DNA条形码技术在白洋淀流域浮游动物调查中的应用
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摘要
DNA条形码在物种鉴定中得到了有效的应用,有助于分类学和生物多样性研究.本研究基于线粒体COI基因序列,使用邻接法(neighbor joining method,NJ)和最大似然法(maximum Likelihood,ML)构建系统发育树,对2018年5月在白洋淀流域采集的浮游动物样品进行初步研究.结果表明,在对桡足类的系统发育树分析时,NJ树和ML树的结果保持一致,而且和形态学鉴定结果保持一致.在对枝角类的系统发育树的分析中,NJ树和ML树的结果有所差异,和形态学鉴定结果也有所不同,分析原因,可能是由于拼接序列时剪短了部分序列,使序列间差异性变小引起误差.总体上看,基于COI基因的DNA条形码可以有效地应用到白洋淀流域的浮游动物鉴定中,并可以逐步完善,最终建立一个完整的DNA条形码数据库.
DNA barcode has been effectively used in identification of species,for taxonomy also biodiversity research.This study constructs phylogenetic trees,which based on mitochondrial COI gene sequences,using adjacency method(neighbor joining method,NJ)and maximum likelihood method(maximum likelihood,ML).It was a preliminary study on the acquisition of zooplankton samples in Baiyangdian Watershed in May 2018.The results showed that the phylogenetic tree analysis of copepods,NJ tree and the tree of ML is consistent with the results of morphological identification results.On the tree branch angle of system development analysis,the result of the NJ tree and ML tree was also different with the result of morphological identification.The reason may be due to the stitching part cut short sequences,the sequence error caused by smaller differences.Overall,based on the COI gene,DNA barcode can be effectively applied to zooplankton in Baiyangdian Watershed and it can gradually improve the identification and finally to create a complete DNA barcode database.
DNA barcode has been effectively used in identification of species,for taxonomy also biodiversity research.This study constructs phylogenetic trees,which based on mitochondrial COI gene sequences,using adjacency method(neighbor joining method,NJ)and maximum likelihood method(maximum likelihood,ML).It was a preliminary study on the acquisition of zooplankton samples in Baiyangdian Watershed in May 2018.The results showed that the phylogenetic tree analysis of copepods,NJ tree and the tree of ML is consistent with the results of morphological identification results.On the tree branch angle of system development analysis,the result of the NJ tree and ML tree was also different with the result of morphological identification.The reason may be due to the stitching part cut short sequences,the sequence error caused by smaller differences.Overall,based on the COI gene,DNA barcode can be effectively applied to zooplankton in Baiyangdian Watershed and it can gradually improve the identification and finally to create a complete DNA barcode database.
引文
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[12]程方平,王敏晓,李超伦.基于mtCOI片段序列的南极海域浮游动物DNA条形码研究[J].极地研究,2014,26(2):212-221.DOI:10.13679/j.jdyj.2014.2.212.
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[16]李超伦,王敏晓,程方平,等.DNA条形码及其在海洋浮游动物生态学研究中的应用[J].生物多样性,2011,19(6):805-814.DOI:10.3724/SP.J.1003.2011.10173.
[17]蒋芝华,丁棒棒,王熠,等.石首鱼科海洋鱼类DNA条形码的构建[J].核农学报,2018,32(4):673-680.DOI:10.11869/j.issn.100-8551.2018.04.0673.
[18]陈文炳,邵碧英,缪婷玉,等.多基因DNA条形码鉴定6个鳗鱼物种[J].食品科学,2018,39(2):163-169.DOI:10.7506/spkx1002-6630-201802026.
[19]陈文炳,缪婷玉,彭娟,等.基于16SrRNA基因DNA条形码鉴定美洲鳗、欧洲鳗、日本鳗[J].食品科学,2017,38(4):283-289.DOI:10.7506/spkx1002-6630-201704046.
[20]易啸,王攀攀,王军,等.基于线粒体COI的DNA条形码在对虾科种类鉴定中的研究[J].水产学报,2018,42(1):1-9.DOI:10.11964/jfc.20161210664.
[21]PEREZ K E,DEFREITAS N,SLAPCINSKY J,et al.Molecular phylogeny,evolution of shell shape,and DNA barcoding in polygyridae(Gastropoda:Pulmonata),an endemic North American clade of land snails[J].American Malacological Bulletin,2014,32(1):1-31.DOI:10.4003/006.032.0103.
[22]MISHRA P,KUMAR A,NAGIREDDY A,et al.DNA barcoding:an efficient tool to overcome authentication challenges in the herbal market[J].Plant Biotechnology Journal,2015,14(1):8-21.DOI:10.1111/pbi.12419.
[2]VINCENT R,SZANISZLO S K,URSULA E,et a1.The quest for a general and reliable fungal DNA barcode[J].Open Applied Informatics Journal,2011,5(1):45-61.DOI:10.2174/18741363 010050100 45.
