine fishes from the Yucatan Peninsula,Mexico:potential in fisheries management[J].Marine and Freshwater Research,2010,61(6):655-671.
[42]KO H L,WANG Y Z,CHIU T S,et al.Evaluating the Accuracy of Morphological Identification of Larval Fishes by Applying DNA Barcoding[J].PLOS ONE,2013,8(1):1-7.
[43]周美玉,陈晓,杨圣云.采用DNA条形码技术对厦门海域鱼卵、仔稚鱼种类的鉴定[J].海洋环境科学,2015,34(1):120-135.
[44]高东奎.鱼类浮游生物形态及分子鉴定方法的应用基础研究[D].青岛:中国海洋大学,2015.
[45]陈定标.浙江沿海鱼类DNA条形码及其在鱼卵仔鱼鉴定中的应用[D].舟山:浙江海洋大学,2017.
[46]刘守海,秦玉涛,刘材材,等.DNA条形码技术在仔稚鱼鉴定中的实践[J].海洋开发与管理,2017,34(2):92-95.