6种接骨木DNA条形码分析
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摘要
由于接骨木属植物种间变异小,性状不稳定等原因,其分类一直难以确定.以6种接骨木属植物的总DNA为模板,利用PCR技术扩增8个DNA条形码片段,并进行序列分析.结果表明:接骨木属叶绿体基因来源的条形码rbc L,rpo C1,Mat K,Rpo B,ycf 5序列完全一致,为高度保守序列;psb A-trn H序列虽然进化较快,但其测序结果准确性差,不适于接骨木品种鉴别.6种接骨木核基因来源的ITS条形码进化上也较为保守,根据该条形码可将接骨木区分为2类.核基因来源的ITS2条形码的扩增效率高,种间区分效果好,是较合适的接骨木属植物分子标记之一.应用ITS2条形码可将6种接骨木区分为4类:接骨木;宽叶接骨木;毛接骨木;东北接骨木、钩齿接骨木和朝鲜接骨木.
For few variation of interspecies and unstabilities of characteristics,the classification of Sambucus have not been determined.Taking the total DNA from 6 species of Sambucus as templates,8 DNA barcodes fragments were amplified by PCR respectively.The results of sequencing showed that the five sequences of DNA barcodes from chloroplast genes,rbc L,rpo C1,Mat K,Rpo B and ycf 5 were coincidence respectively in 6 species of Sambucus,which are not suitable to be used in identification of sambucus.Although the evolution of psb A-trn H fragment were faster than others,but for the low accuracy in sequencing,it is not an ideal DNA barcode for Sambucus.The DNA barcode ITS from nuclear gene is conserved in Sambucus,and 6 species could be only identified into 2 groups by this fragment.The barcode ITS2,which could be amplified efficiency form total DNA is an optional molecular marker to Sambucus.Using ITS2 fragment,the 6 species of Sambucus were divided into four groups:S.williamsii Hance,S.latipinna Nakai,S.buergeriana Blume and the fourth(S.manshurica Kitag,S.foetidissima Nakai and S.coreana Kom).
For few variation of interspecies and unstabilities of characteristics,the classification of Sambucus have not been determined.Taking the total DNA from 6 species of Sambucus as templates,8 DNA barcodes fragments were amplified by PCR respectively.The results of sequencing showed that the five sequences of DNA barcodes from chloroplast genes,rbc L,rpo C1,Mat K,Rpo B and ycf 5 were coincidence respectively in 6 species of Sambucus,which are not suitable to be used in identification of sambucus.Although the evolution of psb A-trn H fragment were faster than others,but for the low accuracy in sequencing,it is not an ideal DNA barcode for Sambucus.The DNA barcode ITS from nuclear gene is conserved in Sambucus,and 6 species could be only identified into 2 groups by this fragment.The barcode ITS2,which could be amplified efficiency form total DNA is an optional molecular marker to Sambucus.Using ITS2 fragment,the 6 species of Sambucus were divided into four groups:S.williamsii Hance,S.latipinna Nakai,S.buergeriana Blume and the fourth(S.manshurica Kitag,S.foetidissima Nakai and S.coreana Kom).
引文
[1]高云珍,刘忠颖.接骨木资源的开发与综合利用[J].绿色科技,2015(1):114-116.
[2]张弼弘,刘宝光,刘颖,等.接骨木的开发及利用[J].林业科技,2003,28(5):53-54.
[3]王启珍.接骨木食用药用价值及开发利用[J].中国野生植物资源,2002,21(3):24-25.
[4]胡荣,陈可贵.接骨木油脂的开发利用研究[J].林产化工通讯,1991(6):18-19.
[5]徐亮,陈功锡,张代贵,等.接骨木属植物研究进展[J].中国野生植物资源,2010,29(5):1-5,10.
[6]杜凤国,祝廷成,朱俊义,等.中国接骨木属花粉表面纹饰类型的研究[J].北华大学学报(自然科学版),2007,8(3):271-275.
[7]Bolòs O D,Vigo J.Flora dels Paisos Catalans,vol III[M].Barcelona:Barcino,1995.
[8]Schmid R,Bolli R,Schmid R,et al.Revision of the Genus Sambucus[J].Taxon,1994,43(4):675.
[9]徐炳声.中国植物志:第72卷[M].北京:科学出版社,1988.
[10]陈可贵,杜凤国,戚继忠,等.接骨木属植物分种研究[J].吉林林学院学报,1993,9(3):44-48.