[3]薛银刚,许霞,蔡焕兴,等.DNA条形码技术在水生生物分类中的研究进展[J].环境监控与预警,2012,4(6):23-26.DOI:10.3969/j.issn.1674 6732.2012.06.007.
[4]LIU Z,SONG N,YANAGIMOTO T,et al.Identification of Odontamblyopus iacepedii,via morphology and DNA barcoding[J].Biochemical Systematics&Ecology,2016,66:281-285.DOI:10.1016/j.bse.2016.04.016.
[5]杨倩倩,刘苏汶,俞晓平.DNA条形码分析方法研究进展[J].应用生态学报,2018,29(03):1006-1014.DOI:10.13287/j.1001-9332.201803.032.
[6]何静超,胡岚岚,郭晨辉.小五台山蟹蛛DNA条形码分子鉴定[J].河北大学学报(自然科学版),2016,36(3):286-292.DOI:10.3969/j.issn.1000-1565.2016.03.011.
[7]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.DOI:10.3969/j.issn.0253-4193.2014.12.001.
[8]张宛宛,谢玉为,杨江华,等.DNA宏条形码(metabarcoding)技术在浮游植物群落监测研究中的应用[J].生态毒理学报,2017,12(1):15-24.DOI:10.7524/AJE.1673-5897.20160729002.
[9]ZAIKO A,MARTINEZ J L,SCHMIDT-PETERSEN J,et al.Metabarcoding approach for the ballast water surveillance-An advantageous solution or an awkward challenge[J].Marine Pollution Bulletin,2015,92(1-2):25-34.DOI:10.1016/j.marpolbul.2015.01.008.
[10]CORSE E,COSTEDOAT C,CHAPPAZ R,et al.A PCR-based method for diet analysis in freshwater organisms using18SrDNA barcoding on faeces[J].Molecular Ecology Resources,2010,10(1):96-108.DOI:10.1111/j.1755-0998.2009.02795.
[11]高彦春,王晗,龙笛.白洋淀流域水文条件变化和面临的生态环境问题[J].资源科学,2009,31(9):1506-1513.DOI:10.3321/j.issn:1007-7588.2009.09.008.
[12]程方平,王敏晓,李超伦.基于mtCOI片段序列的南极海域浮游动物DNA条形码研究[J].极地研究,2014,26(2):212-221.DOI:10.13679/j.jdyj.2014.2.212.
[13]FOLMER O,BLACK M,HOEH W,et al.DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates[J].Molecular Marine Biology and Biotechnology,1994,3(5):294-299.DOI:10.4028/www.scientific.net/DDF.7.460.
[14]HEBERT P D N,STOECKLE M Y,ZEMLAK T S,et al.Identification of birds through DNA barcodes[J].Plos Biology,2004,2(10):e312.DOI:10.1371/journal.pbio.0020312.
[15]HEBERT P D N,PENTON E H,BURNS J M,et al.Ten species in one:DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator[J].Proceedings of the National Academy of Sciences of the United States of America,2004,101(41):14812-14817.DOI:10.1073/pnas.0406166101.
[16]李超伦,王敏晓,程方平,等.DNA条形码及其在海洋浮游动物生态学研究中的应用[J].生物多样性,2011,19(6):805-814.DOI:10.3724/SP.J.1003.2011.10173.
[17]蒋芝华,丁棒棒,王熠,等.石首鱼科海洋鱼类DNA条形码的构建[J].核农学报,2018,32(4):673-680.DOI:10.11869/j.issn.100-8551.2018.04.0673.
[18]陈文炳,邵碧英,缪婷玉,等.多基因DNA条形码鉴定6个鳗鱼物种[J].食品科学,2018,39(2):163-169.DOI:10.7506/spkx1002-6630-201802026.
[19]陈文炳,缪婷玉,彭娟,等.基于16SrRNA基因DNA条形码鉴定美洲鳗、欧洲鳗、日本鳗[J].食品科学,2017,38(4):283-289.DOI:10.7506/spkx1002-6630-201704046.
[20]易啸,王攀攀,王军,等.基于线粒体COI的DNA条形码在对虾科种类鉴定中的研究[J].水产学报,2018,42(1):1-9.DOI:10.11964/jfc.20161210664.
[21]PEREZ K E,DEFREITAS N,SLAPCINSKY J,et al.Molecular phylogeny,evolution of shell shape,and DNA barcoding in polygyridae(Gastropoda:Pulmonata),an endemic North American clade of land snails[J].American Malacological Bulletin,2014,32(1):1-31.DOI:10.4003/006.032.0103.
[22]MISHRA P,KUMAR A,NAGIREDDY A,et al.DNA barcoding:an efficient tool to overcome authentication challenges in the herbal market[J].Plant Biotechnology Journal,2015,14(1):8-21.DOI:10.1111/pbi.12419.