[11]Kumar R,Das A J,Juwarkar A A.Reclamation of petrol oil contaminated soil by rhamnolipids producing PGPR strains for growing Withania somnifera a medicinal shrub[J].World J Microbiol Biotechnol,2015,31(2):307-313.
[12]韩瑞芳,董晓敏,刘天明.应用16S r DNA全序列测序技术鉴定生鲜乳中的细菌种类[J].食品工业科技,2015,36(15):152-156.
[13]赖秀秀.基于16S r DNA的基因测序在腹透相关腹膜炎早期诊断中的应用[D].杭州:浙江大学,2015.
[14]Lenhart T R,Duncan K E,Beech I B,et al.Identification and characterization of microbial biofilm communities associated with corroded oil pipeline surfaces[J].Biofouling,2014,30(7):823-835.
[15]LIN Xiao Yan,WANG Yi,WANG Hai Long,et al.Isolation and Characterization of a Bensulfuron-Methyl-Degrading Strain L1 of Bacillus[J].Pedosphere,2010(1):111-119.
[16]Weigt L A,Driskell A C,Ormos A,et al.Introduction to animal DNA barcoding protocols[J].Methods Mol Biol,2012,858:11-16.
[17]Waugh J,Huynen L,Millar C,et al.DNA barcoding of animal species-response to De Salle[J].Bioessays,2008,30(1):92-93.
[18]Wang X,Hou F X,Wang Y X,et al.Identification of original species of Mantidis ootheca(Sangpiaoxiao)based on DNA barcoding[J].Zhongguo Zhong Yao Za Zhi,2015,40(20):3963-3966.
[19]Evans N,Paulay G.DNA barcoding methods for invertebrates[J].Methods Mol Biol,2012,858:47-77.
[20]Damm S,Schierwater B,Hadrys H.An integrative approach to species discovery in odonates:from character-based DNA barcoding to ecology[J].Mol Ecol,2010,19(18):3881-3893.
[21]Bergmann T,Hadrys H,Breves G,et al.Character-based DNA barcoding:a superior tool for species classification[J].Berl Munch Tierarztl Wochenschr,2009,122(11-12):446-450.
[22]Vassou S L,Kusuma G,Parani M.DNA barcoding for species identification from dried and powdered plant parts:a case study with authentication of the raw drug market samples of Sida cordifolia[J].Gene,2015,559(1):86-93.
[23]Yan L J,Liu J,Moller M,et al.DNA barcoding of Rhododendron(Ericaceae),the largest Chinese plant genus in biodiversity hotspots of the Himalaya-Hengduan Mountains[J].Mol Ecol Resour,2015,15(4):932-944.
[24]Bruni I,Galimberti A,Caridi L,et al.A DNA barcoding approach to identify plant species in multiflower honey[J].Food Chem,2015,170:308-315.
[25]Parvathy V A,Swetha V P,Sheeja T E,et al.Detection of plant-based adulterants in turmeric powder using DNA barcoding[J].Pharm Biol,2015,53(12):1774-1779.
[26]Techen N,Parveen I,Pan Z,et al.DNA barcoding of medicinal plant material for identification[J].Curr Opin Biotechnol,2014,25:103-110.
[27]Saarela J M,Sokoloff P C,Gillespie L J,et al.DNA barcoding the Canadian Arctic flora:core plastid barcodes(rbc L+mat K)for 490 vascular plant species[J].PLo S One,2013,8(10):e77982.
[28]Liu J,Provan J,Gao L M,et al.Sampling strategy and potential utility of indels for DNA barcoding of closely related plant species:a case study in taxus[J].Int J Mol Sci,2012,13(7):8740-8751.
[29]Bruni I,De Mattia F,Martellos S,et al.DNA barcoding as an effective tool in improving a digital plant identification system:a case study for the area of Mt.Valerio,Trieste(NE Italy)[J].PLo S One,2012,7(9):e43256.
[30]Cowan R S,Fay M F.Challenges in the DNA barcoding of plant material[J].Methods Mol Biol,2012,862:23-33.
[31]Kumar S,Stecher G,Tamura K.MEGA7:Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets[J].Mol Biol Evol,2016,33(7):1870-1874.
[32]Saitou N,Nei M.The neighbor-joining method:a new method for reconstructing phylogenetic trees[J].Mol Biol Evol,1987,4(4):406-425.
[33]Tamura K,Nei M,Kumar S.Prospects for inferring very large phylogenies by using the neighbor-joining method[J].Proc Natl Acad Sci U S A,2004,101(30):11030-11035.
[34]Selvaraj D,Sarma R K,Shanmughanandhan D,et al.Evaluation of DNA barcode candidates for the discrimination of the large plant family Apocynaceae[J].Plant Systematics and Evolution,2015,301(4):1-11.
[35]Singh H K,Parveen I,Raghuvanshi S,et al.The loci recommended as universal barcodes for plants on the basis of floristic studies may not work with congeneric species as exemplified by DNA barcoding of Dendrobium species[J].BMC Res Notes,2012,5:42.
[36]Newmaster S G,Fazekas A J,Steeves R A,et al.Testing candidate plant barcode regions in the Myristicaceae[J].Mol Ecol Resour,2008,8(3):480-490.
[37]珔StorchováH,Olson M S.The architecture of the chloroplast psb A-trn H non-coding region in angiosperms[J].Plant Systematics and Evolution,2007,268(1):235-256.
[38]Chen S,Yao H,Han J,et al.Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species[J].PLo S One,2010,5(1):e8613.
[39]张改霞,金钺,贾静,等.药用植物羌活种子DNA条形码鉴定研究[J].中国中药杂志,2016,41(3):390-395.
[40]赵莎,庞晓慧,宋经元,等.应用ITS2条形码鉴定中药材合欢皮、合欢花及其混伪品[J].中国中药杂志,2014,39(12):2164-2168.
[41]刘义梅,张乐华,陈士林,等.ITS2序列鉴别10种杜鹃属药用植物[J].中药材,2011,34(9):1342-1345.
[42]韩建萍,石林春,陈士林,等.ITS2序列鉴定筋骨草及其近缘种[J].世界科学技术-中医药现代化,2008,10(6):86-89.
[2]张弼弘,刘宝光,刘颖,等.接骨木的开发及利用[J].林业科技,2003,28(5):53-54.
[3]王启珍.接骨木食用药用价值及开发利用[J].中国野生植物资源,2002,21(3):24-25.
[4]胡荣,陈可贵.接骨木油脂的开发利用研究[J].林产化工通讯,1991(6):18-19.
[5]徐亮,陈功锡,张代贵,等.接骨木属植物研究进展[J].中国野生植物资源,2010,29(5):1-5,10.
[6]杜凤国,祝廷成,朱俊义,等.中国接骨木属花粉表面纹饰类型的研究[J].北华大学学报(自然科学版),2007,8(3):271-275.
[7]Bolòs O D,Vigo J.Flora dels Paisos Catalans,vol III[M].Barcelona:Barcino,1995.
[8]Schmid R,Bolli R,Schmid R,et al.Revision of the Genus Sambucus[J].Taxon,1994,43(4):675.
[9]徐炳声.中国植物志:第72卷[M].北京:科学出版社,1988.
[10]陈可贵,杜凤国,戚继忠,等.接骨木属植物分种研究[J].吉林林学院学报,1993,9(3):44-48.
[11]Kumar R,Das A J,Juwarkar A A.Reclamation of petrol oil contaminated soil by rhamnolipids producing PGPR strains for growing Withania somnifera a medicinal shrub[J].World J Microbiol Biotechnol,2015,31(2):307-313.
[12]韩瑞芳,董晓敏,刘天明.应用16S r DNA全序列测序技术鉴定生鲜乳中的细菌种类[J].食品工业科技,2015,36(15):152-156.
[13]赖秀秀.基于16S r DNA的基因测序在腹透相关腹膜炎早期诊断中的应用[D].杭州:浙江大学,2015.
[14]Lenhart T R,Duncan K E,Beech I B,et al.Identification and characterization of microbial biofilm communities associated with corroded oil pipeline surfaces[J].Biofouling,2014,30(7):823-835.
[15]LIN Xiao Yan,WANG Yi,WANG Hai Long,et al.Isolation and Characterization of a Bensulfuron-Methyl-Degrading Strain L1 of Bacillus[J].Pedosphere,2010(1):111-119.
[16]Weigt L A,Driskell A C,Ormos A,et al.Introduction to animal DNA barcoding protocols[J].Methods Mol Biol,2012,858:11-16.
[17]Waugh J,Huynen L,Millar C,et al.DNA barcoding of animal species-response to De Salle[J].Bioessays,2008,30(1):92-93.
[18]Wang X,Hou F X,Wang Y X,et al.Identification of original species of Mantidis ootheca(Sangpiaoxiao)based on DNA barcoding[J].Zhongguo Zhong Yao Za Zhi,2015,40(20):3963-3966.
[19]Evans N,Paulay G.DNA barcoding methods for invertebrates[J].Methods Mol Biol,2012,858:47-77.
[20]Damm S,Schierwater B,Hadrys H.An integrative approach to species discovery in odonates:from character-based DNA barcoding to ecology[J].Mol Ecol,2010,19(18):3881-3893.
[21]Bergmann T,Hadrys H,Breves G,et al.Character-based DNA barcoding:a superior tool for species classification[J].Berl Munch Tierarztl Wochenschr,2009,122(11-12):446-450.
[22]Vassou S L,Kusuma G,Parani M.DNA barcoding for species identification from dried and powdered plant parts:a case study with authentication of the raw drug market samples of Sida cordifolia[J].Gene,2015,559(1):86-93.
[23]Yan L J,Liu J,Moller M,et al.DNA barcoding of Rhododendron(Ericaceae),the largest Chinese plant genus in biodiversity hotspots of the Himalaya-Hengduan Mountains[J].Mol Ecol Resour,2015,15(4):932-944.
[24]Bruni I,Galimberti A,Caridi L,et al.A DNA barcoding approach to identify plant species in multiflower honey[J].Food Chem,2015,170:308-315.
[25]Parvathy V A,Swetha V P,Sheeja T E,et al.Detection of plant-based adulterants in turmeric powder using DNA barcoding[J].Pharm Biol,2015,53(12):1774-1779.
[26]Techen N,Parveen I,Pan Z,et al.DNA barcoding of medicinal plant material for identification[J].Curr Opin Biotechnol,2014,25:103-110.
[27]Saarela J M,Sokoloff P C,Gillespie L J,et al.DNA barcoding the Canadian Arctic flora:core plastid barcodes(rbc L+mat K)for 490 vascular plant species[J].PLo S One,2013,8(10):e77982.
[28]Liu J,Provan J,Gao L M,et al.Sampling strategy and potential utility of indels for DNA barcoding of closely related plant species:a case study in taxus[J].Int J Mol Sci,2012,13(7):8740-8751.
[29]Bruni I,De Mattia F,Martellos S,et al.DNA barcoding as an effective tool in improving a digital plant identification system:a case study for the area of Mt.Valerio,Trieste(NE Italy)[J].PLo S One,2012,7(9):e43256.
[30]Cowan R S,Fay M F.Challenges in the DNA barcoding of plant material[J].Methods Mol Biol,2012,862:23-33.
[31]Kumar S,Stecher G,Tamura K.MEGA7:Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets[J].Mol Biol Evol,2016,33(7):1870-1874.
[32]Saitou N,Nei M.The neighbor-joining method:a new method for reconstructing phylogenetic trees[J].Mol Biol Evol,1987,4(4):406-425.
[33]Tamura K,Nei M,Kumar S.Prospects for inferring very large phylogenies by using the neighbor-joining method[J].Proc Natl Acad Sci U S A,2004,101(30):11030-11035.
[34]Selvaraj D,Sarma R K,Shanmughanandhan D,et al.Evaluation of DNA barcode candidates for the discrimination of the large plant family Apocynaceae[J].Plant Systematics and Evolution,2015,301(4):1-11.
[35]Singh H K,Parveen I,Raghuvanshi S,et al.The loci recommended as universal barcodes for plants on the basis of floristic studies may not work with congeneric species as exemplified by DNA barcoding of Dendrobium species[J].BMC Res Notes,2012,5:42.
[36]Newmaster S G,Fazekas A J,Steeves R A,et al.Testing candidate plant barcode regions in the Myristicaceae[J].Mol Ecol Resour,2008,8(3):480-490.
[37]珔StorchováH,Olson M S.The architecture of the chloroplast psb A-trn H non-coding region in angiosperms[J].Plant Systematics and Evolution,2007,268(1):235-256.
[38]Chen S,Yao H,Han J,et al.Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species[J].PLo S One,2010,5(1):e8613.
[39]张改霞,金钺,贾静,等.药用植物羌活种子DNA条形码鉴定研究[J].中国中药杂志,2016,41(3):390-395.
[40]赵莎,庞晓慧,宋经元,等.应用ITS2条形码鉴定中药材合欢皮、合欢花及其混伪品[J].中国中药杂志,2014,39(12):2164-2168.
[41]刘义梅,张乐华,陈士林,等.ITS2序列鉴别10种杜鹃属药用植物[J].中药材,2011,34(9):1342-1345.
[42]韩建萍,石林春,陈士林,等.ITS2序列鉴定筋骨草及其近缘种[J].世界科学技术-中医药现代化,2008,10(6):86-89.